Team:TU Darmstadt/Labjournal/Degradation

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WORK IN PROGRESS DO NO INTERFERE!!!
 
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= Degradation =
 
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This page features the work carried out by the [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation degradation team]. The main objectives were the production of a BioBrick containing ''[https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC Fusarium solani cutinase]'' or ''[https://2012.igem.org/Team:TU_Darmstadt/Materials/Est13 Est13 esterase]'' two enzymes potentially enabling ''E.coli'' of [https://2012.igem.org/Team:TU_Darmstadt/Materials/PET PET] degradation and over-expression stems for activity screening.
 
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== Activity tests of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] ==
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<span style="font-size:200%;"><span style="color:#00689D;">Degradation</span></span>
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=== Week 1 / CW 35 ===
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==== Friday, 31.08.12 ====
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
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{| class="wikitable"
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|-
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! Component !! test tube 1 !! test tube 2 !! test tube 3 !! test tube 4
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|-
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| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL
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|-
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| PET particle || yes || yes || yes || yes
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|-
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| bacteria || yes || yes || yes || no
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|-
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| induced || 1.5% L-arabinose || 1.5% L-arabinose || no || no
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|}
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* test seemed to have worked: but an induced test tube without PET-granula was missing
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=== Week 2 / CW 36 ===
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==== Tuesday, 04.09.12 ====
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
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{| class="wikitable"
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|-
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! Component !! test tube 1 !! test tube 2 !! test tube 3 !! test tube 4 !! test tube 5
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|-
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| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL
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|-
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| PET particle || yes || yes || no || yes || yes
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|-
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| bacteria || yes || yes || yes || no || yes
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|-
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| induced || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || no || no
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|}
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*  test tube 3: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin AMP]
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* looks good but test tube 2 shows no significant change of colour
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==== Wednesday, 05.09.12 ====
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
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{| class="wikitable"
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|-
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! Component !! tube 1 !! tube 2 !! tube 3 !! tube 4 !! tube 5 !! tube 6 !! tube 7 !! tube 8 !! tube 9
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|-
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| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL
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|-
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| PET particle || yes || yes || yes || yes || no || no || yes || yes || yes
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|-
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| bacteria || yes || yes || yes || yes || yes || yes || yes || yes || no
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|-
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| induced || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || no || no || no
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|}
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* test tube 9: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin AMP]
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* all induced tubes turned yellow, even without PET-granula as a substrate
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* no more avtivity tests, we are awaiting the evaluation of test expression series of the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter] conjugated to [https://2012.igem.org/Team:TU_Darmstadt/Materials/GFP GFP]
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==== Trouble shooting ====
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This page features the work carried out by the [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation degradation team]. The main objectives were the production of a BioBrick containing ''[https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC Fusarium solani cutinase]'' or ''[https://2012.igem.org/Team:TU_Darmstadt/Materials/Est13 Est13 esterase]'' two enzymes potentially enabling ''E.coli'' of [https://2012.igem.org/Team:TU_Darmstadt/Materials/PET PET] degradation and over-expression stems for activity screening.
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* evaluation shows a very high sensisty of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter [BBa_K808000]] even to low concentrations of [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] (expression starts at around 0.01%)
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* induction of the [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] with 1.5% [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose arabinose] ended fatal due to extrem expression of the transmembrane construct [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 RBS-PhoA-His6tag-pNBEst13-Myctag-EstA]
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* starting test expressions with lower [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] concentrations ranging from 0.05% - 1%
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<span style="color:red;">Team II Kill Curves</span>
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==== Thursday, 06.09.12 ====
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The [https://2012.igem.org/Team:TU_Darmstadt/Team#Degradation degradation group] consists of six undergraduates and two PhD student advisors. Our objective is the expression of a fusion protein on the surface of ''E. coli'' to enable a microbial polyethylenterephtalate (PET) degradation.  
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 [BBa_K808032]] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
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{| class="wikitable"
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|-
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! Component !! tube 1 !! tube 2 !! tube 3 !! tube 4 !! tube 5 !! tube 6 !! tube 7 !! tube 8 !! tube 9 !! tube 10 !! tube 11
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|-
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| DYT-medium || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL
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|-
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| PET particle || yes || yes || yes || yes || yes || yes || no || no || no || no || no
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|-
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| bacteria || yes || yes || yes || yes || yes || yes || yes || yes || yes || yes || no
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|-
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| induced || 1% L-arabinose || 1% L-arabinose || 0.75% L-arabinose || 0.75% L-arabinose || no || no || 1% L-arabinose || 1% L-arabinose || 0.75% L-arabinose || 0.75% L-arabinose|| no
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|}
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* test tube 11: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin AMP]
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[[File:TU_Darmstadt_logo.png|200px]]
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* all induced tubes turned yellow, even without PET-granula as a substrate
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=== Week 3 / CW 37 ===
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We identified three potential PET degradation enzymes from literature. Two of them are cutinases HiC (''Humicola insolens'' cutinase) and FsC (''Fusarium solani'' cutinase), the other namely pNB-Est13 beeing an esterase. After a short examination we dropped the HiC due to a temperature optimum of 80+°C. Shortly after the FsC was dropped as well, due to its toxicity for ''E.coli''.[[File:Project_overview_degradation.png|450px|thumb|right|Enzymatical degradation of polyethylen terephtalate (PET) to terephtalic acid (TPA)]]
-
==== Monday, 10.09.12 ====
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In order to maximise the activity we decided to anchor and display the cutinase/esterase directly on the surface of the producing bacterial cell. Surface-exposed enzymes are directly accessible to the respective substrates which no longer have to traverse the cellular membrane barriers. Furthermore, the enzyme reaction occurs in a chemically more defined environment as compared to the interior of a microbial cell. We use the outer membrane proteins of ''Pseudomonas aeruginosa'' (EstA) as a membrane anchor and the signaling sequence of PhoA translocators to display the enzyme on the outer surface of ''E. coli'' cells. In addition the fusion protein contains a his-tag and a myc-tag for  detection via flow cytometry after antibody staining or Western blot.The [https://2012.igem.org/Team:TU_Darmstadt/Team#Degradation degradation group] consists of six undergraduates and two PhD student advisors. Our objective is the expression of a fusion protein on the surface of ''E. coli'' to enable a microbial polyethylenterephtalate (PET) degradation.  
-
* we stopped the trial of quantification via PET-substrates because in terms of color the change of pH value (due to acid groups that are released by degradtion) is not very exactly. In order to get reproducible data, we are using new activity assays.
+
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* next bacterial assays are going to be in 96 well plates using a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#pNP-Assay pNP-Assay]
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation] of [[MG1655]] with [[BBa_K808032]] and [[BBa_K808030]] (from [[Thursday, 23.08.12]])
+
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* activity assay on [[LB-Tributyrin-CAM-plates]] with L-arabinose concentrations: 0.1%, 0.2%, 0.4%
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** colony 1-5 are [[DH5 alpha]] containing [[BBa_K808032]] but colony 6 is just [[DH5 alpha]] carrying [[BBa_K808030]]
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** incubated over night at 37°C
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#LB-Agar-Tributyrin activity assay on LB-Tributyrin-CAM-plates] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] concentrations: 0.1%, 0.2%, 0.4%
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[[File:TU_Darmstadt_logo.png|200px]]
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-
[[File:TU_Darmstadt_logo.png|200px]]
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[[File:TU_Darmstadt_logo.png|200px]]
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== Protein Expression ==
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At first the signal sequence (PhoA), the catalytic domain (FsC/Est13) and EstA were assembled inline from their respective vectors. This is due to the fact, that by combining multiple parts in the standardized BioBrick vectors, scars with stop codons are generated that would effectively prevent the fusionproteins expression. In consideration of the DNA constructs length we pursued two PCR based synthesis strategies. One being the SKV (standard cloning procedure) the other being the SOE (standard overlap procedure). The first using primers and restriction sites for assembly the latter using overlapping primers. During both assembly procedures restriction sites of PstI, EcorI, SpeI or XbaI were eliminated from the coding sequence by mutagene PCR. In the end we completely changed our assembly strategy, using synthesis products and BsaI sites to put our parts together. After completion the fusionprotein and its subunits were transfered to the BioBrick standard and sent to the registry.
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=== CW 24 ===
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For further characterisation the enzymes were overexpressed in E. coli strains Top10, DH5α, Mg1655, screened on tributyrin agar and detected via flow cytometry after performing an antibody staining. The material science group went even further and tried to examine them using AFM.
-
==== Thursday, 14.06.2012 ====
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] for protein expression of [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
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** each [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] is performed in 5 batches à 50 µL.
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** Parameter: T<sub>A</sub> = 57°C, t<sub>A</sub> = 35 s, t<sub>E</sub> = 65 s
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] vector for expression with pEX vector
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#: gene of interest: [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] for designed part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
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#: primers: [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX_FsC_His_SfiI_up pEX FsC His SfiI up] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX_FsC_stop_SfiI_lo pEX FsC Stop SfiI lo]
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==== Friday, 15.06.2012 ====
 
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control [[File:TU_Darmstadt_logo.png|200px]]
 
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=== CW 25 ===
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== SOE PCR ==  
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==== Wednesday, 20.06.2012 ====
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[[File:Splicing_by_Overlapp_extension.svg.png|300px|left|thumb|schematic drawing of SOE PCR. the red gene has to be assembled upstream of the blue gene. Pay attention to the primer overlapps.]]
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for preparation [[File:TU_Darmstadt_logo.png|200px]]
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] products
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*: Concentration of produced [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence: 40 ng/µL
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==== Thursday, 21.06.2012 ====
 
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] product from 14.06.
 
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** Enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/SfiI SfiI]
 
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** [https://2012.igem.org/Team:TU_Darmstadt/Materials/NEB_buffers#NEBuffer_4_.28green.29 NEBuffer: 4]
 
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** Digestion time: over night
 
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** Digestion temperature: 50°C
 
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==== Friday, 22.06.2012 ====
 
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] vector
 
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*: Concentration range: 240-488 ng/µL
 
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX]
 
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** Enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/SfiI SfiI]
 
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** NEBuffer: 4
 
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** Digestion time: 3 days
 
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** Digestion temperature: 50°C
 
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=== CW 26 ===
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SOE PCR stands for ''Splicing by Overlapp Extension PCR''. It is a standard overlapp extension procedure, enabling the assembly of genes wihtout performing any cloning, digesting or ligation inbetween.  
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==== Monday, 25.06.2012 =====
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All you need to do ist running PCRs with specific primers. If gene A is the upstream part and gene B has to be assembled downstream of gene A, primer lo of gene A should have an overlapp of around 20 nucleotides complementary to the first 20 nucleotides of gene B. Primer up of gene B should haven a complementary overlapp of 20 nucleotides to the end of gene A.
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control [[File:TU_Darmstadt_logo.png|200px]]
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*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] [[File:TU_Darmstadt_logo.png|200px]] and digested [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence from 21.06. [[File:TU_Darmstadt_logo.png|200px]]
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*: Concentrations: [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX]: 77 ng/µL, [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence: 18 ng/µL
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* [[Ligation]] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence with the ratio 1:3 and 1:5
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{| class="wikitable"
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|-
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! Component !! 1:3 !! 1:5
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|-
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| [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence || 1.12 µL || 2.2 µL
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|-
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| [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] || 0.64 µL || 0.64 µL
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|-
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| Ligase buffer || 4 µL || 4 µL
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|-
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| [https://2012.igem.org/Team:TU_Darmstadt/Materials/T4_DNA_Ligase T4 DNA ligase] || 1 µL || 1 µL
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|-
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| H<sub>2</sub>O || 33 µL || 30 µL
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|}
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* Ligation time: over night
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==== Tuesday, 26.06.2012 ====
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We stopped using SOE PCR after a couple of weeks. It is a good method to perform mutationial PCR but to assemble genes of the length of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] it is not the best. Due to bad yields of gel extraction after the first assembly steps we stopped SOE PCR and went on with [https://2012.igem.org/wiki/index.php?title=Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]. But eventually we got our chimeric genes synthesized by [http://de-de.invitrogen.com/site/de/de/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis.html GeneArt].
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation Bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/TOP10 TOP10] with the ligation product [[pEX-FsC]] from 25.06.
+
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==== Wednesday, 27.06.2012 ====
 
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* Two positive clones on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM] plates picked for liquid culture
 
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*: 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM] cultures at 180 rmp and 37°C, over night
 
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==== Thursday, 28.06.2012 ====
 
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [[pEX-Fsc]] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/TOP10 TOP10]
 
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*: Concentration: 45 ng/µL and 405 ng/µL
 
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation Bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [[BmH7118]] with the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] product [[pEX-FsC]]
 
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=== CW 27 ===
 
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==== Monday, 02.07.2012 ====
 
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* [[Protein expression of FsC]] at different temperatures (16°C, 25°C, 30°C and 37°C) for the final step of the expression
 
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==== Tuesday, 03.07.2012 ====
 
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_Periplasmatic_Proteins Purification of Periplasmatic Proteins] for all expression temperatures
 
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==== Wednesday, 04.07.2012 ====
 
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] without cell disrupter
 
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* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of all collected samples
 
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{| class="wikitable"
 
-
|-
 
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! Expression at 16°C !! Expression at 25°C
 
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|-
 
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| [[File:TU_Darmstadt_logo.png|200px]] || [[File:TU_Darmstadt_logo.png|200px]]
 
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|-
 
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! Expression at 30°C !! Expression at 37°C
 
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|-
 
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| [[File:TU_Darmstadt_logo.png|200px]] || [[File:TU_Darmstadt_logo.png|200px]]
 
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|}
 
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* The best results were maintained at an expression temperature of 30°C
 
-
==== Friday, 06.07.2012 ====
 
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* Inoculation of 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol CAM] with [[BmH7118]] containing [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX#pEX-FsC pEX-FsC]
 
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* Incubation for 3 days at 20°C
 
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=== CW 28 ===
 
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==== Monday, 09.07.2012 ====
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [[pEX-FsC]] from 06.07.
 
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*: Concentration: 470 ng/µL
 
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* Preparation for sequencing at [[Eurofins]]
 
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*: Barcode 043 [[pEX-FsC]] with primer [[M13 Reverse up]]
 
-
*: Barcode 044 [[pEX-FsC]] with primer [[ClaI pIII lo]]
 
-
* Plasmid DNA: 5µL
 
-
* Primer: 3µL
 
-
* H<sub>2</sub>O: 7µL
 
-
==== Wednesday, 11.07.2012 ====
 
-
* [[Protein expression of FsC]] according to standard protocol
 
-
 
-
==== Thursday, 12.07.2012 ====
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples [[File:TU_Darmstadt_logo.png|200px]]
 
-
 
-
=== CW 29 ===
 
-
==== Monday, 16.07.2012 ====
 
-
* [[Protein expression of FsC]] according to standard protocol
 
-
 
-
==== Tuesday, 17.07.2012 ====
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples [[File:TU_Darmstadt_logo.png|200px]]
 
-
 
-
=== CW 31 ===
 
-
==== Monday, 30.07.2012 ====
 
-
*[[Protein expression of FsC]] according to standard protocol
 
-
 
-
==== Tuesday, 31.07.2012 ====
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples [[File:TU_Darmstadt_logo.png|200px]]
 
-
 
-
== SOE PCR ==
 
=== Week 1 / CW 17 ===
=== Week 1 / CW 17 ===
==== Tuesday, 24.04.12 ====
==== Tuesday, 24.04.12 ====
-
* Production of [[electrocompetent cells]] [[DH5alpha]] and [[BL21]]  
+
* Production of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electrocompetent_cells electrocompetent cells] [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5alpha] and [http://ecoliwiki.net/colipedia/index.php/Category:Strain:BL21 BL21]
-
* Pouring of [[LB-Agar]] plates with ampecilin resistance (AMP)
+
* Pouring of [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB-Agar] plates with ampecilin resistance (AMP)
-
* setting of [[DYT media]]
+
* setting of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT media]
-
* [[Electroporation]] of [[BL21]] with the following plasmids
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of BL21 with the following plasmids
-
** [[pEST100]], carrying a CM-resistance, the genes of [[phoA]], [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] and [[EstA]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100], carrying a CMP-resistance, the genes of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 phoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA]
-
** [[pET26b(+)]], carrying a Kan-resistance and the gene of [[pNB-Est13]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)], carrying a Kan-resistance and the gene of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13]
-
** [[pET16]], carrying an Amp-resistance , and is needed for our [[SKV]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b], carrying an Amp-resistance , and is needed for our [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]
** transformed Bl21 cells are incubated over night at 37°C in DYT-media and crossed out on LB-Agar plates
** transformed Bl21 cells are incubated over night at 37°C in DYT-media and crossed out on LB-Agar plates
 +
==== Wednesday, 25.04.12 ====
==== Wednesday, 25.04.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of  the 3 overnigth [[Bl21]] cultures and [[concentration meassurement via Nanodrop]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of  the 3 overnigth [http://ecoliwiki.net/colipedia/index.php/Category:Strain:BL21 Bl21] cultures and [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Quantification_/_NanoDrop concentration meassurement via Nanodrop]
-
** [[pEST100]] = 140 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] = 140 ng/µL
-
** [[pET26b(+)]] = 200 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)] = 200 ng/µL
-
** [[pET16]] = 200 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] = 200 ng/µL
 +
 
==== Thursday, 26.04.12 ====
==== Thursday, 26.04.12 ====
-
* [[pEST100]] and [[pET26b(+)]] serve as templates for the follwoing [[PCR 1]]s  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)] serve as templates for the following [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s  
Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SKV]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]
-
#: primers: [[SKV a1 up XbaI]] & [[SKV a1 lo NdeI]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SKV a1 up XbaI & SKV a1 lo NdeI
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [[pNB-Est13]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Esterase13
-
#: primers: [[SOE A up]] & [[SOE a1 lo]]
+
#: primers: SOE A up & SOE a1 lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100]
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
#: gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with FsC
-
#: primers: [[SOE A up]] & [[SOE a2 lo]]
+
#: primers: SOE A up & SOE a2 lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[EstA part1]]
+
#: gene of interest: FsC for SOE PCR with Promo-LacO-RBS-Phoa and EstA part1
-
#: primers: [[SOE b2 up]] & [[SOE b2 lo]]
+
#: primers: SOE b2 up & SOE b2 lo
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
-
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13 part2]]
+
#: gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
-
#: primers: [[SOE b1 up]] & [[SOE Est13 mut lo]]
+
#: primers: SOE b1 up & SOE Est13 mut lo
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
-
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] with [[pNB-Est13 part1]] and [[EstA part1]]
+
#: gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
-
#: primers: [[SOE Est13 mut up]] & [[SOE b1 lo]]
+
#: primers: SOE Est13 mut up & SOE b1 lo
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] (Agarose gele elektrophoresis) for qualitiy control
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for qualitiy control
[[File:120426_PCR_1-3_dunkel_siehe_Laborbuch_26.4.tif]]
[[File:120426_PCR_1-3_dunkel_siehe_Laborbuch_26.4.tif]]
* 2-5 1.PCR, 6-9 2.PCR, 10-13 3.PCR
* 2-5 1.PCR, 6-9 2.PCR, 10-13 3.PCR
[[File:120426_PCR_4-6_siehe_Laborbuch_26.4.tif]]
[[File:120426_PCR_4-6_siehe_Laborbuch_26.4.tif]]
* 2-5 4.PCR, 6-9 5.PCR, 710-13. 6.PCR
* 2-5 4.PCR, 6-9 5.PCR, 710-13. 6.PCR
 +
==== Friday, 27.04.12 ====
==== Friday, 27.04.12 ====
-
* clean up of 1. PCR on [[pEST100]] from [[Thursday, 26.04.12]] via [[Ammonium acetate - Ehtanol DNA precipitation]], solved in 54 µl ddH<sub>2</sub>O
+
* clean up of 1. PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_26.04.12 Thursday, 26.04.12] via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Ammonium_sulfate_precipitation Ammonium acetate - Ehtanol DNA precipitation], solved in 54 µl ddH<sub>2</sub>O
-
* restriction of cleaned up 1. PCR and [[pET16b]] with XbaI and NdeI over weekend at 37°C  
+
* restriction of cleaned up 1. PCR and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] with XbaI and NdeI over weekend at 37°C  
-
** Annotation: From now on [[SKV]] will be protocolled in [[SKV]] wiki.
+
** Annotation: From now on [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV] will be protocolled in SKV wiki.
 +
 
=== Week 2 / CW 18 ===
=== Week 2 / CW 18 ===
==== Monday, 30.04.12 ====
==== Monday, 30.04.12 ====
-
* [[SOE PCR]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]  
-
** [[pNB-Est13 part1]] & [[pNB-Est13 part2]], primers: [[SOE b1 up]] & [[SOE b1 lo]]
+
** pNB-Est13 part1 & pNB-Est13 part2, [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE b1 up & SOE b1 lo
-
** [[Promo-LacO-RBS-Phoa]] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC], primers: [[SOE A up]] & [[SOE b2 lo]]
+
** Promo-LacO-RBS-Phoa & FsC, primers: SOE A up & SOE b2 lo
** Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E1</sub> = 20s, t<sub>E1</sub> = 35s
** Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E1</sub> = 20s, t<sub>E1</sub> = 35s
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of SOE PCR
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of SOE PCR
[[File:120430 SOE PCR1 dunkel siehe Laborbuch 30.4.png]]
[[File:120430 SOE PCR1 dunkel siehe Laborbuch 30.4.png]]
-
* [[SOE PCR]] of [[Promo-LacO-RBS-Phoa-FsC]] worked, [[pNB-Est13]] did not due to missing clean up via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis], precipitation is insufficient, we do it again
+
* SOE PCR of Promo-LacO-RBS-Phoa-FsC worked, pNB-Est13 did not due to missing clean up via Agarose gel electrophoresis, precipitation is insufficient, we do it again
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
-
# PCR on [[pET26b(+)]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)]
-
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13 part2]]
+
#: gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
-
#: primers: [[SOE b1 up]] & [[SOE Est13 mut lo]]
+
#: primers: SOE b1 up & SOE Est13 mut lo
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
-
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] with [[pNB-Est13 part1]] and [[EstA part1]]
+
#: gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
-
#: primers: [[SOE Est13 mut up]] & [[SOE b1 lo]]
+
#: primers: SOE Est13 mut up & SOE b1 lo
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
* Agarose gel electrophoresis
** 1. PCR worked well 2. PCR did not
** 1. PCR worked well 2. PCR did not
[[File:120430_PCR_-2_der_beiden_EST_Fragmente_1234_est_lo_5678_est_up.tif‎]]
[[File:120430_PCR_-2_der_beiden_EST_Fragmente_1234_est_lo_5678_est_up.tif‎]]
Line 329: Line 138:
==== Wednesday, 02.05.12 ====  
==== Wednesday, 02.05.12 ====  
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [[pNB-Est13]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
-
#: primers: [[SOE A up]] & [[SOE a1 lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE A up & SOE a1 lo
-
# PCR on [[pET26b(+)]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)]
-
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13 part2]]
+
#: gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
-
#: primers: [[SOE b1 up]] & [[SOE Est13 mut lo]]
+
#: primers: SOE b1 up & SOE Est13 mut lo
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
-
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] with [[pNB-Est13 part1]] and [[EstA part1]]
+
#: gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
-
#: primers: [[SOE Est13 mut up]] & [[SOE b1 lo]]
+
#: primers: SOE Est13 mut up & SOE b1 lo
: T<sub>A</sub> = 57°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
: T<sub>A</sub> = 57°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
: every PCR is performed in 3 batches à 50 µL
: every PCR is performed in 3 batches à 50 µL
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[File:120502 PCR 1.png]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]
-
[[File:120502 PCR 2 und 3.png]]
+
-
* [[Promega gel extraction]]
+
** c(1.PCR)=6 ng/µL
** c(1.PCR)=6 ng/µL
** c(2.PCR)=12 ng/µL
** c(2.PCR)=12 ng/µL
** c(3.PCR)=13 ng/µL
** c(3.PCR)=13 ng/µL
-
* [[SOE PCR]] of 2.PCR and 3.PCR in order to form [[pNB-Est13]] for SOE PCR with [[Promo-LacO-RBS-Phoa]] and [[EstA]]
+
* SOE PCR of 2.PCR and 3.PCR in order to form pNB-Est13 for SOE PCR with Promo-LacO-RBS-Phoa and EstA
: T<sub>A1</sub> = 60°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 25 s
: T<sub>A1</sub> = 60°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 25 s
: T<sub>A</sub> = 60°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 35 s
: T<sub>A</sub> = 60°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 35 s
Line 353: Line 160:
==== Tuesday, 03.05.12 ====
==== Tuesday, 03.05.12 ====
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of SOE PCR from yesterday
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of SOE PCR from yesterday
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]  
-
** c[[pNB-Est13]] 7 ng/µL
+
** c(pNB-Est13) 7 ng/µL
==== Friday, 04.05.12 ====
==== Friday, 04.05.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [[pNB-Est13]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
-
#: primers: [[SOE A up]] & [[SOE a1 lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE A up & SOE a1 lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13]]
+
#: gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13
-
#: primers: [[SOE c1 up]] & [[SOE EstA mut PstI out lo]]
+
#: primers: SOE c1 up & SOE EstA mut PstI out lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
#: gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and FsC
-
#: primers: [[SOE c2 up]] & [[SOE EstA mut PstI out lo]]
+
#: primers: SOE c2 up & SOE EstA mut PstI out lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part2]] for [[SOE PCR]] with [[EstA part1]]
+
#: gene of interest: EstA part2 for SOE PCR with EstA part1
-
#: primers: [[SOE EstA mut PstI out up]] & [[SOE D lo]]
+
#: primers: SOE EstA mut PstI out up & SOE D lo
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> = 35 s
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> = 35 s
** every PCR is performed in 3 batches à 50 µL
** every PCR is performed in 3 batches à 50 µL
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[File:120504 pcr Esta1 Est13 + EstA1 Fsc.png]]
 
-
[[File:120504 pcr Esta2.png]]
 
-
[[File:120504 pcr PhoAEst13lapp.png]]
 
=== Week 3 / CW 19 ===
=== Week 3 / CW 19 ===
==== Tuesday  08.05.12 ====
==== Tuesday  08.05.12 ====
-
* [[SOE PCR]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]
-
: gene of interest: [[Promo-LacO-RBS-Phoa-pNBEst13]] for [[SOE PCR]] with [[EstA]]
+
: gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
-
: primers: [[SOE A up]] & [[SOE b1 lo]]
+
: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE A up & SOE b1 lo
-
: template: [[pNB-Est13]] from last friday & [[Promo-LacO-RBS-Phoa]] from [[Wednesday, 02.05.12]]
+
: template: pNB-Est13 from last friday & Promo-LacO-RBS-Phoa from Wednesday, 02.05.12
** annotation: T<sub>A1</sub> = 60°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** annotation: T<sub>A1</sub> = 60°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** T<sub>A2</sub> = 60°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1 min
** T<sub>A2</sub> = 60°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1 min
* did not work
* did not work
==== Wednesday, 09.05.12 ====
==== Wednesday, 09.05.12 ====
-
* [[PCR 1]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR 1]
-
# PCR on [[pET26b(+)]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)]
-
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13 part2]]
+
#: gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
-
#: primers: [[SOE b1 up]] & [[SOE Est13 mut lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE b1 up & SOE Est13 mut lo
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
-
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] with [[pNB-Est13 part1]] and [[EstA part1]]
+
#: gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
-
#: primers: [[SOE Est13 mut up]] & [[SOE b1 lo]]
+
#: primers: SOE Est13 mut up & SOE b1 lo
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[pNB-Est13]]
+
#: gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13
-
#: primers: [[SOE c1 up]] & [[SOE EstA mut PstI out lo]]
+
#: primers: SOE c1 up & SOE EstA mut PstI out lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
#: gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and FsC
-
#: primers: [[SOE c2 up]] & [[SOE EstA mut PstI out lo]]
+
#: primers: SOE c2 up & SOE EstA mut PstI out lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part2]] for [[SOE PCR]] with [[EstA part1]]
+
#: gene of interest: EstA part2 for SOE PCR with EstA part1
-
#: primers: [[SOE EstA mut PstI out up]] & [[SOE D lo]]
+
#: primers: SOE EstA mut PstI out up & SOE D lo
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> = 35 s
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> = 35 s
** every PCR is performed in 2 batches à 50 µL
** every PCR is performed in 2 batches à 50 µL
Line 409: Line 213:
=== Week 4 / CW 20 ===
=== Week 4 / CW 20 ===
==== Monday, 14.05.12 ====
==== Monday, 14.05.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of remaining PCRs from [[Wednesday, 09.05.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction] of remaining PCRs from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_09.05.12 Wednesday, 09.05.12]
-
** c([[pNB-Est13 part1]])=24 ng/µL
+
** c(pNB-Est13 part1)=24 ng/µL
-
** c([[pNB-Est13 part2]])=26 ng/µL
+
** c(pNB-Est13 part2)=26 ng/µL
-
** c([[EstA part2]])=13 ng/µL
+
** c(EstA part2)=13 ng/µL
-
* new [[SOE EstA mut PstI out lo]] is orderd from Sigma-Aldrich
+
* new SOE EstA mut PstI out lo is orderd from Sigma-Aldrich
-
* [[SOE PCR]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]  
-
: gene of interest: [[pNB-Est13]] for [[SOE PCR]] with [[EstA]] and [[Promo-LacO-RBS-Phoa]]
+
: gene of interest: pNB-Est13 for SOE PCR with EstA and Promo-LacO-RBS-Phoa
-
: primers: [[SOE b1 up]] & [[SOE b1 lo]]
+
: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE b1 up & SOE b1 lo
-
: template: [[pNB-Est13 part1]] from last friday & [[pNB-Est13 part2]]
+
: template: pNB-Est13 part1 from last friday & pNB-Est13 part2
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** T<sub>A2</sub> = 57°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1.15 min
** T<sub>A2</sub> = 57°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1.15 min
Line 423: Line 227:
==== Tuesday, 15.05.12 ====
==== Tuesday, 15.05.12 ====
-
* [[Gel extraction]9 of [[SOE PCR]] from yesterday
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction] of SOE PCR from yesterday
-
** c([[pNB-Est13]])=24 ng/µL
+
** c(pNB-Est13)=24 ng/µL
-
* [[SOE PCR]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]  
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[Promo-LacO-RBS-Phoa-pNBEst13]] for [[SOE PCR]] with [[EstA]]
+
#: gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
-
#: primers: [[SOE A up]] & [[SOE b1 lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE A up & SOE b1 lo
-
#: template: [[pNB-Est13]] from yesterday & [[Promo-LacO-RBS-Phoa]] from [[Wednesday, 02.05.12]]
+
#: template: pNB-Est13 from yesterday & Promo-LacO-RBS-Phoa from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_02.05.12 Wednesday, 02.05.12]
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[Promo-LacO-RBS-Phoa-FsC]] for [[SOE PCR]] with [[EstA]]
+
#: gene of interest: Promo-LacO-RBS-Phoa-FsC for SOE PCR with EstA
-
#: primers: [[SOE A up]] & [[SOE b2 lo]]
+
#: primers: SOE A up & SOE b2 lo
-
#: template: [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] from [[Thursday, 26.04.12]] & [[Promo-LacO-RBS-Phoa]] from [[Wednesday, 02.05.12]]
+
#: template: FsC from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_26.04.12 Thursday, 26.04.12] & Promo-LacO-RBS-Phoa from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_02.05.12 Wednesday, 02.05.12]
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> = 35 s
** T<sub>A2</sub> = 57°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1.15 min
** T<sub>A2</sub> = 57°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 1.15 min
** each PCR is performed in 2 batches à 50 µL
** each PCR is performed in 2 batches à 50 µL
 +
==== Wednesday, 16.05.12 ====
==== Wednesday, 16.05.12 ====
-
* [[SOE PCR]] of [[Promo-LacO-RBS-Phoa-pNBEst13] did not work but [[Promo-LacO-RBS-Phoa-FsC]] worked
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR] of Promo-LacO-RBS-Phoa-pNBEst13 did not work but Promo-LacO-RBS-Phoa-FsC worked
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]  
-
** c([[Promo-LacO-RBS-Phoa-FsC]])=10 ng/µL
+
** c(Promo-LacO-RBS-Phoa-FsC)=10 ng/µL
=== Week 5 / Kw 21 ===
=== Week 5 / Kw 21 ===
==== Monday, 23.05.12 ====
==== Monday, 23.05.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [[pNB-Est13]] and [[EstA part2]]
+
#: gene of interest: EstA part1 for SOE PCR with pNB-Est13 and EstA part2
-
#: primers: [[SOE c1 up]] & [[SOE EstA mut PstI out lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE c1 up & SOE EstA mut PstI out lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [[EstA part1]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] and [[EstA part2]]
+
#: gene of interest: EstA part1 for SOE PCR with FsC and EstA part2
-
#: primers: [[SOE c2 up]] & [[SOE EstA mut PstI out lo]]
+
#: primers: SOE c2 up & SOE EstA mut PstI out lo
==== Tuesday, 22.05.12 ====
==== Tuesday, 22.05.12 ====
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]  
-
** c([[EstA part1]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])=4 ng/µL
+
** c(EstA part1 for SOE PCR with FsC)=4 ng/µL
-
** c([[EstA part1]] for [[SOE PCR]] with [[pNB-Est13]])=7 ng/µL
+
** c(EstA part1 for SOE PCR with pNB-Est13)=7 ng/µL
==== Wednesday, 23.05.12 ====
==== Wednesday, 23.05.12 ====
-
* [[SOE PCR]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]  
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[EstA]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
#: gene of interest: EstA for SOE PCR with FsC
-
#: primers: [[SOE c2 up]] & [[SOE D lo]]
+
#: primers: SOE c2 up & SOE D lo
-
#: template: [[EstA part1]] from yesterday & [[EstA part2]] from [[Monday, 14.05.12]]
+
#: template: EstA part1 from yesterday & EstA part2 from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_14.05.12 Monday, 14.05.12]
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> =45 s
** annotation: T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> =45 s
** T<sub>A2</sub> = 65°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 90 s
** T<sub>A2</sub> = 65°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 90 s
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[File:120524 SOE PCR EstAFsc.png]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]  
+
** c(EstA for SOE PCR with pNB-Est13)=42 ng/µL
-
** c([[EstA]] for [[SOE PCR]] with [[pNB-Est13]])=42 ng/µL
+
** c(EstA for SOE PCR with FsC)=23 ng/µL
-
** c([[EstA]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])=23 ng/µL
+
==== Thursday, 24.05.12 ====
==== Thursday, 24.05.12 ====
-
* [[PCR 1]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR 1]
-
# PCR on [[EstA]] for [[SOE PCR]] with [[pNB-Est13]] from yesterday
+
# PCR on EstA for SOE PCR with pNB-Est13 from yesterday
-
#: gene of interest: [[EstA]] for [[SOE PCR]] with [[pNB-Est13]]
+
#: gene of interest: EstA for SOE PCR with pNB-Est13
-
#: primers: [[SOE c1 up]] & [[SOE D lo]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primers]: SOE c1 up & SOE D lo
-
# PCR on [[EstA]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
# PCR on EstA for SOE PCR with FsC
-
#: gene of interest: [[EstA]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
#: gene of interest: EstA for SOE PCR with FsC
-
#: primers: [[SOE c2 up]] & [[SOE D lo]]
+
#: primers: SOE c2 up & SOE D lo
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [[pNB-Est13]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
-
#: primers: [[SOE A up]] & [[SOE a1 lo]]
+
#: primers: SOE A up & SOE a1 lo
-
# PCR on [[pEST100]]
+
# PCR on pEST100
-
#: gene of interest: [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] for [[SOE PCR]] with [[Promo-LacO-RBS-Phoa]] and [[EstA part1]]
+
#: gene of interest: FsC for SOE PCR with Promo-LacO-RBS-Phoa and EstA part1
-
#: primers: [[SOE b2 up]] & [[SOE b2 lo]]
+
#: primers: SOE b2 up & SOE b2 lo
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> =45 s
** annotation: T<sub>A</sub> = 60°C, t<sub>a</sub> = 25 s, t<sub>E</sub> =45 s
: each PCR is performed in 3 batches à 50 µL
: each PCR is performed in 3 batches à 50 µL
Line 489: Line 293:
** both EstAs worked
** both EstAs worked
** Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13 worked
** Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13 worked
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]
-
** c([[EstA]] for [[SOE PCR]] with [[pNB-Est13]])=39 ng/µL
+
** c(EstA for SOE PCR with pNB-Est13)=39 ng/µL
-
** c([[EstA]] for [[SOE PCR]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])=20 ng/µL
+
** c(EstA for SOE PCR with FsC)=20 ng/µL
-
** c([[Promo-LacO-RBS-Phoa]] for [[SOE PCR]] with [[pNB-Est13]])=13 ng/µL
+
** c(Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13)=13 ng/µL
=== Week 6 / Kw 22 ===
=== Week 6 / Kw 22 ===
==== Tuesday, 29.05.12 ====
==== Tuesday, 29.05.12 ====
-
* [[SOE PCR]]s
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR SOE PCR]s
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[Promo-LacO-RBS-Phoa-Fsc-EstA]]
+
#: gene of interest: Promo-LacO-RBS-Phoa-Fsc-EstA  
-
#: primers: [[SOE A up]] & [[SOE D lo]]
+
#: primers: SOE A up & SOE D lo
-
#: template: [[EstA]] from [[Thursday, 24.05.12]] & [[Promo-LacO-RBS-Phoa-Fsc]] from [[Wednesday, 16.05.12]]
+
#: template: EstA from Thursday, 24.05.12  & Promo-LacO-RBS-Phoa-Fsc from Wednesday, 16.05.12
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[Promo-LacO-RBS-Phoa-pNBEst13-EstA]]
+
#: gene of interest: Promo-LacO-RBS-Phoa-pNBEst13-EstA
-
#: primers: [[SOE A up]] & [[SOE D lo]]
+
#: primers: SOE A up & SOE D lo
-
#: template: [[EstA]] from [[Thursday, 24.05.12]] & [[Promo-LacO-RBS-Phoa]] from [[Wednesday, 02.05.12]] & [[pNB-Est13]] from [[Monday, 14.05.12]]
+
#: template: EstA from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_24.05.12 Thursday, 24.05.12] & Promo-LacO-RBS-Phoa from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_02.05.12 Wednesday, 02.05.12] & pNB-Est13 from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_14.05.12 Monday, 14.05.12]
-
# [[SOE PCR]]
+
# SOE PCR
-
#: gene of interest: [[Promo-LacO-RBS-Phoa-pNBEst13]] for [[SOE PCR]] with [[EstA]]
+
#: gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
-
#: primers: [[SOE A up]] & [[SOE b1 lo]]
+
#: primers: SOE A up & SOE b1 lo
-
#: template: [[Promo-LacO-RBS-Phoa]] from [[Wednesday, 02.05.12]] & [[pNB-Est13]] from [[Monday, 14.05.12]]
+
#: template: Promo-LacO-RBS-Phoa from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_02.05.12 Wednesday, 02.05.12] & pNB-Est13 from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_14.05.12 Monday, 14.05.12]
** annotation: each PCR is performed in 3 batches à 50 µL
** annotation: each PCR is performed in 3 batches à 50 µL
** T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> =45 s
** T<sub>A1</sub> = 52°C, t<sub>a1</sub> = 25 s, t<sub>E1</sub> =45 s
** T<sub>A2</sub> = 65°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 90 s
** T<sub>A2</sub> = 65°C, t<sub>a2</sub> = 25 s, t<sub>E2</sub> = 90 s
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
** [[Promo-LacO-RBS-Phoa-Fsc-EstA]] worked
+
** Promo-LacO-RBS-Phoa-Fsc-EstA worked
-
** [[Promo-LacO-RBS-Phoa-pNBEst13]] worked
+
** Promo-LacO-RBS-Phoa-pNBEst13 worked
==== Thursday, 29.05.12 ====
==== Thursday, 29.05.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction]
-
** c([[Promo-LacO-RBS-Phoa-Fsc-EstA]])= 8 ng/µL
+
** c(Promo-LacO-RBS-Phoa-Fsc-EstA)= 8 ng/µL
-
** c([[Promo-LacO-RBS-Phoa-pNBEst13]])= 13 ng/µL
+
** c(Promo-LacO-RBS-Phoa-pNBEst13)= 13 ng/µL
-
Due to better results in [[SKV]] we stopped our tries in SOE PCR assembly of our total construct [[BBa_K808032]]
+
Due to better results in [https://2012.igem.org/wiki/index.php?title=Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV] we stopped our tries in SOE PCR assembly of our chimeric protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030].
== SKV ==
== SKV ==
 +
 +
[[File:molecular cloning.jpg|500px|left|thumb]]
 +
 +
The shortcut SKV stands for "Standard Klonierungs Verfahren", in english standard molecular cloning. The team tried to build up the whole construct without usage of the BioBrick system as a second way. Here the team had to generate many primers with different restriction sites to connect the parts of the construct.
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
=== Week 1 / CW 17 ===
=== Week 1 / CW 17 ===
==== Tuesday, 24.04.12 ====
==== Tuesday, 24.04.12 ====
-
* Production of [[electrocompetent cells]] [[DH5alpha]] and [[BL21]]  
+
* Production of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electrocompetent_cells electrocompetent cells] [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] and [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21]  
-
* Pouring of [[LB-Agar]] plates with ampecilin resistance (AMP)
+
* Pouring of [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB-Agar] plates with ampecilin resistance (AMP)
-
* setting of [[DYT media]]
+
* setting of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT media]
-
* [[Electroporation]] of [[BL21]] with the following plasmids
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of BL21 with the following plasmids
-
** [[pEST100]], carrying a CM-resistance, the genes of [[phoA]], [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] and [[EstA]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100], carrying a CM-resistance, the genes of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 phoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA]
-
** [[pET26b(+)]], carrying a Kan-resistance and the gene of [[pNB-Est13]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)], carrying a Kan-resistance and the gene of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13]
-
** [[pET16]], carrying an Amp-resistance , and is needed for our [[SKV]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b], carrying an Amp-resistance , and is needed for our [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]
 +
 
==== Wednesday, 25.04.12 ====
==== Wednesday, 25.04.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of  the 3 overnigth [[Bl21]] cultures and [[concentration meassurement via Nanodrop]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of  the 3 overnigth [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21] cultures and [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Quantification_/_NanoDrop concentration meassurement via Nanodrop]
-
** [[pEST100]] = 140 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] = 140 ng/µL
-
** [[pET26b(+)]] = 200 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)] = 200 ng/µL
-
** [[pET16]] = 200 ng/µL
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] = 200 ng/µL
 +
 
==== Thursday, 26.04.12 ====
==== Thursday, 26.04.12 ====
-
* [[pEST100]] and [[pET26b(+)]] serve as templates for the following [[PCR I]]s  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)] serve as templates for the following [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s  
Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
Annotation: Every PCR is done in 4 assays à 50 µL, T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
-
# PCR on [[pEST100]]
+
# [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR 1]on pEST100
-
#: gene of interest: [[Promo-LacO-RBS-Phoa]] for [[SKV]]
+
#: gene of interest: Promo-LacO-RBS-Phoa for [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]
-
#: primers: [[SKV a1 up XbaI]] & [[SKV a1 lo NdeI]]
+
#: [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation Primer]s: SKV a1 up XbaI & SKV a1 lo NdeI
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] (Agarose gele elektrophoresis) for qualitiy control
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] (Agarose gele elektrophoresis) for qualitiy control
-
[[120426 PCR 1-3 siehe Laborbuch 26.4.tif]]
+
[[File: 120426_PCR_1-3_siehe_Laborbuch_26.4-1.png]]
 +
* 2-12= phoA
 +
 
==== Friday, 27.04.12 ====
==== Friday, 27.04.12 ====
-
* clean up of 1. PCR on [[pEST100]] from [[Thursday, 26.04.12]] via [[Ammonium acetate - Ehtanol DNA precipitation]], solved in 54 µl ddH<sub>2</sub>O
+
* clean up of 1. PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_26.04.12_2 Thursday, 26.04.12] via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Ammonium_sulfate_precipitation Ammonium acetate - Ehtanol DNA precipitation], solved in 54 µl ddH<sub>2</sub>O
-
* restriction of cleaned up 1. PCR and [[pET16b]] with XbaI and NdeI over weekend at 37°C
+
* restriction of cleaned up 1. PCR and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] with XbaI and NdeI over weekend at 37°C
 +
 
=== Week 2 / CW 18 ===
=== Week 2 / CW 18 ===
==== Monday, 30.04.12 ====
==== Monday, 30.04.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of DNA digestion from [[Friday, 27.04.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of DNA digestion from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Friday.2C_27.04.12_2 Friday, 27.04.12]
-
[[120430 Testrestrikt.XbaINdeI.tif]]
+
* Only one single band on Agarose gel electrophoresis
-
* Only one single band on [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] image
+
** For saveness two single digests are performed at 20 µL batches. One with XbaI and the other with NdeI. Incubation for 2 hours.
** For saveness two single digests are performed at 20 µL batches. One with XbaI and the other with NdeI. Incubation for 2 hours.
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of single digests  
+
* Agarose gel electrophoresis of single digests  
-
[[File:TU_Darmstadt_logo.png|200px]]
+
** Enzymes cut once each, so digest should have worked.
** Enzymes cut once each, so digest should have worked.
-
* [[Ligation]] of [[PhoA]] in cut (XbaI / NdeI) [[pET16b(+)]]
+
[[File: 120430_Testrestrikt.XbaINdeI_zugeschnitten.png]]
-
** Annotation: 30 µL batch, 1:5 ratio, Ligation at 4°C for 2 days till [[Wednesday, 02.05.12]]
+
** 2= uncut [[pET16b]]
 +
** 3= [[pET16b]] cut with NdeI
 +
** 4= [[pET16b]] cut with XbaI
 +
 
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of PhoA in cut (XbaI / NdeI) [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]
 +
** Annotation: 30 µL batch, 1:5 ratio, Ligation at 4°C for 2 days till Wednesday, 02.05.12
 +
 
=== Week 4/CW 20 ===
=== Week 4/CW 20 ===
==== Monday, 07.05.====
==== Monday, 07.05.====
-
*[[Electroporation]] of [[DH5alpha]] with 5 µl of the ligation which was performed 2 days before.
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with 5 µl of the ligation which was performed 2 days before.
-
* clean up of the PCR-product PhoA [[Friday, 04.05.]]
+
 
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of half of the product with XbaI/NdeI for 1,5h at 37°C
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of the remaining PCR product PhoA with XbaI/NdeI for 1,5h at 37°C [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_26.04.12_2 Thursday, 26.04.]
 +
 
* PhoA is cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* PhoA is cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* concentration:7,36 ng/µl,10,6 ng/µl
* concentration:7,36 ng/µl,10,6 ng/µl
-
*[[Ligation]] of PhoA x [[pET16b(+)]] for 2h, at the rate of (Vector/Insert) 1:5, 1:3
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of PhoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] for 2h, at the rate of (Vector/Insert) 1:5, 1:3
-
Annotation: If it does not say anything else, [[Ligation]] is always done in 20µl batches.
+
Annotation: If it does not say anything else, Ligation is always done in 20µl batches.
 +
 
==== Tuesday, 08.05. ====
==== Tuesday, 08.05. ====
-
* Transformation of [[DH5alpha]] with [[PhoA]] x [[pET16b(+)]] was not successfull, so it was performed again [[Monday, 07.05.]]
+
* Transformation of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with PhoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] was not successfull, so it was performed again [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_07.05. Monday, 07.05.]
-
* DNA digestion of [[pET16b(+)]]
+
* DNA digestion of pET16b
** 100 µl are cut with XbaI/NdeI, incubaton-time: 1,5h at 37°C
** 100 µl are cut with XbaI/NdeI, incubaton-time: 1,5h at 37°C
-
** product is cleaned up by [[Ammonium acetate - Ehtanol DNA precipitation]]
+
** product is cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Ammonium_sulfate_precipitation Ammonium acetate - Ehtanol DNA precipitation]
**concentration: 85 ng/µl
**concentration: 85 ng/µl
 +
==== Wednesday, 09.05.====
==== Wednesday, 09.05.====
-
* [[Colony-PCR]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR]  
-
** gene of interest: [[PhoA]]
+
** gene of interest: PhoA
-
** primer:[[SKV a1 up XbaI]], [[SKV a1 lo NdeI]] 
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primer]:SKV a1 up XbaI, SKV a1 lo NdeI
-
* PhoA was not inserted, but 2 colonies were picked and inoculated in 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB] Amp medium to look at it again due to a test-restriction.  
+
* PhoA was not inserted, but 2 colonies were picked and inoculated in 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB] Amp medium to look at it again due to a test-restriction.
 +
 
==== Thursday, 10.05.====
==== Thursday, 10.05.====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [[PhoA]] x [[pET16b(+)]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of PhoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep]: [[PhoA]] x [[pET16b(+)]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep]: [[(PhoA x pET16b)]]  
** enzymes: XbaI/NdeI, incubation: 1,5 h, 37°C
** enzymes: XbaI/NdeI, incubation: 1,5 h, 37°C
-
** digest shows that [[PhoA]] was not inserted
+
** digest shows that PhoA was not inserted
-
** [[Ligation]] is performed again [[Monday, 07.05.]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] is performed again [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_07.05. Monday, 07.05.]
-
* Amplification of the genes [[FSC]], [[Est13]] and [[EstA]] via [[PCR gg 1]]
+
* Amplification of the genes FSC, Est13 and EstA via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR1]
* templates:
* templates:
-
** [[FSC]]: pEST100
+
** FSC: pEST100
-
** [[Est13]]: pET26b
+
** Est13: pET26b
-
** [[EstA]]: product of [[SOE-PCR]]
+
** EstA: product of [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SOE_PCR SOE-PCR]
-
* primer:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primer]:
-
** [[SKV b1 up NdeI]], [[SKV b1 lo NcoI]]
+
** SKV b1 up NdeI, SKV b1 lo NcoI
-
** [[SKV b2 up NdeI]], [[SKV b2 lo NCOI]]
+
** SKV b2 up NdeI, SKV b2 lo NCOI
-
** [[SKV c1 up NcoI]], [[SKV c1 lo EcoRI]]
+
** SKV c1 up NcoI, SKV c1 lo EcoRI
 +
 
==== Friday, 11.05. ====
==== Friday, 11.05. ====
-
* an analytic, 1% agarose-gel proves that the amplification of [[FSC]], [[Est13]] and [[EstA]] was successfull.
+
* an analytic, 1% agarose-gel proves that the amplification of FSC, Est13 and EstA was successfull.
-
[[File:TU_Darmstadt_logo.png|200px]]
+
* But to amplify Est13 it was used the product of the [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SOE_PCR SOE PCR] which had not been cleaned up, so the large Fragments of the SOE-primers might have disturbed the amplification. The PCR of Est13 had to be performed again ([https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_16.05. Wednesday, 16.05.])
-
* DNA digestion of [[pET16b(+)]] to produce template for a new ligation of [[PhoA]]
+
[[File: 120511_-_Kopie1.png]]
 +
* 2,3,5,6= Est13
 +
* 7,8,9,10= EstA
 +
* 11,12= FSC
 +
* DNA digestion of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] to produce template for a new ligation of PhoA
** concentration: 76,3 ng/µl
** concentration: 76,3 ng/µl
** enzymes: XbaI, NdeI
** enzymes: XbaI, NdeI
** incubation: for 2 days, 37°C
** incubation: for 2 days, 37°C
-
* [[LIgation]] of [[PhoA]] x [[pET16b(+)]] cut with XbaI and NdeI is carried out using different rates of Vector and insert:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of PhoA x pET16b cut with XbaI and NdeI is carried out using different rates of Vector and insert:
** ratio vector/insert= 3:1, 1:1, 1:3, 1:5, 1:7, 1:10
** ratio vector/insert= 3:1, 1:1, 1:3, 1:5, 1:7, 1:10
-
** PhoA= 10,6 ng/µl [[Monday,07.05.]]
+
** PhoA= 10,6 ng/µl [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_07.05. Monday,07.05.]
** incubation: 2 days, 4°C
** incubation: 2 days, 4°C
 +
=== Week5/CW21 ===
=== Week5/CW21 ===
==== Monday, 14.05.====
==== Monday, 14.05.====
-
* the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [[pET16b(+)]] cut with XbaI and NdeI is isolated by [[Ammonium acetate - Ehtanol DNA precipitation]]
+
* the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b] cut with XbaI and NdeI is isolated by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Ammonium_sulfate_precipitation Ammonium acetate - Ehtanol DNA precipitation]
-
* [[LIgation]] of [[phoA]] x [[pET16b(+)]] is used to transform [[DH5alpha]] via [[Electroporation]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of [[(phoA x pET16b)]] is used to transform [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation]
 +
 
==== Tuesday, 15.05.====
==== Tuesday, 15.05.====
-
*[[Colony-PCR]]
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR]
-
**primer:
+
**[https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primer:]
-
**[[SKV a1 up XbaI]],  
+
**SKV a1 up XbaI,  
-
**[[SKV a1 lo NdeI]]
+
**SKV a1 lo NdeI
-
*[[File:TU_Darmstadt_logo.png|200px]]
+
 
-
*PhoA is inserted, so 10 clones are picked to grow them in 5ml DYT over night.
+
[[File: 120515_colony_PCR_+_SkV_Est13_beschriftet.png]]
 +
 
 +
*PhoA is inserted, so 10 clones (2-9,11,12) are picked to be grown in 5ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] over night.
 +
 
==== Wednesday, 16.05.====
==== Wednesday, 16.05.====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of 10 clones, the plasmid-DNA is isolated out of 3ml culture per clone.
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of 10 clones, the plasmid-DNA is isolated out of 3ml culture per clone.
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] with NdeI and NcoI of the plasmids [[PhoA]] x [[pET16b(+)]] 1-4, so [[FSC]] and [[Est13]] can be added to the construct.
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] with NdeI and NcoI of the plasmids ([[phoA]] x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]) 1-4, so FSC and Est13 can be added to the construct.
-
* [[FSC]] is cut with NdeI and NcoI   
+
* FSC is cut with NdeI and NcoI   
** digests are performed in 20µl total volume at 37°C for 1,5h and cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
** digests are performed in 20µl total volume at 37°C for 1,5h and cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
* [[File:TU_Darmstadt_logo.png|200px]]
+
 
-
* [[PCR1]] of [[EST13]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR1] of EST13  
** template: product of SOE-PCR, cleaned up by the Promega-Kit
** template: product of SOE-PCR, cleaned up by the Promega-Kit
-
** primer: [[SKV b1 up NdeI]], [[SKV b1 lo NcoI]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation primer]: SKV b1 up NdeI, SKV b1 lo NcoI
 +
** an analytical Agarose gel electrophoresis is performed
 +
 
 +
[[File: 120516_SOE_PCR_PhoA_Est13_+_SkV_Est13_FsC2.png]]
 +
** 7-10 = [[Est 13]]
 +
 
==== Friday, 18.05.====
==== Friday, 18.05.====
-
*[[Ligation]] of [[FSC]] x ([[phoA]] x [[pET16b(+)]])
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of FSC x (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
** ratio vector/insert: 3:1, 1:1, 1:3
** ratio vector/insert: 3:1, 1:1, 1:3
**concentration:
**concentration:
-
*([[phoA]] x [[pET16b(+)]])= 3,72 ng/µl
+
*(phoA x pET16b)= 3,72 ng/µl
-
*[[FSC]]= 12,22 ng/µl
+
*FSC= 12,22 ng/µl
 +
 
=== Week 6/CW 22 ===
=== Week 6/CW 22 ===
==== Monday, 21.05.====
==== Monday, 21.05.====
-
* [[Elektroporation]] of [[DH5alpha]] with the [[Ligation]] of [[FSC]] x ([[phoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Elektroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of ([[FSC]]) x ([[phoA]] x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of ([[phoA]] x [[pET16b(+)]])(150µl,160µl) for the insertion of [[Est13]]/[[FSC]] and [[Est13]](50µl)
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of (phoA x pET16b)(150µl,160µl) for the insertion of Est13/FSC
** enzymes: NdeI, NcoI
** enzymes: NdeI, NcoI
** incubation: 1,5h, 37°C
** incubation: 1,5h, 37°C
-
** cleaned up via[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
** cleaned up via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
** c([[phoA]] x [[pET16b(+)]])= 23,5 ng/µl
+
** the DNA fragment at 600 bp proves that the vector has been cut with NdeI and NcoI.
-
** c([[Est13]]= 7,7 ng/µ
+
[[File: 120523_pET16b_Verdau_pET16b_NN1.png]]
 +
** c([[phoA]] x [[pET16b]])= 23,5 ng/µl
 +
 
 +
*Restriction digest of Est13
 +
**cleaned up via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
 +
** c([[Est13]])= 7,7 ng/µl
 +
 
==== Tuesday, 22.05.====
==== Tuesday, 22.05.====
-
* [[Ligation]] of [[Est13]] and ([[phoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of Est13 and ([[phoA]] x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
-
** both components have been cut with NdeI and NcoI [[Monday, 21.05.]]
+
** both components have been cut with NdeI and NcoI [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_21.05. Monday, 21.05.]
** ratio vector/insert: 1:10, 1:5, 1:3
** ratio vector/insert: 1:10, 1:5, 1:3
** incubation: 2h, 25°C
** incubation: 2h, 25°C
-
** [[Electroporation]] of dH5alpha using the [[Ligation]] of [[Est13]] x ([[phoA]] x [[pET16b(+)]], 5 µl per 100µl cells
+
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of dH5alpha using the Ligation of [[Est13]] x ([[phoA]] x [[pET16b]]), 5 µl per 100µl cells
 +
 
==== Wednesday, 23.05. ====
==== Wednesday, 23.05. ====
-
* [[colony-PCR]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR]
** aim is to check the insertion of [[Est13]]
** aim is to check the insertion of [[Est13]]
-
** Primer:[[SKV b1 up NdeI]], [[SKV b1 lo NcoI]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation Primer]:SKV b1 up NdeI, SKV b1 lo NcoI
-
** 8 colonies have been picked and the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] proves, that [[Est 13]] has not been inserted into ([[phoA]] x [[pET16b(+)]]
+
** 8 colonies have been picked and the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] proves, that Est 13 has not been inserted into (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]
-
==== Wednesday, 23.05.====
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of FSC and Est13 in ([[phoA]] x [[pET16b]])
-
* [[Ligation]] of [[FSC]] and [[Est13]] in ([[phoA]] x [[pET16b(+)]]
+
** ratio vector/insert: 1:3, 1:5
** ratio vector/insert: 1:3, 1:5
-
** c(templates):[[Monday, 21.05.]]
+
** c(templates):[https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_21.05. Monday, 21.05.]
-
*[[Elektroporation]] of [[DH5alpha]] with [[Est13]] in ([[phoA]] x [[pET16b(+)]]
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Elektroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with Est13 in (phoA x pET16b)
 +
 
==== Thursday, 24.05. ====
==== Thursday, 24.05. ====
-
* [[colony-PCR]] proves, that [[Est13]] has been inserted into ([[phoA]] x [[pET16b(+)]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR] proves, that [[Est13]] has been inserted into (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
-
** plates are covered with colonies, 8 colonies are chosen for [[colony-PCR]]
+
** plates are covered with colonies, 8 colonies are chosen for colony-PCR
** colony No.5 is chosen to be inoculated in 5µ DYT/Amp medium
** colony No.5 is chosen to be inoculated in 5µ DYT/Amp medium
-
* [PCR 1] is performed again to amplify [[FSC]] and [[Est13]]
+
[[File:120524_o_Est13_FsC_u_Kolonie_PCR_Est131.png]]
 +
 
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR1] is performed again to amplify FSC and Est13
**products are cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
**products are cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
**[[File:TU_Darmstadt_logo.png|200px]]
+
 
==== Friday, 25.05. ====
==== Friday, 25.05. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [[FSC]] and [[Est13]] [[Thursday, 24.05.]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of FSC and Est13 [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_24.05. Thursday, 24.05.]
** enzymes: NdeI, NcoI
** enzymes: NdeI, NcoI
** incubation: 2days, 37°C
** incubation: 2days, 37°C
-
=== week 7/CW 23 ===
+
 
 +
=== Week 7/CW 23 ===
==== Tuesday, 29.05. ====
==== Tuesday, 29.05. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [[FSC]] and [[Est13]] is cleaned up via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of FSC and Est13 is cleaned up via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
* [[MIniprep]] of [[Est13]] x ([[phoA]] x [[pET16b(+)]] via Promega-Kit
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep#Promega_kit Miniprep] of Est13 x (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]) via Promega-Kit
-
* [[Ligation]] of [[FSC]] x ([[phoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of FSC x (phoA x pET16b)
** ratio vector/insert: 1:3, 1:5, 1:10
** ratio vector/insert: 1:3, 1:5, 1:10
** incubation: 2h, 25°C
** incubation: 2h, 25°C
-
* [[Electroporation]] of DH5alpha with 5µl of the [[LIgaton]]: [[FSC]] x ([[phoA]] x [[pET16b(+)]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with 5µl of the Ligaton: FSC x (phoA x pET16b)
-
* [[PCR 1]] to amplify [[EstA]], (Thursday, 10.05.)
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR#PCR_I_NEB_Phusion_.2850_.C2.B5L_batch.29 PCR1] to amplify EstA, [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Thursday.2C_10.05. (Thursday, 10.05.)]
** 4 assays à 50 µL, T<sub>A</sub> = 66°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90s
** 4 assays à 50 µL, T<sub>A</sub> = 66°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90s
** cleaned up via Kit
** cleaned up via Kit
 +
** An analytical electrophoresis is performed
 +
 +
*[[File:120529_EstASKVund_SOEXXX1.png]]
 +
==== Wednesday, 30.05. ====
==== Wednesday, 30.05. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [[EstA]] (product of PCR, 80 µl) and Plasmid: ([[Est13]] x [[phoA]] x [[pET16b(+)]])  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of EstA (product of PCR, 80 µl) and Plasmid: (Est13 x phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])  
** enzymes: EcoRI, NcoI
** enzymes: EcoRI, NcoI
** incubation: 1,5h, 37°C
** incubation: 1,5h, 37°C
-
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
** The [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] shows, that two DNA fragments are cut out of the vector (Est13 x phoA x pET16b). This might be a hint that Est13 is not inserted.
-
** [[File:TU_Darmstadt_logo.png|200px]]
+
[[File: 120530_VPE_+_EstA_Reinigung_Verdau1.png]]
-
** c([[EstA]]) = 6,7 ng/µl
+
** 1-3 = (Est13 x phoA x pET16b)
-
** c([[Est13]] x [[phoA]] x [[pET16b(+)]])= 23 ng/µl  
+
** 4-5 = EstA
-
* [[Electroporation]] of [[FSC]] x ([[phoA]] x [[pET16b(+)]] worked well, plates are covered with colonies which are picked to be grown in 5ml DYT/Amp medium over night.
+
** c(EstA) = 6,7 ng/µl
 +
** c(Est13 x phoA x pET16b)= 23 ng/µl  
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of (FSC x phoA x pET16b) worked well, plates are covered with colonies which are picked to be grown in 5ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT]/[https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin Amp] medium over night.
 +
 
==== Thursday, 31.05. ====
==== Thursday, 31.05. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the amplified ([[FSC]] x [[phoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the amplified (FSC x phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
-
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] to ligate [[EstA]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] to ligate EstA
** enzymes:NcoI, EcoRI
** enzymes:NcoI, EcoRI
** incubation: 1,5h, 37°C  
** incubation: 1,5h, 37°C  
-
* to be sure that the plasmid ([[Est13]] x [[phoA]] x [[pET16b(+)]]) really carries [[Est13]] and [[PhoA]], an analytic [[PCR1]] is performed. Also [[pEt16b(+)]] is used as template with different primers.
+
* to be sure that the plasmid (Est13 x phoA x pET16b) really carries Est13 and PhoA, an analytic [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] is performed. Also pEt16b is used as template with different primers.
* templates:
* templates:
-
** [[pEt16b(+)]] [[Wednesday, 25.04.]]
+
** pET16b [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_25.04.12_2 Wednesday, 25.04.]
-
** ([[phoA]] x [[pET16b(+)]]) [[Wednesday, 16.05.]]
+
** (phoA]] x pET16b) [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_16.05. Wednesday, 16.05.]
-
** ([[Est13]] x [[phoA]] x [[pET16b(+)]]) [[Monday,29.05.]]
+
** (Est13 x phoA x pET16b) [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Tuesday.2C_29.05. Tuesday,29.05.]
-
* primers, used on each template:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation Primer]s, used on each template:
-
** [[SKV b1 up NdeI]], [[SKV b1 lo NcoI]]
+
** SKV b1 up NdeI, SKV b1 lo NcoI
-
** [[SKV a1 up XbaI]], [[SKV a1 lo NdeI]]
+
** SKV a1 up XbaI, SKV a1 lo NdeI
*conditions:  
*conditions:  
** T<sub>A</sub> = 66°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90s
** T<sub>A</sub> = 66°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90s
* the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] shows, that there is no binding-specifity concerning the genes of interest and the primers, but primers have been checked on mistakes.
* the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] shows, that there is no binding-specifity concerning the genes of interest and the primers, but primers have been checked on mistakes.
-
* to solve the problem, the [[LIgation]] of [[FSC]] and [[Est13]] shall be repeated from the beginning.
+
* to solve the problem, the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of FSC and Est13 shall be repeated from the beginning.
-
* [[File:TU_Darmstadt_logo.png|200px]]
+
[[File:120531ae_Est131.png]]
-
* Additionally,the decision was to go on with the Ligation of [[EstA]] into the Plasmids ([[Est13]] x [[phoA]] x [[pET16b(+)]]) and ([[FSC]] x [[phoA]] x [[pET16b(+)]]), in case that the PCR was proceeded under wrong conditions.
+
* Additionally,the decision was to go on with the Ligation of EstA into the Plasmids (Est13 x phoA x pET16b) and (FSC x phoA x pET16b), in case that the PCR was proceeded under wrong conditions.
 +
 
==== Friday, 01.06. ====
==== Friday, 01.06. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of ([[phoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])
** enzymes: NcoI, NdeI
** enzymes: NcoI, NdeI
** incubation: 1,5 h, 37°C
** incubation: 1,5 h, 37°C
-
* [[LIgation]] of [[Est13]] and [[FSC]]x([[PhoA]]x[[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of Est13 and FSC x (PhoA x pET16b)
** ratio vector/insert: 1:3, 1:5
** ratio vector/insert: 1:3, 1:5
-
** c([[Est13]])= 3 ng/µl
+
** c([[Est13)= 3 ng/µl
-
** c([[FSC]])= 11 ng/µl
+
** c(FSC)= 11 ng/µl
-
** c([[[[phoA]] x [[pET16b(+)]])= 29 ng/µl
+
** c(phoA x pET16b)= 29 ng/µl
** incubation: over night, 25°C
** incubation: over night, 25°C
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of ([[FSC]]x ([[PhoA]] x [[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of (FSC x (PhoA x pET16b)
* enzymes: NcoI, EcoRI
* enzymes: NcoI, EcoRI
* incubation: 1,5h, 37°C
* incubation: 1,5h, 37°C
-
=== week 8/CW 24 ===
+
 
 +
=== Week 8/CW 24 ===
==== Monday, 04.06. ====
==== Monday, 04.06. ====
-
* restriction of  ([[FSC]]x([[PhoA]]x[[pET16b(+)]]) and ([[phoA]]x[[pET16b(+)]]) is cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
* restriction of  (FSC x (phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]) and (phoA x pET16b) is cleaned up by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
**[[File:TU_Darmstadt_logo.png|200px]]
+
**c(FSCx (phoA x pET16b) = 14 ng/µl
-
**c([[FSC]]x ([[PhoA]] x [[pET16b(+)]]) = 14 ng/µl
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation]: (FSC x phoA x pET16b), (EST13 x phoA x pET16b) [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Friday.2C_01.06. Friday, 01.06]
-
*[[Electroporation]] of [[DH5alpha]] with [[Ligation]]: ([[FSC]]x[[PhoA]]x[[pET16b(+)]]), ([[EST13]]x[[PhoA]]x[[pET16b(+)]]) [[Friday, 01.06]]
+
 
==== Tuesday, 05.06. ====
==== Tuesday, 05.06. ====
-
*[[colony-PCR]] on [[EST13]] & [[FSC]] is negative.
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR] on EST13 & FSC is negative.
 +
 
==== Wednesday, 06.06. ====
==== Wednesday, 06.06. ====
-
* [[Electroporation]] of [[DH5alpha]] with [[Ligation]]-assays from 01.06.
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] with [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation]-assays from 01.06.
-
* [[Ligation]] of [[EstA]][[Wednesday,30.05]] and the Plasmids ([[Est13]]x[[phoA]]x[[pET16b(+)]]),([[FSC]]x[[phoA]]x[[pET16b(+)]]) from [[Monday,04.06.]]
+
* Ligation of EstA [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_30.05. Wednesday,30.05] and the Plasmids (Est13 x phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]),(FSC x phoA x pET16b) from [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Monday.2C_04.06. Monday,04.06.]
** ratio vector/insert: 1:3,1:5
** ratio vector/insert: 1:3,1:5
** incubation: 2h, 25°C
** incubation: 2h, 25°C
-
**[[Electroporation]] of [[DH5alpha]] with ([[EstA]]x[[Est13]]x[[phoA]]x[[pET16b(+)]]) and ([[EstA]]x[[FSC]]x[[phoA]]x[[pET16b(+)]])
+
**Electroporation of DH5alpha with (EstA x Est13 x phoA x pET16b) and (EstA x FSC x phoA x pET16b)
 +
 
==== Friday, 08.06. ====
==== Friday, 08.06. ====
* No cells are grown on plates, so the plates are incubated for another two days at RT.
* No cells are grown on plates, so the plates are incubated for another two days at RT.
-
=== week8/ CW24 ===
+
 
 +
=== Week8/ CW24 ===
==== Monday, 11.06.====
==== Monday, 11.06.====
-
* all plates are covered with cells, so a [[colony-PCR]] is performed on either [[Est13]],[[FSC]] or [[EstA]]
+
* all plates are covered with cells, so a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR colony-PCR] is performed on either Est13,FSC or EstA
-
* primer:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation Primer]:
-
** [[SKV b1 up NdeI]], [[SKV b1 lo NcoI]]
+
** SKV b1 up NdeI, SKV b1 lo NcoI
-
** [[SKV b2 up NdeI]], [[SKV b2 lo NCOI]]
+
** SKV b2 up NdeI, SKV b2 lo NCOI
-
** [[SKV c1 up NcoI]], [[SKV c1 lo EcoRI]]
+
** SKV c1 up NcoI, SKV c1 lo EcoRI
** Every PCR is done in 8 assays à 50 µL, T<sub>A</sub> = 57°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90 s
** Every PCR is done in 8 assays à 50 µL, T<sub>A</sub> = 57°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 90 s
 +
==== Tuesday, 12.06. ====
==== Tuesday, 12.06. ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] shows, that EstA has been inserted in both Plasmids, ([[Est13]]x[[PhoA]]x[[pET16b(+)]]) and ([[FSC]]x[[PhoA]]x[[pET16b(+)]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] shows, that EstA has been inserted in both Plasmids, (Est13 x phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]) and (FSC x phoA x pET16b)
-
* [[File:TU_Darmstadt_logo.png|200px]]
+
 
-
* colonies No.3,4 ([[EstA]]x[[FSC]]x[[PhoA]]x[[pET16b(+)]]) and No.15,16 ([[EstA]]x[[Est13]]x[[PhoA]]x[[pET16b(+)]]) seem to be positive on EstA and are picked to be grown in 5ml DYT/Amp medium.
+
* colonies No.3,4 (EstA x FSC x phoA x pET16b) and No.15,16 (EstA x Est13 x phoA x pET16b) seem to be positive on EstA and are picked to be grown in 5ml DYT/Amp medium.
-
*[[colony-PCR]] on [[Est13]] and [[FSC]] shows a lot of unspecific bands, so cloning of the genes from the beginning has to be dropped.
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony-PCR] on Est13 and FSC shows a lot of unspecific bands, so cloning of the genes from the beginning has to be dropped.
-
**[[File:TU_Darmstadt_logo.png|200px]]  
+
[[File: 120612_SKVcolony-PCR%2CVPFE%2CVPEE.png]]
 +
 
==== Wednesday, 13.06. ====
==== Wednesday, 13.06. ====
-
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the clones No. 3,4,15 and 16. [[Tuesday, 12.06.]]
+
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the clones No. 3,4,15 and 16. [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Tuesday.2C_12.06. Tuesday, 12.06.]
-
** c([[EstA]]x[[FSC]]x[[phoA]]x[[pET16b(+)]])=
+
** c(EstA x FSC x PhoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b])=
** No.3=65,17 ng/µl
** No.3=65,17 ng/µl
** No.4=63,8 ng/µl
** No.4=63,8 ng/µl
-
** c([[EstA]]x[[Est13]]x[[phoA]]x[[pET16b(+)]])=
+
** c(EstA x Est13 x PhoA x pET16b)=
** No.15=66,3 ng/µl
** No.15=66,3 ng/µl
** No.16=59,7 ng/µl
** No.16=59,7 ng/µl
-
* for gene-expression, it is performed a [[Elektroporation]] of [[BL21]]-cells with 1µl of the PLasmid-DNA which has just been isolated.  
+
* for gene-expression, it is performed a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation elektroporation] of [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21]-cells with 1µl of the PLasmid-DNA which has just been isolated.
 +
 
==== Friday, 15.06.====
==== Friday, 15.06.====
-
* Transformation of [[BL21]] worked well
+
* Transformation of [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21] worked well
-
* [[Tributyrinagar plates]] with 1mM IPTG were generated, to induce the Lac-Promotor of [[pET16b(+)]], and to demonstrate the esterase-activity by the lysis of Tributyrin.
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin Tributyrinagar plates] with 1mM IPTG were generated, to induce the Lac-Promotor of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b], and to demonstrate the esterase-activity by the lysis of Tributyrin.
-
* afterwards [[Tributyrinagar plates]] are inoculated with cells which were transformed by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] No.3,4,15,16 on [[Wednesday, 13.06.]]
+
* afterwards Tributyrinagar plates are inoculated with cells which were transformed by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] No.3,4,15,16 on [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#Wednesday.2C_13.06. Wednesday, 13.06.]
** incubation: 37°C, 2 days
** incubation: 37°C, 2 days
-
=== week9/CW25 ===
+
 
 +
=== Week9/CW25 ===
==== Monday, 18.06.====
==== Monday, 18.06.====
-
* [[Tributyrinagar plates]] are covered with cells, but no lysis is visible.
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin Tributyrinagar plates] are covered with cells, but no lysis is visible.
** plates are incubated for another day at 25°C.
** plates are incubated for another day at 25°C.
 +
==== Tuesday, 19.06. ====
==== Tuesday, 19.06. ====
* no lysis, plates stay incubated at 25°C.
* no lysis, plates stay incubated at 25°C.
Line 776: Line 652:
* no lysis
* no lysis
==== Friday, 22.06. ====
==== Friday, 22.06. ====
-
* The plasmids No.3,4 ([[EstA]]x[[FSC]]x[[PhoA]]x[[pET16b(+)]]) and No.15,16 ([[EstA]]x[[Est13]]x[[PhoA]]x[[pET16b(+)]]) are prepared for sequencing at [[Seqlab]]
+
* The plasmids No.3,4 (EstA x FSC x phoA x [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET16b pET16b]) and No.15,16 (EstA x Est13 x phoA x pET16b) are prepared for sequencing.
-
* primer:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation Primer]:
-
* ([[EstA]]x[[FSC]]x[[PhoA]]x[[pET16b(+)]]):
+
* (EstA x FSC x phoA x pET16b):
-
** [[T7 up]]
+
** T7 up
-
** [[T7 lo]]
+
** T7 lo
-
** [[SOE EstA mut up lo]]
+
** SOE EstA mut up lo
-
** [[SOE EstA mut up lo]]
+
** [[SOE EstA mut up lo
-
* ([[EstA]]x[[Est13]]x[[PhoA]]x[[pET16b(+)]]):
+
* (EstA x Est13 x phoA x pET16b):
-
** [[T7 up]]
+
** T7 up
-
** [[T7 lo]]
+
** T7 lo
-
** [[SOE Est13 mut up lo]]
+
** SOE Est13 mut up lo
-
** [[SOE Est13 mut up lo]]
+
** SOE Est13 mut up lo
Sequencing was not successfull.
Sequencing was not successfull.
-
It was discovered later, that there was a contamination of the [[DH5alpha]] cells with other plasmid-DNA, probably caused by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation].  
+
It was discovered later, that there was a contamination of the [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5alpha] cells with other plasmid-DNA, probably caused by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation].  
-
[[Verlinkung Arne]]
+
[https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation#SOE_PCR SOE-PCR]<br />
Due to this fact, the isolated plasmids were always mixed up with other plasmids, and sequencing had to fail.
Due to this fact, the isolated plasmids were always mixed up with other plasmids, and sequencing had to fail.
-
The contamination of the cells may have also caused false-positive results of the [[colony-PCR]]s.  
+
The contamination of the cells may have also caused false-positive results of the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR colony-PCR]s.  
-
We suggest that the cutinase [[FSC]] has an additional lipase-activity,  
+
We suggest that the cutinase FSC has an additional lipase-activity,  
-
which causes a lysis of the cell-membrane and may have an selective effect on [[FSC]]-negative mutants while cultivating the cells.
+
which causes a lysis of the cell-membrane and may have an selective effect on FSC-negative mutants while cultivating the cells.
== BioBricks ==
== BioBricks ==
-
=== Week 1 / Kw 29 ===
+
[http://partsregistry.org/Help:An_Introduction_to_BioBricks BioBricks] are standardized parts of synthetic biology. For more information visit the [http://partsregistry.org/Help:An_Introduction_to_BioBricks BioBrick registry]. As a contribution to iGEM it is necessary to submit the isolated enzymes and proteins in the [http://partsregistry.org/Part:pSB1C3 pSB1C3] vector.
 +
=== Week 1 / CW 21 ===
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 Est13]: 3 assays à 50 µl T<sub>Anneal</sub> = 57°C @ 20s
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrohporesis] of the PCR products yields no result due to too short annealing time
 +
* PCR of PhoA, FsC and Est13: 3 assays à 50 µl T<sub>Anneal</sub> = 57/62/67°C @ 120s
 +
* 1% Agarose gel electrohporesis and PCR clean-up using the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Wizard SV Gel and PCR Clean-Up System]
 +
:M Est13 PhoA+RBSx2 PhoAx3 PhoA+RBS Est13x2 FsCx3
 +
:[[File:Pcr_ae_03.JPG|300px]]
 +
:Note: Accidental exchange of PhoA+RBS (57°C) and Est13 (57°C)
 +
 
 +
=== Week 2 / CW 22 ===
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] of FsC: 3 assays à 50 µl T<sub>Anneal</sub> = 57/58,6/60°C @ 120s
 +
:Marker FsC x 3
 +
:[[File:Pcr_ae_01.JPG|200px]]
 +
* PCR of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] and Est13: 2 assays à 50 µl T<sub>Anneal</sub> = 57/62°C @ 120s
 +
:M Est13x2 EstAx2
 +
:[[File:Pcr_ae_02.JPG|300px]]
 +
:Note: PCR of Est13 did fail [only primer band]
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electrocompetent_cells electrocompetent] [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] @ 2,5kV/2mm cuvette using 1µl of [http://partsregistry.org/Part:pSB1C3 pSB1C3] insert cultivation on [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol chlor] [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Pouring_LB_plates LB plates] overnight at 37°C -> no colonies -> growth over weekend at ~25°C
 +
 
 +
=== Week 3 / CW 23 ===
 +
* Purity Plate of [http://partsregistry.org/Part:pSB1C3 pSB1C3] cultures 1d at 37°C
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] culture of pSB1C3 [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] at 500 Hz / 37°C overnight
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the pSB1C3 cutures and determination of the concentration via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Quantification_/_NanoDrop NanoDrop] yields of ~120ng/µl at 100µl
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of PhoA, EstA, Est13 and FsC (200 ng each) with [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcoRI] (à 20 µl)
 +
* Clean-up of the restriction digest via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Salting_Out ammonium sulfate precipitation] utterly fails
 +
 
 +
=== Week 4 / CW 24 ===
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of PhoA, EstA, Est13 and FsC (200 ng each) with [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcoRI] (à 20 µl)
 +
* Clean-up of the restriction digest via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrohporesis] and PCR clean-up using the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Wizard SV Gel and PCR Clean-Up System]] -> only FsC and Vector
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Pouring_LB_plates Pouring plates] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] 50x
 +
* 1:3 and 1:5 [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of [http://partsregistry.org/Part:pSB1C3 pSB1C3] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] at 25°C overnight
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electrocompetent_cells electrocompetent] [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] @ 2,5kV/2mm cuvette using 5µl of pSB1C3-FsC insert; cultivation on Cmp LB plates overnight at 37°C
 +
 
 +
=== Week 5 / CW 25 ===
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] and [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] of EstA, Est13 and PhoA
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrohporesis] of the PCR products
 +
:M PhoA EstA EstA Est13 Est13 FsC Fsc Kol.1 Kol.2
 +
:[[File:Pcr_ae_04.JPG|300px]]
 +
* PCR of EstA, Est13 and PhoA (Templates: PhoA = pEst100; EstA,Est13 = komp. Est13 mutated): 3 assays à 50 µl T<sub>Anneal</sub> = 57/62°C @ 120s
 +
* 1% Agarose gel electrohporesis and PCR clean-up using the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Wizard SV Gel and PCR Clean-Up System]
 +
 
 +
=== Week 6 / CW 26 ===
 +
* Cultivation of [http://partsregistry.org/Part:pSB1C3 pSB1C3] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] (3ml) @ 37°C
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the pSB1C3 cutures and determination of the concentration via [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Quantification_/_NanoDrop NanoDrop] yields of ~47,02/52,11 ng/ml @ 30 µl each
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of EstA, Est13, PhoA and pSB1C3 (200 ng each) with PstI & EcoRI (à 20 µl) @ 37°C for 1:55h
 +
* Heat inactivation of the restriction digest @ 55°C for 25min
 +
 
 +
=== Week 7 / CW 27 ===
 +
Gelelectrophoresis of the restriction digest.
 +
:M PhoA EstA Est13 - pSB1C3
 +
:[[File:Pcr_ae_05.JPG|300px]]
 +
Extraction of the PhoA, EstA, Est13 and pSB1C3 from the agarose gel. Ligation and transformation of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;].
 +
=== Week 8 / CW 28 ===
 +
Colony PCR of the cultures.
 +
:M PhoA PhoA PhoA PhoA EstA EstA Est13 Est13
 +
:[[File:Pcr_ae_06.JPG|300px]]
 +
Gel was run too long. Therefore no conclusion in regard of the transformation success was possible.
 +
=== Week 9 / CW 29 ===
==== Tuesday, 17.07.12 ====
==== Tuesday, 17.07.12 ====
-
* [[PCR 1]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR 1]
: each PCR is performed in 5 batches à 50 µL.
: each PCR is performed in 5 batches à 50 µL.
: T<sub>A</sub> = 57°C, t<sub>A</sub> = 30 s, t<sub>E</sub> = 2 min
: T<sub>A</sub> = 57°C, t<sub>A</sub> = 30 s, t<sub>E</sub> = 2 min
-
# PCR on [[pEST100]]  
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]  
-
#: gene of interest: [[PhoA]] for designing part [[BBa_K808028]]  
+
#: gene of interest: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] for designing part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 BBa_K808028]  
#: primers: [[BBa PhoA up]] & [[BBa PhoA down]]
#: primers: [[BBa PhoA up]] & [[BBa PhoA down]]
-
# PCR on [[pET26b(+)]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)]
-
#: gene of interest: [[pNB-Est13 part1]] for designing part [[BBa_K808026]] via [[SOE PCR]]
+
#: gene of interest: pNB-Est13 part1 for designing part [[BBa_K808026]] via SOE PCR
#: primers: [[BBa Est13 up]] & [[SOE Est13 mut lo]]
#: primers: [[BBa Est13 up]] & [[SOE Est13 mut lo]]
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)  
#: gene of interest: [[pNB-Est13 part2]] for designing part [[BBa_K808026]] via [[SOE PCR]]
#: gene of interest: [[pNB-Est13 part2]] for designing part [[BBa_K808026]] via [[SOE PCR]]
#: primers: [[BBa Est13 down]] & [[SOE Est13 mut up]]
#: primers: [[BBa Est13 down]] & [[SOE Est13 mut up]]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control
-
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
+
* preparative Agarose gel electrophoresis  
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] products
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] products
** 1. PCR (gene of interest: [[phoA]]): c(PhoA)=19 ng/µL
** 1. PCR (gene of interest: [[phoA]]): c(PhoA)=19 ng/µL
** 2. PCR (gene of interest: [[pNB-Est13 part1]]): c(pNB-Est13 part1)=39 ng/µL
** 2. PCR (gene of interest: [[pNB-Est13 part1]]): c(pNB-Est13 part1)=39 ng/µL
** 3. PCR (gene of interest: [[pNB-Est13 part2]]): c(pNB-Est13 part2)=40 ng/µL
** 3. PCR (gene of interest: [[pNB-Est13 part2]]): c(pNB-Est13 part2)=40 ng/µL
-
* [[SOE PCR]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SOE-PCR SOE PCR]
: gene of interest: [[pNB-Est13]] for designing part [[BBa_K808028]]  
: gene of interest: [[pNB-Est13]] for designing part [[BBa_K808028]]  
: primers: [[BBa Est13 up]] & [[BBa Est13 down]]
: primers: [[BBa Est13 up]] & [[BBa Est13 down]]
Line 829: Line 763:
==== Wednesday, 18.07.12 ====
==== Wednesday, 18.07.12 ====
-
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of [[SOE PCR]] (from [[Tuesday, 17.07.12]])
+
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SOE-PCR SOE PCR] (from [[Tuesday, 17.07.12]])
-
[[120718 SOE PCR Est13.jpg]]
+
[[File:120718 SOE PCR Est13.jpg]]
* preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]  
* preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]  
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of SOE PCR produkt
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of SOE PCR produkt
-
* [[PCR 1]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR 1]  
: gene of interest: [[EstA]] from [[SKV]] [[Date]] for designing part [[BBa_K808027]]
: gene of interest: [[EstA]] from [[SKV]] [[Date]] for designing part [[BBa_K808027]]
: primers: [[BBa EstA up]] and [[BBa EstA down]]
: primers: [[BBa EstA up]] and [[BBa EstA down]]
Line 840: Line 774:
** GC Buffer is used
** GC Buffer is used
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[120718 EstA mit bba.jpg]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of PCR product
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] product
+
** gene of interest: [[EstA]]: c(pNB-Est13 part2)=119 ng/µL
** gene of interest: [[EstA]]: c(pNB-Est13 part2)=119 ng/µL
** stored in freezer
** stored in freezer
==== Thursday, 19.07.12 ====
==== Thursday, 19.07.12 ====
-
* inoculation of 5 mL [[DYT-media]] with 5 µL CAM and [[DH5alpha]] carrying pSB1C3 with part [[BBa_K808025]] ([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])
+
* inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media] with 5 µL [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] and [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] carrying pSB1C3 with part [[BBa_K808025]] ([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])
* [[DNA Digestion]] of the following parts
* [[DNA Digestion]] of the following parts
-
## [[PhoA]] from [[Tuesday, 17.07.12]]
+
## [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] from [[Tuesday, 17.07.12]]
-
## [[pNB-Est13]] from[[Tuesday, 17.07.12]]
+
## [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] from[[Tuesday, 17.07.12]]
-
## [[EstA]] from [[Wednesday, 18.07.12]]
+
## [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] from [[Wednesday, 18.07.12]]
-
## [[pSB1C3]]1
+
## [http://partsregistry.org/Part:pSB1C3 pSB1C3] 1
-
## [[pSB1C3]]2
+
## pSB1C3 2
-
** enzymes used: [[EcorI-HF]] & [[PstI-HF]] / for  [[pSB1C3]]2 [[SpeI]] is used instead of [[PstI]]
+
** enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcorI-HF] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF] / for  pSB1C3 2 [https://2012.igem.org/Team:TU_Darmstadt/Materials/SpeI SpeI] is used instead of PstI
-
** in NEBuffer 4
+
** in [https://2012.igem.org/Team:TU_Darmstadt/Materials/NEB_buffers NEBuffer 4]
** Digestion time: 2 h  
** Digestion time: 2 h  
* adding of [[Dephosphatase Antarctica]] from NEB on digested [[pSB1C3]] 1 & 2
* adding of [[Dephosphatase Antarctica]] from NEB on digested [[pSB1C3]] 1 & 2
-
* [[Ligation]] into digested and 5' dephosphorylated [[pSB1C3]] 1
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] into digested and 5' dephosphorylated pSB1C3 1
-
** [[pNB-Est13]]
+
** pNB-Est13
-
** [[PhoA]]
+
** PhoA
-
** [[EstA]]
+
** EstA  
-
* [[bacterial transformation]] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [[DH5alpha]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;]
==== Friday, 20.07.12 ====
==== Friday, 20.07.12 ====
* the following [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] from [[Thursday, 19.07.12]] worked
* the following [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] from [[Thursday, 19.07.12]] worked
-
**[[Ligation]] into digested and 5' dephosphorylated [[pSB1C3]]
+
**[https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] into digested and 5' dephosphorylated [[pSB1C3]]
-
*** [[pNB-Est13]]
+
*** pNB-Est13
-
*** [[PhoA]]
+
*** PhoA
-
* inoculation of 5 mL [[DYT-media]] with 5 µL CAM and two positive colonies from each transformation (from pNB-Est13 3 colonies are taken) .
+
* inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media] with 5 µL [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] and two positive colonies from each transformation (from pNB-Est13 3 colonies are taken) .
-
** in addition [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] is already on plate, but to controle it, 2 [[colony PCR]]s are performed
+
** in addition [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] is already on plate, but to controle it, 2 [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR colony PCR]s are performed
-
* [[Ligation]] of [[EstA]] into digested and 5' dephosphorylated [[pSB1C3]]
+
* Ligation of EstA into digested and 5' dephosphorylated [http://partsregistry.org/Part:pSB1C3 pSB1C3]
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [[DH5alpha]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of inoculated FsC in pSB1C3 ([[BBa_K808025]]) from [[Thursday, 19.07.12]] failed
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of inoculated FsC in pSB1C3 ([[BBa_K808025]]) from [[Thursday, 19.07.12]] failed
-
* inoculation of 5 mL [[DYT-media]] with 5 µL CAM and [[DH5alpha]] carrying pSB1C3 with part [[BBa_K808025]] ([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])
+
* inoculation of 5 mL DYT-media with 5 µL Cmp and [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] carrying pSB1C3 with part [[BBa_K808025]] ([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC])
** incubation at 37°C over weekend of transformations and picked colonies
** incubation at 37°C over weekend of transformations and picked colonies
-
=== Week 2 / CW 30 ===
+
 
 +
=== Week 10 / CW 30 ===
==== Monday, 23.07.12 ====
==== Monday, 23.07.12 ====
-
* [[Colony PCR]] of picked colonies from [[Friday, 20.07.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] of picked colonies from [[Friday, 20.07.12]]
-
[[120723 BBaPhoA BBa PhoA BBa FsC BBa FsC BBa Est13 BBa Est13 BBa Est13.jpg]]
+
[[File:120723 BBaPhoA BBa PhoA BBa FsC BBa FsC BBa Est13 BBa Est13 BBa Est13.jpg]]
-
* 2-3 [[PhoA]] colonies, 4-5 [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] colonies, 6-8 [[pNB-Est13]] colonies
+
* 2-3 PhoA colonies, 4-5 [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] colonies, 6-8 pNB-Est13 colonies
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of one inoculated colony in DYT-media with CAM from [[Friday, 20.07.12]]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of one inoculated colony in DYT-media with CAM from [[Friday, 20.07.12]]
-
** c([[PhoA]] in [[pSB1C3]])=220 ng/µL
+
** c(PhoA in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=220 ng/µL
-
** c([[pNB-Est13]] in [[pSB1C3]])=50 ng/µL
+
** c(pNB-Est13 in pSB1C3)=50 ng/µL
-
* inoculation of 2 x 5 mL [[DYT-media]]-CAM with [[pSB1C3]] carrying [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
+
* inoculation of 2 x 5 mL [[DYT-media]]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with pSB1C3 carrying [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
-
* second transformation of [[EstA]] from [[Friday, 20.07.12]] worked, but too many colonies!  
+
* second transformation of EstA from [[Friday, 20.07.12]] worked, but too many colonies!  
** purity plate is done
** purity plate is done
 +
==== Tuesday, 24.07.12 ====
==== Tuesday, 24.07.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the 2 [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] [[DYT-media]]-CAM cultures with [[pSB1C3]] carrying [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] from yesterday
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of the 2 [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] cultures with [http://partsregistry.org/Part:pSB1C3 pSB1C3] carrying [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] from yesterday
-
** c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]])=168 ng/µL
+
** c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in pSB1C3)=168 ng/µL
-
* purity plate of [[EstA]] in [[pSB1c3]] is positive
+
* purity plate of [[EstA]] in pSB1c3 is positive
** colonies picked
** colonies picked
-
** [[Colony PCR]] with positive control by amplfifying an [[SKV]]-[[EstA]]
+
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] with positive control by amplfifying an EstA from [https://2012.igem.org/wiki/index.php?title=Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV]
-
** Annotation: T<sub>A</sub> = 57°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min, done with NEB- Phusion so its similiar to [[PCR 1]]
+
** Annotation: T<sub>A</sub> = 57°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min, done with NEB- Phusion so its similiar to [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR 1]
** GC Buffer is used
** GC Buffer is used
 +
==== Wednesday, 25.07.12 ====
==== Wednesday, 25.07.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of [[Colony PCR]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR]
** worked out well
** worked out well
[[120725 Colony BBaEstA positiv probe auf SKV EstA.jpg]]
[[120725 Colony BBaEstA positiv probe auf SKV EstA.jpg]]
-
* 2 [[EstA]] colony, 4 [[EstA]] from SKV as a control
+
* 2 EstA colony, 4 EstA from [https://2012.igem.org/wiki/index.php?title=Team:TU_Darmstadt/Labjournal/Degradation#SKV SKV] as a control
-
* [[ Miniprep]] of inoculated 5 ml [[DYT-media]]-CAM
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of inoculated 5 ml DYT-media-Cmp
-
** c([[EstA]] in [[pSB1C3]])=350 ng/µL
+
** c(EstA in pSB1C3)=350 ng/µL
 +
 
==== Thursday, 26.07.12 ====
==== Thursday, 26.07.12 ====
* Sequencing is ordered. The following premixes are used :
* Sequencing is ordered. The following premixes are used :
-
** 10 µL of c([[PhoA]] in [[pSB1C3]])=220 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
+
** 10 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=220 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
-
** 10 µL of c([[PhoA]] in [[pSB1C3]])=220 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
+
** 10 µL of c(PhoA in [[pSB1C3]])=220 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
-
** 7 µL of c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]])=168 ng/µL, 1µL [[VR]], 7 µL ddH<sub>2</sub>O
+
** 7 µL of c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in pSB1C3)=168 ng/µL, 1µL [[VR]], 7 µL ddH<sub>2</sub>O
-
** 7 µL of c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]])=168 ng/µL, 1µL [[VF2]], 7 µL ddH<sub>2</sub>O
+
** 7 µL of c(FsC in pSB1C3)=168 ng/µL, 1µL [[VF2]], 7 µL ddH<sub>2</sub>O
-
** 5 µL of c([[EstA]] in [[pSB1C3]])=350 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
+
** 5 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] in pSB1C3)=350 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
-
** 5 µL of c([[EstA]] in [[pSB1C3]])=350 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
+
** 5 µL of c(EstA in pSB1C3)=350 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
-
** 5 µL of c([[pNB-Est13]] in [[pSB1C3]])=50 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
+
** 5 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in pSB1C3)=50 ng/µL, 1µL [[VR]], 9 µL ddH<sub>2</sub>O
-
** 5 µL of c([[pNB-Est13]] in [[pSB1C3]])=50 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
+
** 5 µL of c(pNB-Est13 in pSB1C3)=50 ng/µL, 1µL [[VF2]], 9 µL ddH<sub>2</sub>O
-
* in order to prepare [[DMSO stocks]] and [[Minipreps]] 5 mL [[DYT-media]]-CAM are inoculated with following colonies containing
+
* in order to prepare [[DMSO stocks]] and [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Minipreps] 5 mL DYT-media-Cmp are inoculated with following colonies containing
-
** [[pNB-Est13]] in [[pSB1C3]]
+
** pNB-Est13 in pSB1C3
-
** [[PhoA]] in [[pSB1C3]]
+
** PhoA in pSB1C3
-
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]]
+
** FsC in pSB1C3
-
** [[EstA]] in [[pSB1C3]]
+
** EstA in pSB1C3
** Annotation: incubation is done at 37°C over night
** Annotation: incubation is done at 37°C over night
 +
==== Friday, 27.07.12 ====
==== Friday, 27.07.12 ====
-
* inoculated [[pNB-Est13]] in [[pSB1C3]] from [[Thursday, 26.07.12]] has not grown over night
+
* inoculated pNB-Est13 in [http://partsregistry.org/Part:pSB1C3 pSB1C3] from [[Thursday, 26.07.12]] has not grown over night
-
** new colony pcked from plate and incubated in 5 mL [[DYT-media]]-CAM at 37°C over night
+
** new colony pcked from plate and incubated in 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] at 37°C over night
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of 3 mL from the following over night [[DYT-media]] cultures from [[Thursday, 26.07.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of 3 mL from the following over night DYT-media cultures from [[Thursday, 26.07.12]]
-
** c([[PhoA]] in [[pSB1C3]])=440 ng/µL
+
** c(PhoA in pSB1C3)=440 ng/µL
-
** c([[pNB-Est13]] in [[pSB1C3]])=450 ng/µL
+
** c(pNB-Est13 in pSB1C3)=450 ng/µL
-
** c([https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]])=90 ng/µL
+
** c(FsC in pSB1C3)=90 ng/µL
-
=== Week 3 / CW 31 ===
+
=== Week 11 / CW 31 ===
==== Monday, 30.07.12 ====
==== Monday, 30.07.12 ====
-
* [[bacterial transformation]] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [[DH5alpha]] with c([[pNB-Est13]] in [[pSB1C3]])=50 ng/µL from [[Monday, 23.07.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] with c(pNB-Est13 in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=50 ng/µL from [[Monday, 23.07.12]]
 +
 
==== Tuesday, 31.07.12 ====
==== Tuesday, 31.07.12 ====
* no results in sequencing our BioBricks / parts from [[Thursday, 26.07.12]] except for [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]]
* no results in sequencing our BioBricks / parts from [[Thursday, 26.07.12]] except for [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]]
Line 942: Line 881:
* Symptoms
* Symptoms
-
** very much transformants on crossed out plates after [[bacterial transformation]] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation]
+
** very much transformants on crossed out plates after [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation]
-
** at first [[Colony PCR]] is positive
+
** at first [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] is positive
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep]s result in very high yields (exceeding >200 ng/µL)
** [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep]s result in very high yields (exceeding >200 ng/µL)
-
** second [[Colony PCR]] is negative
+
** second Colony PCR is negative
** sequencing failed
** sequencing failed
-
** BUT [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [[pSB1C3]]  
+
** BUT [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] in [http://partsregistry.org/Part:pSB1C3 pSB1C3]  
*** has had not very much transformants
*** has had not very much transformants
*** has had a seuqencing result
*** has had a seuqencing result
Line 953: Line 892:
* Diagnosis:  
* Diagnosis:  
-
** our [[bacterial transformation]] is done by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation]
+
** our bacterial transformation is done by Electroporation
** therefor we use electroporation cuvettes, stored in DNA precipitating liquids like isopropanol or ethanol after being washed out.
** therefor we use electroporation cuvettes, stored in DNA precipitating liquids like isopropanol or ethanol after being washed out.
** long before we started these electroporation cuvettes were in use.
** long before we started these electroporation cuvettes were in use.
Line 961: Line 900:
** after a short period of time, bacterial colonies start to seperate and repel their plasmids, selecting only the most "comfortables"
** after a short period of time, bacterial colonies start to seperate and repel their plasmids, selecting only the most "comfortables"
** probably our plasmids, containing big genes on ligated vectors, are pushed out during this phase of selection
** probably our plasmids, containing big genes on ligated vectors, are pushed out during this phase of selection
-
** this slow decrease of plasmid could explain the missing second positive signal of [[Colony PCR]]
+
** this slow decrease of plasmid could explain the missing second positive signal of Colony PCR
* Strategy
* Strategy
-
** switching our method from [[Electroporation]] to [[Heatshock transformation]]
+
** switching our method from Electroporation to [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation]
-
 
+
==== Wednesday, 01.08.12 ====
==== Wednesday, 01.08.12 ====
-
* due to change of strategy the following [[PCR 1]]s are performed
+
* due to change of strategy the following [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR 1]s are performed
-
# PCR on [[pEST100]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100]
#: gene of interest: [[PhoA]] BioBrick for assembly of part [[BBa_K808028]]
#: gene of interest: [[PhoA]] BioBrick for assembly of part [[BBa_K808028]]
#: primers: [[BBa PhoA up]] & [[BBa PhoA down]]
#: primers: [[BBa PhoA up]] & [[BBa PhoA down]]
-
# PCR on [[pEST100]]
+
# PCR on pEST100
#: gene of interest: [[EstA part1]] for [[SOE PCR]] of EstA ([[BBa_K808027]])
#: gene of interest: [[EstA part1]] for [[SOE PCR]] of EstA ([[BBa_K808027]])
#: primers: [[BBa Est A up]] & [[SOE EstA mut PstI out lo]]
#: primers: [[BBa Est A up]] & [[SOE EstA mut PstI out lo]]
-
# PCR on [[pEST100]]
+
# PCR on pEST100
#: gene of interest: [[EstA part2]] for [[SOE PCR]] of EstA ([[BBa_K808027]])
#: gene of interest: [[EstA part2]] for [[SOE PCR]] of EstA ([[BBa_K808027]])
#: primers: [[BBa EstA mut up]] & [[BBa EstA down]]
#: primers: [[BBa EstA mut up]] & [[BBa EstA down]]
-
# PCR on [[pET26b(+)]]
+
# PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)]
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] of pNB-Est13 ([[BBa_K808026]])
#: gene of interest: [[pNB-Est13 part1]] for [[SOE PCR]] of pNB-Est13 ([[BBa_K808026]])
#: primers: [[BBa Est13 up]] & [[BBa Est13 mut lo]]
#: primers: [[BBa Est13 up]] & [[BBa Est13 mut lo]]
-
# PCR on [[pET26b(+)]]
+
# PCR on pET26b(+)
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] of pNB-Est13 ([[BBa_K808026]])
#: gene of interest: [[pNB-Est13 part2]] for [[SOE PCR]] of pNB-Est13 ([[BBa_K808026]])
#: primers: [[BBa Est13 lo]] & [[BBa Est13 mut up]]
#: primers: [[BBa Est13 lo]] & [[BBa Est13 mut up]]
Line 988: Line 926:
* due to time pressure there will be no qualitative but only preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* due to time pressure there will be no qualitative but only preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
** [[PhoA]] only on analytical scale but on same [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with [[EstA part1]]
** [[PhoA]] only on analytical scale but on same [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with [[EstA part1]]
-
[[120801 soe pcr esta1 pcr phoa.jpg]]
 
-
* 1 cut out [[EstA part1]], 2 [[PhoA]]
 
-
[[120801 soe pcr est131 est132.jpg]]
 
-
* 2 cut out [[pNB-Est13 part1]], 3 cut out [[pNB-Est13 part2]]
 
-
[[120801 soe pcr esta2.jpg]]
 
-
* cut out [[EstA part2]]
 
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [[EstA part1]], [[EstA part2]], [[pNB-Est13 part1]] and [[pNB-Est13 part2]]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] of [[EstA part1]], [[EstA part2]], [[pNB-Est13 part1]] and [[pNB-Est13 part2]]
** c([[EstA part1]])=19 ng/µL
** c([[EstA part1]])=19 ng/µL
Line 999: Line 931:
** c([[pNB-Est13 part1]])=45 ng/µL
** c([[pNB-Est13 part1]])=45 ng/µL
** c([[pNB-Est13 part2]])=48 ng/µL
** c([[pNB-Est13 part2]])=48 ng/µL
-
* [[SOE PCR]]s
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SOE-PCR SOE PCR]s
# SOE PCR
# SOE PCR
#: gene of interest: [[EstA]]
#: gene of interest: [[EstA]]
Line 1,012: Line 944:
** stored over night at 10°C
** stored over night at 10°C
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[120801 SOE PCR Est13 EstA EstApart2 kontrolle.jpg]]
+
** lane 2 [[pNB-Est13]], lane 3 [[ESTA]], lane 4[[EstA part2]]
-
* 2 [[pNB-Est13]], 3 [[ESTA]], 4[[EstA part2]]
+
[[File:120801 SOE PCR Est13 EstA EstApart2 kontrolle.jpg]]
 +
 
* [[PCR Clean up]] by Promega Kit of [[PhoA]], [[pNB-Est13]], [[EstA]]  
* [[PCR Clean up]] by Promega Kit of [[PhoA]], [[pNB-Est13]], [[EstA]]  
* [[DNA Digestion]] of the following parts
* [[DNA Digestion]] of the following parts
Line 1,019: Line 952:
## [[pNB-Est13]]  
## [[pNB-Est13]]  
## [[EstA]]  
## [[EstA]]  
-
** enzymes used: [[EcorI-HF]] & [[PstI-HF]]  
+
** enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcorI-HF] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF]  
-
** in NEBuffer 4
+
** in [https://2012.igem.org/Team:TU_Darmstadt/Materials/NEB_buffers NEBuffer 4]
** each digestion is performed in a 60 µL batch
** each digestion is performed in a 60 µL batch
-
** Digestion time: 1.5 h  
+
** Digestion time: 1.5 h
 +
 
==== Thursday, 02.08.12 ====
==== Thursday, 02.08.12 ====
* [[Ligation]] into digested and 5' dephosphorylated [[pSB1C3]]
* [[Ligation]] into digested and 5' dephosphorylated [[pSB1C3]]
Line 1,032: Line 966:
** 1:5 & 1:10 ratio
** 1:5 & 1:10 ratio
** incubation at room temperature for 30 min
** incubation at room temperature for 30 min
-
* [[Heatschock transformation]] of [[DH5alpha]] with our ligation batches
+
* [[Heatschock transformation]] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] with our ligation batches
* incubation over night at 37°C  
* incubation over night at 37°C  
==== Friday, 03.08.12 ====
==== Friday, 03.08.12 ====
-
* transformation succeeded
+
* transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
-
** colonies picked to inoculate 5 ml [[DYT-media]]-CM
+
** colonies picked to inoculate 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp]
 +
 
==== Saturday, 04.08.12 ====
==== Saturday, 04.08.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colonies
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colonies
Line 1,042: Line 977:
** c([[pNB-Est13]] in [[pSB1C3]])=148ng/µL
** c([[pNB-Est13]] in [[pSB1C3]])=148ng/µL
** c([[EstA]] in [[pSB1C3]])=227 ng/µL
** c([[EstA]] in [[pSB1C3]])=227 ng/µL
-
* test [[DNA Digestion]] with EcoRI-HF and PstI-HF
+
* test [[DNA Digestion]] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcoRI-HF] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF]
* [[PCR 2]] on preped plasmids with primers [[VR]] & [[VF2]], and the respective BBa primers
* [[PCR 2]] on preped plasmids with primers [[VR]] & [[VF2]], and the respective BBa primers
: T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
: T<sub>A</sub> = 60°C, t<sub>a</sub> = 35s, t<sub>E</sub> = 25 s
Line 1,049: Line 984:
[[120804 Verdau PhoA, EstA, Est13, PCR auf EstA, Est 13, PhoA, Kontrolle auf Insert und Vektor.jpg]]
[[120804 Verdau PhoA, EstA, Est13, PCR auf EstA, Est 13, PhoA, Kontrolle auf Insert und Vektor.jpg]]
* digestion: 2 [[PhoA]], 3 [[EstA]], 4 [[pNB-Est13]] PCR: 6 [[EstA]] with BBa primers, 7 [[EstA]] with [[VR]] & [[VF2]], 8 [[pNB-Est13]] with BBa primers, 10 [[pNB-Est13]] with [[VR]] & [[VF2]], 11 [[PhoA]] with BBa primers, 12 [[PhoA]] with [[VR]] & [[VF2]]
* digestion: 2 [[PhoA]], 3 [[EstA]], 4 [[pNB-Est13]] PCR: 6 [[EstA]] with BBa primers, 7 [[EstA]] with [[VR]] & [[VF2]], 8 [[pNB-Est13]] with BBa primers, 10 [[pNB-Est13]] with [[VR]] & [[VF2]], 11 [[PhoA]] with BBa primers, 12 [[PhoA]] with [[VR]] & [[VF2]]
-
* tests succeeded
+
* tests [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
** Sequencing of the following parts
** Sequencing of the following parts
*** c([[PhoA]] in [[pSB1C3]])=227 ng/µL
*** c([[PhoA]] in [[pSB1C3]])=227 ng/µL
Line 1,055: Line 990:
*** c([[EstA]] in [[pSB1C3]])=227 ng/µL
*** c([[EstA]] in [[pSB1C3]])=227 ng/µL
* Annotation: failure in mixing sequencing premixes
* Annotation: failure in mixing sequencing premixes
-
* retransformation of [[DH5alpha]] by [[Heatshock transformation]] with the following plasmids with 1 µL each
+
* retransformation of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] by [[Heatshock transformation]] with the following plasmids with 1 µL each
** c([[PhoA]] in [[pSB1C3]])=227 ng/µL
** c([[PhoA]] in [[pSB1C3]])=227 ng/µL
** c([[pNB-Est13]] in [[pSB1C3]])=148ng/µL
** c([[pNB-Est13]] in [[pSB1C3]])=148ng/µL
** c([[EstA]] in [[pSB1C3]])=227 ng/µL
** c([[EstA]] in [[pSB1C3]])=227 ng/µL
-
=== Week 4 / Kw 32 ===
+
 
 +
=== Week 12 / CW 32 ===
Assembly of our composite part RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) is reached by synthesis (from GENEART) of 2 different gene parts:
Assembly of our composite part RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) is reached by synthesis (from GENEART) of 2 different gene parts:
* [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]]
* [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]]
Line 1,066: Line 1,002:
* both products can be assembled by using BsaI. An restriction enzyme, with an restriction site in a defined distance to its recognition site
* both products can be assembled by using BsaI. An restriction enzyme, with an restriction site in a defined distance to its recognition site
==== Monday, 06.08.12 ====
==== Monday, 06.08.12 ====
-
* [[Heatshock transformation]] of [[DH5alpha]] with 1 µL synthesis products (c=100 ng/µL):
+
* [[Heatshock transformation]] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] with 1 µL synthesis products (c=100 ng/µL):
** [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]]
** [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]]
** [[BsaI-Myctag-EstA- bba suffix]]
** [[BsaI-Myctag-EstA- bba suffix]]
Line 1,080: Line 1,016:
* incubation at 37°C over night
* incubation at 37°C over night
==== Tuesday, 07.08.12 ====
==== Tuesday, 07.08.12 ====
-
* [[Colony PCR]] on 4 colonies of each transformation of synthesis product from [[Monday, 06.08.12]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] on 4 colonies of each transformation of synthesis product from [[Monday, 06.08.12]]
** Annotation: PCR is done with house-taq, similar to [[PCR 2]]
** Annotation: PCR is done with house-taq, similar to [[PCR 2]]
** T<sub>A</sub> = 57°C, t<sub>A</sub> = 30 s, t<sub>E</sub> = 90 s
** T<sub>A</sub> = 57°C, t<sub>A</sub> = 30 s, t<sub>E</sub> = 90 s
-
* [[Colony PCR]] succeeded
+
* Colony PCR [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
** from [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]] colonies 5, 2, 11 are picked
** from [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]] colonies 5, 2, 11 are picked
** from [[BsaI-Myctag-EstA- bba suffix]] colonies 1, 10, 16 are picked
** from [[BsaI-Myctag-EstA- bba suffix]] colonies 1, 10, 16 are picked
-
* inoculation of 5 ml [[DYT-media]]-KAN with colonies
+
* inoculation of 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with colonies
* incubation over night at 37°C
* incubation over night at 37°C
* inoculated 5 mL cultures from [[Monday, 06.08.12]] are stored at 4°C
* inoculated 5 mL cultures from [[Monday, 06.08.12]] are stored at 4°C
 +
==== Wednesday, 08.08.12 ====
==== Wednesday, 08.08.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of following 5 mL cultures
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of following 5 mL cultures
Line 1,114: Line 1,051:
*** digestion for 3 h
*** digestion for 3 h
* preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* preperative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
-
[[120808 Restriktion mit E BsaI PhoA Est13 und bsai s EstA.jpg]]
 
* 3-4 cut out [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]], 5-6 cut out [[BsaI-Myctag-EstA- bba suffix]]
* 3-4 cut out [[bba prefix-PhoA-His6tag-pNBEst13-BsaI site]], 5-6 cut out [[BsaI-Myctag-EstA- bba suffix]]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction]
Line 1,129: Line 1,065:
**** primers [[VF2]] & [[VR]], 1.5 µL each
**** primers [[VF2]] & [[VR]], 1.5 µL each
**** 9 µL ddH<sub>2</sub>O
**** 9 µL ddH<sub>2</sub>O
 +
==== Thursday, 09.08.12 ====
==== Thursday, 09.08.12 ====
-
* [[Heatshock transformation]]  of [[DH5alpha]] with 10 µL of each ligation batch from yesterday
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation]  of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] with 10 µL of each ligation batch from yesterday
 +
 
==== Friday, 10.08.12 ====
==== Friday, 10.08.12 ====
* transformation from yesterday suceeded
* transformation from yesterday suceeded
Line 1,136: Line 1,074:
==== Saturday, 11.08.12 ====
==== Saturday, 11.08.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colonies from yesterday
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colonies from yesterday
-
** testing ligation by [[DNA Digestion]] of plasmids with [[EcorI-HF]] & [[PstI-HF]]
+
** testing ligation by [[DNA Digestion]] of plasmids with [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcorI-HF] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF]
-
* [[Colony PCR]] on picked colonies
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] on picked colonies
** Annotation: T<sub>A</sub> = 55°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min, done with house-taq so its similiar to [[PCR 2]]
** Annotation: T<sub>A</sub> = 55°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min, done with house-taq so its similiar to [[PCR 2]]
-
** primers: [[VR]] & [[VF2]]
+
** primers: VR & VF2
-
* Ligation and transformation succeeded
+
* Ligation and transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
[[120811 PCR (VR,VF2) und Verdau (EcoRI,PstI) auf BBa Gesamt von Geneart.jpg]]
[[120811 PCR (VR,VF2) und Verdau (EcoRI,PstI) auf BBa Gesamt von Geneart.jpg]]
-
* 2-5 [[bba prefix-PhoA-His6tag-pNBEst13-Myctag-EstA- bba suffix]] running at round about 3 kb  
+
* 2-5 [[bba prefix-PhoA-His6tag-pNBEst13-Myctag-EstA- bba suffix]] running at round about 3 kb
-
=== Week 5 / CW 33 ===
+
 
 +
=== Week 13 / CW 33 ===
==== Monday, 13.08.12 ====
==== Monday, 13.08.12 ====
* Preparation for designing part [[BBa_K808032]] which is an arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA  
* Preparation for designing part [[BBa_K808032]] which is an arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA  
Line 1,162: Line 1,101:
[[120813 PCR Q5 auf bba gesamt konstrukt.jpg]]  
[[120813 PCR Q5 auf bba gesamt konstrukt.jpg]]  
* 2-4 [[bba prefix-RBS-PhoA-His6tag-pNBEst13-Myctag-EstA-bba suffix]]
* 2-4 [[bba prefix-RBS-PhoA-His6tag-pNBEst13-Myctag-EstA-bba suffix]]
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s succeeded
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR]s [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
-
* [[PCR clean up]] of 1.-3. PCR
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA PCR clean up] of 1.-3. PCR
-
* [[DNA Digestion]] of [[pSB1C3]] carrying [[RFP]] part [[????]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest DNA Digestion] of [[pSB1C3]] carrying [[RFP]] part [[????]]
-
** enzymes used: [[XbaI]] & [[PstI]]
+
** enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/XbaI XbaI] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI]
** performed in 100 µL batch
** performed in 100 µL batch
-
* [[DNA Digestion]] of part [[BBa_K808000]] ([[pSB1C3]] carrying [[Arabinose inducible promotor]])
+
* DNA Digestion of part [[BBa_K808000]] ([[pSB1C3]] carrying [[Arabinose inducible promotor]])
-
** enzymes used: [[SpeI]] & [[PstI]]
+
** enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/SpeI SpeI] & PstI
** performed in 100 µL batch
** performed in 100 µL batch
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]  
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]  
Line 1,177: Line 1,116:
** c(cut S/P [[BBa_K808000]]: [[Arabinose inducible promotor]]) possibility 2= 14 ng/µL
** c(cut S/P [[BBa_K808000]]: [[Arabinose inducible promotor]]) possibility 2= 14 ng/µL
** c(cut X/P [[pSB1C3]] carrying [[RFP]])=20 ng/µL
** c(cut X/P [[pSB1C3]] carrying [[RFP]])=20 ng/µL
-
* [[Ligation]] at 4°C over night of the following combinations:
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] at 4°C over night of the following combinations:
# 1.PCR & 2.PCR in [[pSB1C3]] carrying [[RFP]]
# 1.PCR & 2.PCR in [[pSB1C3]] carrying [[RFP]]
# 3.PCR in [[pSB1C3]] carrying [[RFP]]
# 3.PCR in [[pSB1C3]] carrying [[RFP]]
Line 1,184: Line 1,123:
# 1.PCR & 2. PCR in [[BBa_K808000]] possibility 2
# 1.PCR & 2. PCR in [[BBa_K808000]] possibility 2
# 3.PCR in [[BBa_K808000]] possibility 2
# 3.PCR in [[BBa_K808000]] possibility 2
 +
==== Tuesday, 14.08.12 ====
==== Tuesday, 14.08.12 ====
-
* [[Heatshock transformation]] of ligation batches 1-6 from yesterday
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation] of ligation batches 1-6 from yesterday
 +
 
==== Wednesday, 15.08.12 ====
==== Wednesday, 15.08.12 ====
-
* transformation succeeded
+
* transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
-
* inoculation of 5 mL [[DYT-media]]-CAM of the following colonies
+
* inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] of the following colonies
** colony 1.1
** colony 1.1
** colony 2.1
** colony 2.1
Line 1,200: Line 1,141:
** colony 6.2
** colony 6.2
*** incubation over night at 37°C
*** incubation over night at 37°C
-
* [[Colony PCR]] on colonies 1.1-6.2 with house-taq  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] on colonies 1.1-6.2 with house-taq  
-
** primers: [[VR]] & [[VF2]]
+
** primers: VR & VF2
 +
 
==== Thursday 16.08.12 ====
==== Thursday 16.08.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of colonies from yesterday
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of colonies from yesterday
-
* [[DNA Digestion]] of preped colonies with [[EcorI-HF]] & [[PstI-HF]]
+
* [[DNA Digestion]] of preped colonies with [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcorI-HF] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF]
** incubation for 1.5 h at 37°C
** incubation for 1.5 h at 37°C
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
** FAILURE, because bands on gel are inconsistent
** FAILURE, because bands on gel are inconsistent
-
[[120816 Testrestriktion der pSB1C3 mit e und p colony platten 1 - 6.jpg]]
+
[[File:120816 Testrestriktion der pSB1C3 mit e und p colony platten 1 - 6.jpg]]
* 2 colony 1.1, 3 colony 2.1, 3 colony 2.2, 4 colony 3.1, 5 colony 4.1, 6 colony 4.2, 7 colony 5.1, 8 colony 5.2
* 2 colony 1.1, 3 colony 2.1, 3 colony 2.2, 4 colony 3.1, 5 colony 4.1, 6 colony 4.2, 7 colony 5.1, 8 colony 5.2
* for further information see discussion below
* for further information see discussion below
-
* new inoculation of 5 mL [[DYT-media]]-CAM of Colonies 1.1 - 5.2
+
* new inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] of Colonies 1.1 - 5.2
==== Trouble shooting ====
==== Trouble shooting ====
Line 1,217: Line 1,159:
What should have been transformed:
What should have been transformed:
-
* colony 1.1: 1.PCR & 2.PCR in [[pSB1C3]]
+
* colony 1.1: 1.PCR & 2.PCR in [http://partsregistry.org/Part:pSB1C3 pSB1C3]
-
** should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) in [[pSB1C3]] (length: ~ 3.1 kb)
+
** should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) in pSB1C3 (length: ~ 3.1 kb)
-
* colony 2.1: 3.PCR in [[pSB1C3]] upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1
+
* colony 2.1: 3.PCR in pSB1C3 upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1
-
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in [[pSB1C3]] (length: ~ 4.3kb)
+
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in pSB1C3 (length: ~ 4.3kb)
* colony 2.2: similar to colony 2.1
* colony 2.2: similar to colony 2.1
-
* colony 3.1: 3.PCR in [[pSB1C3]] upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 2
+
* colony 3.1: 3.PCR in pSB1C3 upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 2
-
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in [[pSB1C3]] (length: ~ 4.3kb) like colony 2.1
+
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in pSB1C3 (length: ~ 4.3kb) like colony 2.1
-
* colony 4.1: 3.PCR in [[pSB1C3]]
+
* colony 4.1: 3.PCR in pSB1C3
** should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) in [[pSB1C3]] (length: ~ 3.1 kb)
** should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808030]]) in [[pSB1C3]] (length: ~ 3.1 kb)
* colony 4.2: similiar to colony 4.1
* colony 4.2: similiar to colony 4.1
-
* colony 5.1: 1.PCR & 2.PCR in [[pSB1C3]] upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1
+
* colony 5.1: 1.PCR & 2.PCR in pSB1C3 upstream of part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1
-
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in [[pSB1C3]] (length: ~ 4.3kb)
+
** should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA ([[BBa_K808032]]) in pSB1C3 (length: ~ 4.3kb)
* colony 5.2: similar to colony 5.1
* colony 5.2: similar to colony 5.1
Conclusion:  
Conclusion:  
*estimated gene length was aorund 4,3 kb (colony 5.1, 5.2, 2.1, 2.2 = part [[BBa_K808032]]) or 3,1 kb (colony 1.1, 4.1, 4.2 part [[BBa_K808030]])
*estimated gene length was aorund 4,3 kb (colony 5.1, 5.2, 2.1, 2.2 = part [[BBa_K808032]]) or 3,1 kb (colony 1.1, 4.1, 4.2 part [[BBa_K808030]])
-
* digestion with [[EcoRI-HF]] & [[PstI-HF]] of all [[ligations]] from [[Thursday 16.08.12]] in part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1 shows bands at round about 3 - 3.5 kb
+
* digestion with EcoRI-HF & PstI-HF of all [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation ligations] from [[Thursday 16.08.12]] in part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1 shows bands at round about 3 - 3.5 kb
* when digested with same enzymes of ligations into part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 2, bands are shown at round about 1 - 1.5 kb
* when digested with same enzymes of ligations into part [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 2, bands are shown at round about 1 - 1.5 kb
* this leads to our concluison that [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1 was the not digested DNA band, because resulting gene length of cut insert correlates with length of [[BBa_K808000]] ([[Arabinose inducible promotor]])
* this leads to our concluison that [[BBa_K808000]] ([[Arabinose inducible promotor]]) possibility 1 was the not digested DNA band, because resulting gene length of cut insert correlates with length of [[BBa_K808000]] ([[Arabinose inducible promotor]])
* for a sharper solution an [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with 0.5 % agarose is performed for digestions of colonies 1.1, 3.1, 4.1, 4.2  plus batches from [[Colony PCR]] from [[Wednesday, 15.08.12]]
* for a sharper solution an [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with 0.5 % agarose is performed for digestions of colonies 1.1, 3.1, 4.1, 4.2  plus batches from [[Colony PCR]] from [[Wednesday, 15.08.12]]
-
[[120816 Colony 1.1 3.1 4.1 4.2 Colony Pcr 1-8.tif]]
+
[[File:120816 Colony 1.1 3.1 4.1 4.2 Colony Pcr 1-8.tif]]
* 2-5 colonies 1.1, 3.1, 4.1, 4.2, 6 - 13 colony 1.1, 2.1, 2.2, 3.1, 4.1, 4.2, 5.1, 5.2
* 2-5 colonies 1.1, 3.1, 4.1, 4.2, 6 - 13 colony 1.1, 2.1, 2.2, 3.1, 4.1, 4.2, 5.1, 5.2
-
 
==== Friday, 17.08.12 ====
==== Friday, 17.08.12 ====
Line 1,281: Line 1,222:
** colony 5.1
** colony 5.1
-
=== Week 6 / CW 34 ===
+
=== Week 14 / CW 34 ===
==== Monday 20.08.12 ====
==== Monday 20.08.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of incoucaltes colonies from [[Friday, 17.08.12]]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of incoucaltes colonies from [[Friday, 17.08.12]]
Line 1,294: Line 1,235:
** colony 5.1 using [[VR]], [[SOE EstA mut lo]], [[SOE EstA mut up]] & [[VF2]], 1.5 µL each
** colony 5.1 using [[VR]], [[SOE EstA mut lo]], [[SOE EstA mut up]] & [[VF2]], 1.5 µL each
==== Tuesday 21.08.12 ====
==== Tuesday 21.08.12 ====
-
* [[Ligation]] of [[BBa_K808000]] upstream of [[BBa_K808032]] in [[pSB1C3]] ( to design [[BBa_K808032]])  from [[Friday, 17.08.12]] worked well
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of [[BBa_K808000]] upstream of [[BBa_K808032]] in [[pSB1C3]] ( to design [[BBa_K808032]])  from [[Friday, 17.08.12]] worked well
-
* 6 colonies are picked in order to perform a [[Colony PCR]] and for inoculation of 5 mL [[DYT-media]]-CAM
+
* 6 colonies are picked in order to perform a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Colony_PCR Colony PCR] and for inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp]
** colony A 4.1/2.1 ligated at 4°C  
** colony A 4.1/2.1 ligated at 4°C  
** colony B 4.1/2.1 ligated at 37°C  
** colony B 4.1/2.1 ligated at 37°C  
Line 1,302: Line 1,243:
** colony E 4.2/2.2 ligated at 4°C
** colony E 4.2/2.2 ligated at 4°C
** colony F 4.2/2.2 ligated at 37°C
** colony F 4.2/2.2 ligated at 37°C
-
* [[Colony PCR]]
+
* Colony PCR
: T<sub>A</sub> = 55°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 5 min
: T<sub>A</sub> = 55°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 5 min
-
: primers: [[VF2]] & [[VR]]
+
: primers: VF2 & VR
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis]
** did not work due to immense gene legth ( around 4 kb)
** did not work due to immense gene legth ( around 4 kb)
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] for testing is planned
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] for testing is planned
-
** inoculation of 5 mL [[DYT-media]]-CAM with colony E,F,C,D
+
** inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with colony E,F,C,D
 +
 
==== Wednesday, 22.08.12 ====
==== Wednesday, 22.08.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of inoculated 5 mL [[DYT-media]]-CAM with colony E,F,C,D
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of inoculated 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with colony E,F,C,D
** c(colony C 1.1/5.1 ligated at 4°C)=46 ng/µL
** c(colony C 1.1/5.1 ligated at 4°C)=46 ng/µL
** c(colony D 1.1/5.1 ligated at 37°c)=46 ng/µL
** c(colony D 1.1/5.1 ligated at 37°c)=46 ng/µL
** c(colony E 4.2/2.2 ligated at 4°C)=60 ng/µL
** c(colony E 4.2/2.2 ligated at 4°C)=60 ng/µL
** c(colony F 4.2/2.2 ligated at 37°C)=58 ng/µL
** c(colony F 4.2/2.2 ligated at 37°C)=58 ng/µL
-
* [[DNA Digestion]] of 15 µL of preped plasmids with [[EcoRI-HF]] & [[PstI-HF]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest DNA Digestion] of 15 µL of preped plasmids with [[EcoRI-HF]] & [[PstI-HF]]
** expected insert length: 4.4 kb ([[BBa_K808000]]+[[BBa_K808030]])  
** expected insert length: 4.4 kb ([[BBa_K808000]]+[[BBa_K808030]])  
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with 0.8% agarose
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] with 0.8% agarose
-
[[Verdau vom Gesamtkonstrukt 4.2_2.2 und 5.1_1.1 beide temperaturen.tif]]
+
** ligation worked well, bands are in estimated length
-
* all bands are in same heights, so ligation worked well
+
** lane 2-5: colony 4.2/2.2, lane 6-9: colony 5.1/1.1
-
* ligation worked well, bands are in estimated length
+
[[File:Verdau vom Gesamtkonstrukt 4.2_2.2 und 5.1_1.1 beide temperaturen.tif]]
-
* due to rather bad results of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] colonies are used for inoculation of 5 mL [[DYT-media]]-CAM again
+
* due to rather bad results of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] colonies are used for inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] again
** incubation over night at 37°C
** incubation over night at 37°C
* evaluation of sequencing from [[Wednesday, 08.08.12]]  
* evaluation of sequencing from [[Wednesday, 08.08.12]]  
Line 1,329: Line 1,271:
** but at leat FsC is sequenced completely
** but at leat FsC is sequenced completely
* new sequencing of  
* new sequencing of  
-
** [[PhoA]] in [[pSB1C3]], primers [[VF2]] & [[VR]], 1.5 µL each
+
** PhoA in [[pSB1C3]], primers VF2 & VR, 1.5 µL each
-
** [[EstA]] in [[pSB1C3]], primers [[SOE EstA mut up]] & [[BBa EstA down]], 1.5 µL each
+
** EstA in [[pSB1C3]], primers [[SOE EstA mut up]] & [[BBa EstA down]], 1.5 µL each
* [[PCR 1]] performed on [[BBa_K808032]](preped colony C 1.1/5.1 ligated at 4°C)
* [[PCR 1]] performed on [[BBa_K808032]](preped colony C 1.1/5.1 ligated at 4°C)
** T<sub>A</sub> = 57°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min
** T<sub>A</sub> = 57°C, t<sub>A</sub> = 25 s, t<sub>E</sub> = 2 min
Line 1,336: Line 1,278:
** performed in 3 batches à 50 µL
** performed in 3 batches à 50 µL
* analytical [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] 2% agarose
* analytical [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] 2% agarose
-
* [PCR Clean up]]  
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA PCR Clean up]  
-
* [[DNA Digestion]] of PCR product with [[EcoRI-HF]] & [[PstI-HF]] over night at 37°C
+
* DNA Digestion of PCR product with [https://2012.igem.org/Team:TU_Darmstadt/Materials/EcoRI EcoRI-HF] & [https://2012.igem.org/Team:TU_Darmstadt/Materials/PstI PstI-HF] over night at 37°C
 +
 
==== Thursday, 23.09.12 ====
==== Thursday, 23.09.12 ====
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of colonies from  
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of colonies from  
Line 1,345: Line 1,288:
** c(colony F 4.2/2.2 ligated at 37°C)=128 ng/µL
** c(colony F 4.2/2.2 ligated at 37°C)=128 ng/µL
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of digested [[pNB-Est13]] from yesterday
* preparative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] of digested [[pNB-Est13]] from yesterday
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] leads to c([[pNB-Est13]]- cut E/P)=25 ng/µL
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Gel_extraction Gel extraction] leads to c(pNB-Est13- cut E/P)=25 ng/µL
-
* [[Ligation]] of digested [[pNB-Est13]] in digested [[pSB1C3]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of digested pNB-Est13 in digested [[pSB1C3]]
** 1:5 ratio is used
** 1:5 ratio is used
-
* [[Heatshock transformation]] of [[DH5alpha]] with 10 µL of ligation batch
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation]] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] with 10 µL of ligation batch
* incubation of transformed cells at 37°C over night
* incubation of transformed cells at 37°C over night
 +
==== Friday, 24.08.12 ====
==== Friday, 24.08.12 ====
-
* transformation of ligation from yesterday succeeded, colony picked and inoculation of 5 mL [[DYT-media]]-CAM
+
* transformation of ligation from yesterday [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000], colony picked and inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp]
* sequencing of  
* sequencing of  
-
** [[BBa_K808032]] (colony C 1.1/5.1 ligated at 4°C), primers [[VF2]], [[XbaI Rbs Phoa up]], [[BBa Ara Promo lo]], [[SE Est13 mut up]], [[SOE Est13 mut lo]], [[BBa EstA down]], [[VR]], 1.5 µL each,  
+
** [[BBa_K808032]] (colony C 1.1/5.1 ligated at 4°C), primers VF2, [[XbaI Rbs Phoa up]], [[BBa Ara Promo lo]], [[SE Est13 mut up]], [[SOE Est13 mut lo]], [[BBa EstA down]], VR, 1.5 µL each,
-
=== Week 7 / CW 35 ===
+
 
 +
=== Week 15 / CW 35 ===
==== Monday, 27.08.12 ====
==== Monday, 27.08.12 ====
-
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colony from [[BBa_K808026]] ([[pNB-Est13]] in [[pSB1C3]])
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of picked colony from [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])
-
** c([[pNB-Est13]] in [[pSB1C3]])=116 ng/µL
+
** c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=116 ng/µL
-
* sequencing of [[pNB-Est13]] in [[pSB1C3]]
+
* sequencing of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3]
-
** using primers [[VF2]], [[VR]], [[SOE Est13 mut up]], [[SOE Est13 mut lo]]
+
** using primers VF2, VR, [[SOE Est13 mut up]], [[SOE Est13 mut lo]]
-
* test expression of [[BBa_K808032]] (colony C 1.1/5.1 ligated at 4°C) in [[DH5alpha]]
+
* test expression of [[BBa_K808032]] (colony C 1.1/5.1 ligated at 4°C) in [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;]
** [[BBa_K808032]] is an arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA
** [[BBa_K808032]] is an arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA
-
** inoculation of 50 mL [[DYT-media]]-CAM with [[DH5alpha]] carrying [[BBa_K808032]]
+
** inoculation of 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5&alpha;] carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
*** stop incubation at at OD<sub>600</sub>=0.7
*** stop incubation at at OD<sub>600</sub>=0.7
*** storaging cultures on ice for 15mins
*** storaging cultures on ice for 15mins
*** inducing with ~ 1.5% L-arabinose (using 3.75 mL of 20% mw L-arobinose solution)
*** inducing with ~ 1.5% L-arabinose (using 3.75 mL of 20% mw L-arobinose solution)
*** incubation at 20°C, 25°C and 30°C over night
*** incubation at 20°C, 25°C and 30°C over night
 +
==== Tuesday, 28.08.12 ====
==== Tuesday, 28.08.12 ====
-
* [[antibody staining]]
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Antibody_staining antibody staining]
-
* detection of surface expression of [[BBa_K808032]] by using [[FACS]]
+
* detection of surface expression of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] by using [[FACS]]
-
* positive signal increases with higher temperature, staining succeeded
+
* positive signal increases with higher temperature, staining [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
-
* [[Protein ourification]] of test expression without rinnung IMAC afterwards, just using supernatant and cell debris pellet
+
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification protein purification] of test expression without running IMAC afterwards, just using supernatant and cell debris pellet
** 32 µL of supernatant is used
** 32 µL of supernatant is used
** 3 mL pellet of each testexpression is treated with more SDS as a detergent, in order to solve membrane proteins
** 3 mL pellet of each testexpression is treated with more SDS as a detergent, in order to solve membrane proteins
-
* running two [[SDS-tris gel]]s with an myc positive probe  
+
* running two [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page SDS-tris gel]s with an myc positive probe  
-
* one of these gels is used for performing a [[Westernblot]]
+
* one of these gels is used for performing a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Western_Blot Westernblot]
** using mouse-antimyc antibody as first antibody and goat-antimouse-AP as second antibody
** using mouse-antimyc antibody as first antibody and goat-antimouse-AP as second antibody
-
[[120831 Westermblot auf Gesamt konstrukt aus DH5 alpha 5111.tif]]
+
** lane 2-4: supernatant of induced and disrupted cells. Level of induction decreases from lane 2 (1.5% arabinose) to lane 4 (0.5% arabinose)
-
* both are not very good in their solution, we do it again with [[Laemmli gel]]s
+
** lane 6-8: Pellet of induced and disrupted cells, treated with high SDS concentrations. Level of induction decreases from lane 6 (1.5% arabinose) to lane 8 (0.5% arabinose).
 +
** Lane 9-10 show myc positive probes.
 +
** The blot shows that our expression worked of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] and proofs the membrane intercalation of our chimeric protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808030] because the blot only gives positive signals when high concentrations of detergent where used to treat the cell debris pellet.
 +
[[File:120831 Westermblot auf Gesamt konstrukt aus DH5 alpha 5111.tif]]
 +
* both are not very good in their solution, we do it again with [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Laemmli.29 Laemmli gel]s
 +
 
==== Wednesday, 29.08.12 ====
==== Wednesday, 29.08.12 ====
* evalutation of sequencing from last week:
* evalutation of sequencing from last week:
Line 1,387: Line 1,338:
** arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA
** arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA
==== Thursday, 30.08.12 ====
==== Thursday, 30.08.12 ====
-
* running 2 [[SDS-Laemmli gel]]s
+
* running 2 [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Laemmli.29 SDS-Laemmli gel]s
** pellet is treated with n-Dodecyl-ß-maltoside (DDM) in order to solve membrane proteins  
** pellet is treated with n-Dodecyl-ß-maltoside (DDM) in order to solve membrane proteins  
-
[[File:TU_Darmstadt_logo.png|200px]]
+
* one gel is used to perform a second [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Western_Blot Western blot] with a myc positive probe
-
* one gel is used to perform a second [[Western blot]] with a myc positive probe
+
[[File:120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111.png]]
-
[[120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111.tif]]
+
* 2 supernatant 30°C, 3 pellet (treated with detergent) 30°C, 4 supernatant 25°C, 5 pellet (treated with detergent) 25°C, 6 supernatant 20°C, 7 pellet (treated with detergent) 20°C, 8 myc positive probe
* 2 supernatant 30°C, 3 pellet (treated with detergent) 30°C, 4 supernatant 25°C, 5 pellet (treated with detergent) 25°C, 6 supernatant 20°C, 7 pellet (treated with detergent) 20°C, 8 myc positive probe
-
* as we can see, only the treated 120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111pellets show positive signals when treated with antibodies, so we have expressed our membrane protein [[BBa_K808032]]
+
* as we can see, only the treated 120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111pellets show positive signals when treated with antibodies, so we have expressed our membrane protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
* now our lab can start with quantification of enzymatic activites of [[BBa_K808032]] on PET or model substrates
* now our lab can start with quantification of enzymatic activites of [[BBa_K808032]] on PET or model substrates
 +
 +
== Activity tests of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] ==
 +
 +
We were able to generate our BioBricks [http://partsregistry.org/Part:BBa_K808030 BBa_K808030] (chimeric, membrane bound, hydrolytic protein) and [http://partsregistry.org/Part:BBa_K808032 BBa_K808032] ( arabinose inducible operon, regulating the expression of BBa_K808030). Funcionality of both parts will be described by a bunch of tests:
 +
 +
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page SDS PAGE]
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Western_Blot Western blot]
 +
* [http://en.wikipedia.org/wiki/Flow_cytometry#Labels flow cytometry]  (after [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Antibody_staining antibody staining])
 +
* screening for hydrolysis by bacterial colonies using [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin#About Tributyrin agar plates]
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#pNP-Assay pNP-Assay] with living cells using para-Nitrophenylbutyrate
 +
 +
* As hosts we will use ''E.coli'' strains [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10], [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5alpha] or [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655]
 +
 +
=== Week 1 / CW 35 ===
 +
==== Friday, 31.08.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#DYT-medium Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
 +
{| class="wikitable"
 +
|-
 +
! Component !! test tube 1 !! test tube 2 !! test tube 3 !! test tube 4
 +
|-
 +
| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL
 +
|-
 +
| PET particle || yes || yes || yes || yes
 +
|-
 +
| bacteria || yes || yes || yes || no
 +
|-
 +
| induced || 1.5% L-arabinose || 1.5% L-arabinose || no || no
 +
|}
 +
* test seemed to have worked: but an induced test tube without PET-granula was missing
 +
 +
=== Week 2 / CW 36 ===
 +
==== Tuesday, 04.09.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#DYT-medium Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
{| class="wikitable"
 +
|-
 +
! Component !! test tube 1 !! test tube 2 !! test tube 3 !! test tube 4 !! test tube 5
 +
|-
 +
| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL
 +
|-
 +
| PET particle || yes || yes || no || yes || yes
 +
|-
 +
| bacteria || yes || yes || yes || no || yes
 +
|-
 +
| induced || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || no || no
 +
|}
 +
*  test tube 3: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin Amp]
 +
* looks good but test tube 2 shows no significant change of colour
 +
 +
==== Wednesday, 05.09.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#DYT-medium Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
{| class="wikitable"
 +
|-
 +
! Component !! tube 1 !! tube 2 !! tube 3 !! tube 4 !! tube 5 !! tube 6 !! tube 7 !! tube 8 !! tube 9
 +
|-
 +
| DYT-medium || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL || 8 mL
 +
|-
 +
| PET particle || yes || yes || yes || yes || no || no || yes || yes || yes
 +
|-
 +
| bacteria || yes || yes || yes || yes || yes || yes || yes || yes || no
 +
|-
 +
| induced || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || 1.5% L-arabinose || no || no || no
 +
|}
 +
* test tube 9: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin Amp]
 +
* all induced tubes turned yellow, even without PET-granula as a substrate
 +
* no more avtivity tests, we are awaiting the evaluation of test expression series of the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter] conjugated to [https://2012.igem.org/Team:TU_Darmstadt/Materials/GFP GFP]
 +
 +
==== Trouble shooting ====
 +
* evaluation shows a very high sensisty of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter [BBa_K808000]] even to low concentrations of [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] (expression starts at around 0.01%)
 +
* induction of the [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] with 1.5% [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose arabinose] ended fatal due to extrem expression of the transmembrane construct [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 RBS-PhoA-His6tag-pNBEst13-Myctag-EstA]
 +
* starting test expressions with lower [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] concentrations ranging from 0.05% - 1%
 +
 +
==== Thursday, 06.09.12 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#DYT-medium Activity assay] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/DH5alpha DH5&alpha;] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 [BBa_K808032]] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
 +
{| class="wikitable"
 +
|-
 +
! Component !! tube 1 !! tube 2 !! tube 3 !! tube 4 !! tube 5 !! tube 6 !! tube 7 !! tube 8 !! tube 9 !! tube 10 !! tube 11
 +
|-
 +
| DYT-medium || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL || 5 mL
 +
|-
 +
| PET particle || yes || yes || yes || yes || yes || yes || no || no || no || no || no
 +
|-
 +
| bacteria || yes || yes || yes || yes || yes || yes || yes || yes || yes || yes || no
 +
|-
 +
| induced || 1% L-arabinose || 1% L-arabinose || 0.75% L-arabinose || 0.75% L-arabinose || no || no || 1% L-arabinose || 1% L-arabinose || 0.75% L-arabinose || 0.75% L-arabinose|| no
 +
|}
 +
* test tube 11: [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] without bacteria contains [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Kanamycin Kan], [https://2012.igem.org/Team:TU_Darmstadt/Materials/Ampicillin Amp]
 +
* all induced tubes turned yellow, even without PET-granula as a substrate
 +
 +
=== Week 3 / CW 37 ===
 +
we stopped the trial of quantification via PET-substrates because in terms of color the change of pH value (due to acid groups that are released by degradtion) is not very exactly. In order to get reproducible data, we are using other activity assays:
 +
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#pNP-Assay pNP-Assay]
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#LB-Agar-Tributyrin activity assay on LB-Tributyrin-CAM-plates] used for screening of hydrolytic bacterial colonies.
 +
 +
==== Monday, 10.09.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Heatshock transformation] of [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#LB-Agar-Tributyrin activity assay on LB-Tributyrin-CAM-plates] with [https://2012.igem.org/Team:TU_Darmstadt/Materials/Arabinose L-arabinose] concentrations: 0.1%, 0.2%, 0.4%
 +
** colony 1-5 are [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5 alpha] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] but colony 6 is just DH5 alpha carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
 +
** incubated over night at 37°C
 +
 +
==== Tuesday, 11.09.12 ====
 +
* inoculation of 5 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with K1 and K2 of transformed [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655] from yesterday
 +
* acticity tests on [[LB-Tributyrin-Cmp-plates]] shows good results
 +
** from now on incubation at room temperature
 +
[[File: 120911 dh5alpha k808032 0.1 ara.jpg|200px]]
 +
[[File: 120911 dh5alpha k808032 0.2 ara.jpg|200px]]
 +
[[File:120911 dh5alpha k808032 0.4 ara.jpg|200px]]
 +
 +
==== Wednesday, 12.09.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep#Promega_kit Plasmid preparation] of inoculated [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655] colonies K1 and K2
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest DNA digestion] with EcoRI-HF & PstI-HF
 +
* qualitative [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis AGE]
 +
[[File:120912 Testrestriktion K808032 im ethylenglycol stamm K1 und K2 mit ecori und psti.tif]]
 +
==== Thursday, 13.09.12 ====
 +
* the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Activity_assay#LB-Agar-Tributyrin activity assay on LB-Tributyrin-Cmp-plates] from tuesday gives good results
 +
 +
[[File:120913 dh5alpha k808032 0.1 ara.jpg|200px]] [[File:120913 dh5alpha k808032 0.2 ara.jpg|200px]] [[File:120913 dh5alpha k808032 0.4 ara.jpg|200px]]
 +
 +
* to perform a better expression of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030] we will use [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] as a host for [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]. Its unability to metabolize L-arabinose is crucial for our decision. We hope to generate good expression levels.
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] (after washing ecletroporation cuvettes very carefully) of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
 +
==== Friday, 14.09.12 ====
 +
* yesterdays electroporation worked well
 +
* inoculation of 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with colony from plate of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
 +
==== Saturday, 15.09.12 ====
 +
* making [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Glycerine_stock#Protocol 10% DMSO stocks] from 50 mL [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] culture
 +
 +
=== Week 4/ KW 38 ===
 +
==== Monday, 17.09.12 ====
 +
* inoculation of 4 x 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT-media]-[https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] stocks
 +
* at OD<sub>600</sub>=0,5 the cultures are incduced with:
 +
** 0.02% mw L-arabinose
 +
** 0.2% mw L-arabinose
 +
** 0.5% mw L-arabinose
 +
** one culture is not induced and will serve as a negative control
 +
* after 3 hours an [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Antibody_staining antibody staining] is performed on our expressed [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] containing a myc-epitope
 +
* checking surface expression levels via [http://en.wikipedia.org/wiki/Flow_cytometry#Labels flow cytometry]
 +
** inducing worked well, we can go on with screening the enzymatic activity
 +
 +
[[Image:Flow cytometry 002 ara.png|200px|left|thumb|''E.coli'' Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.02% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.]] [[Image:Flow cytometry 02 ara.png|200px|left|thumb|''E.coli'' Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.2% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.]][[Image:Flow cytometry 05 ara.png|200px|left|thumb|''E.coli'' Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.5% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.]] [[Image:Flow cytometry alle.png|200px|left|thumb|''E.coli'' Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.02%, 0.2%, 0.5% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.]]
 +
 +
==== Tuesday, 18.09.12 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030], serving as a negative  (directly used after 1h of incubation at 37°C in pure DYT-medium)
 +
* activity assay of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin-CAM-plates LB Tributyrin agar] with L-arabinose concentrations: 0.02%, 0.2%, 0.5%
 +
** colonies 1-3 containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] but colony 4 containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification#Procedure Protein purification] from induced cultures and negative control
 +
** cell debris pellets are treated with [http://www.sigmaaldrich.com/catalog/product/sigma/d4641?lang=en&region=US n-Dodecyl ß-D-maltoside] as a detergent
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Laemmli.29 SDS PAGE (Laemmli)] of pellets and supernatants
 +
[[Image: SDS Page of BBa_K808030.png|400px|thumb|left|2: supernatant 0.5% arabinose, 3: treated pellet 0.5% arabinose, 4: supernatant 0.2% arabinose, 5: treated pellet 0.2% arabinose, 7: supernatant 0.02% arabinose, 8: treated pellet 0.02% arabinose, 9: supernatant no arabinose, 10: treated pellet no arabinose ]]
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Western_Blot Westernblot] is successful as well
 +
* to quantify the hydrolytic activity of our induced bacteria we perform a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Bacteria bacterial pNP-Assay].
 +
We use our induced cells (Top10) with an OD<sub>600</sub>=0.1-0.025 (resuspended in PBS-buffer) as catalysts and ''para-Nitrophenylbutyrate'' as a substrate. Induced cells have the [http://partsregistry.org/Part:BBa_K808030 fusion protein (BBa_K808030)] expressed on their surface. The catalytical domain, formed by pNB-Esterase 13 will show hydrolytic activity we can screen for by performing a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay pNP-assay]. The substrate will be hydrolysed, and one degradation construct is ''para-Nitrophenylbutyrate''. If released by hydrolysis, a characeristic absorption at 405 nm can be detected and plotted against the time, resulting in straight lines.  The hydrolytic activity is quantified by the slope of the respective straight line.
 +
[[Image:top_ten_induz_geschwindigkeiten.png|500px|center|thumb|Plot of the bacterial [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#pNP-Assay pNP-Assay] using induced cells (Top10) with an OD<sub>600</sub>=0.1-0.025 (in PBS-buffer) as catalysts and ''para-Nitrophenylbutyrate'' as a substrate.  The hydrolytic activity is quantified by the slope of the respective straight.]]
 +
 +
[[Image:top10_induz(2).png|500px|center|thumb| Plot shows relation of the slopes from Figure 6, representing the hydrolytic activity, in coherence with the level of arabinose concentration in % used for induction.]]
 +
 +
==== Wednesday, 19.09.12 ====
 +
* activity assays on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin-CAM-plates LB Tributyrin agar] worked well (incubation occured just for the night at 30°C)
 +
[[File:120919 top10 k808032 0.02 ara.jpg|200px]]
 +
[[File:120919 top10 k808032 0.2 ara.jpg|200px]]
 +
[[File:120919 top10 k808032 0.5 ara.jpg|200px]]
 +
* activity assays on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin-CAM-plates LB Tributyrin agar]  with 0.5% mw L-arabinose for inducing
 +
** colonies 1-4 [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5 alpha], 5-8 [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10], 9-12 [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655]
 +
** colonies 1,2,5,6,9,10 are carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
** colonies 3,4,7,8,11,12 are carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
 +
 +
==== Tuesday, 18.09.12 ====
 +
* activity assays on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB_Tributyrin-CAM-plates LB Tributyrin agar]  worked well
 +
[[File:120920 k808032 k808030 dh5a top10 mg1655.tif.jpg|300px]]
 +
 +
== Protein Expression ==
 +
=== CW 20 ===
 +
==== Monday 14.05.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Heat_Shock_Transformation Bacterial transformation by heatshock] of [http://www.neb.com/nebecomm/products/productc3029.asp BL21(DE3)SHuffle] with the plasmid [https://2012.igem.org/Team:TU_Darmstadt/Materials/pET26b pET26b(+)pNBDSM13] encoding Esterase 13 recieved by Henkel AG & Co. KGaA
 +
* bacterial suspension was poured out on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB] plates containing [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp]
 +
 +
==== Tuesday 15.06.2012 ====
 +
* one coclony of the retransformation was picked and transfered into 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB-Medium] containing [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp]
 +
* the culture was stirred at 180 rpm at 30°C
 +
 +
==== Wednesday 16.06.12 ====
 +
* centrifugation of the culture and resolving the pellet in 2 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB-Medium] and 15% glycerine
 +
* seperate the cell suspension into 100 µL aliquots
 +
* store the stocks at -80°C
 +
 +
=== CW 24 ===
 +
==== Thursday, 14.06.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] for protein expression of [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC]
 +
** each PCR is performed in 5 batches à 50 µL.
 +
** Parameter: T<sub>A</sub> = 57°C, t<sub>A</sub> = 35 s, t<sub>E</sub> = 65 s
 +
* PCR on [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEST100 pEST100] vector for expression with [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] vector gene of interest: FsC for designed part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
 +
primers: [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX_FsC_His_SfiI_up pEX FsC His SfiI up] and [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX_FsC_stop_SfiI_lo pEX FsC Stop SfiI lo]
 +
 +
==== Friday, 15.06.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control
 +
 +
=== CW 25 ===
 +
==== Wednesday, 20.06.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for preparation
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] products
 +
*: Concentration of produced [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence: 40 ng/µL
 +
 +
==== Thursday, 21.06.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of [https://2012.igem.org/Team:TU_Darmstadt/Protocols/PCR PCR] product from 14.06.
 +
** Enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/SfiI SfiI]
 +
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/NEB_buffers#NEBuffer_4_.28green.29 NEBuffer: 4]
 +
** Digestion time: over night
 +
** Digestion temperature: 50°C
 +
 +
==== Friday, 22.06.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] vector
 +
*: Concentration range: 240-488 ng/µL
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Restriction_digest Restriction digest] of pEX
 +
** Enzymes used: [https://2012.igem.org/Team:TU_Darmstadt/Materials/SfiI SfiI]
 +
** [https://2012.igem.org/Team:TU_Darmstadt/Materials/NEB_buffers#NEBuffer_4_.28green.29 NEBuffer: 4]
 +
** Digestion time: 3 days
 +
** Digestion temperature: 50°C
 +
 +
=== CW 26 ===
 +
==== Monday, 25.06.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Agarose_gel_electrophoresis Agarose gel electrophoresis] for quality control
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_DNA Gel extraction] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] and digested [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence from 21.06.
 +
*: Concentrations: pEX: 77 ng/µL, FsC sequence: 18 ng/µL
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/DNA_Ligation Ligation] of pEX with FsC sequence with the ratio 1:3 and 1:5
 +
{| class="wikitable"
 +
|-
 +
! Component !! 1:3 !! 1:5
 +
|-
 +
| [https://2012.igem.org/Team:TU_Darmstadt/Materials/FsC FsC] sequence || 1.12 µL || 2.2 µL
 +
|-
 +
| [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX] || 0.64 µL || 0.64 µL
 +
|-
 +
| Ligase buffer || 4 µL || 4 µL
 +
|-
 +
| [https://2012.igem.org/Team:TU_Darmstadt/Materials/T4_DNA_Ligase T4 DNA ligase] || 1 µL || 1 µL
 +
|-
 +
| H<sub>2</sub>O || 33 µL || 30 µL
 +
|}
 +
* Ligation time: over night
 +
 +
==== Tuesday, 26.06.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation Bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/TOP10 TOP10] with the ligation product [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX-FsC] from 25.06.
 +
 +
==== Wednesday, 27.06.2012 ====
 +
* Two positive clones on [https://2012.igem.org/Team:TU_Darmstadt/Materials/LB LB] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] plates picked for liquid culture
 +
*: 50 mL [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] cultures at 180 rmp and 37°C, over night
 +
 +
==== Thursday, 28.06.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX-Fsc] in [https://2012.igem.org/Team:TU_Darmstadt/Materials/TOP10 TOP10]
 +
*: Concentration: 45 ng/µL and 405 ng/µL
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Bacterial_transformation Bacterial transformation] by [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Electroporation Electroporation] of [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strains-bmh-71_18-muts-and-es1301-muts/ BmH7118] with the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] product pEX-FsC
 +
 +
=== CW 27 ===
 +
==== Monday, 02.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein expression of FsC] at different temperatures (16°C, 25°C, 30°C and 37°C) for the final step of the expression
 +
 +
==== Tuesday, 03.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Purification_of_Periplasmatic_Proteins Purification of Periplasmatic Proteins] for all expression temperatures
 +
 +
==== Wednesday, 04.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] without cell disrupter
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of all collected samples
 +
{| class="wikitable"
 +
|-
 +
! Expression at 16°C/25°C
 +
|-
 +
| [[File:120711_FsC_16_25.jpeg|500px]]
 +
|-
 +
! Expression at 30°C/37°C
 +
|-
 +
| [[File:120711_FsC_30_37.jpeg|500px]]
 +
|}
 +
* The best results were maintained at an expression temperature of 30°C
 +
 +
==== Friday, 06.07.2012 ====
 +
* Inoculation of 5 ml [https://2012.igem.org/Team:TU_Darmstadt/Materials/DYT DYT] [https://2012.igem.org/Team:TU_Darmstadt/Materials/Chloramphenicol Cmp] with [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strains-bmh-71_18-muts-and-es1301-muts/ BmH7118] containing [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX pEX-FsC]
 +
* Incubation for 3 days at 20°C
 +
 +
=== CW 28 ===
 +
==== Monday, 09.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Miniprep Miniprep] of [https://2012.igem.org/Team:TU_Darmstadt/Materials/pEX#pEX-FsC pEX-FsC] from 06.07.
 +
*: Concentration: 470 ng/µL
 +
* Preparation for sequencing at [https://2012.igem.org/Team:TU_Darmstadt/Sponsors Eurofins]
 +
*: Barcode 043 pEX-FsC with primer [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation M13 Reverse up]
 +
*: Barcode 044 pEX-FsC with primer [https://2012.igem.org/Team:TU_Darmstadt/Materials/Primer_Degradation ClaI pIII lo]
 +
* Plasmid DNA: 5µL
 +
* Primer: 3µL
 +
* H<sub>2</sub>O: 7µL
 +
 +
==== Wednesday, 11.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein expression of FsC] according to standard protocol
 +
 +
==== Thursday, 12.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples
 +
[[File:120713_FsC_30.jpeg|500px]]
 +
 +
=== CW 29 ===
 +
==== Monday, 16.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_Est13 Protein expression of Est13] according to standard protocol
 +
 +
==== Tuesday, 17.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples
 +
[[File:120719_Est13.jpeg|500px]]
 +
 +
=== CW 31 ===
 +
==== Monday, 30.07.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein expression of FsC] according to standard protocol
 +
 +
==== Tuesday, 31.07.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples
 +
[[File:120801_FsC_30.jpeg|500px]]
 +
 +
=== CW 33 ===
 +
==== Friday, 17.08.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein expression of FsC] according to standard protocol
 +
 +
==== Saturday, 18.08.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples
 +
[[File:120819_FsC_30.jpeg|500px]]
 +
 +
=== CW 34 ===
 +
==== Wednesday, 22.08.2012 ====
 +
*[https://2012.igem.org/Team:TU_Darmstadt/Protocols/Protein_Expression#Protein_Expression_FsC Protein expression of FsC] according to standard protocol
 +
 +
==== Thursday, 23.08.2012 ====
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/Proteinpurification Protein purification] by standard protocol
 +
* [https://2012.igem.org/Team:TU_Darmstadt/Protocols/SDS-Page#SDS-PAGE_.28Sch.C3.A4gger.29  SDS-PAGE (Schägger)] analysis of samples
 +
[[File:120824_FsC_30.jpeg|500px]]
 +
 +
==Enzyme Activity Assays==
 +
To characterise our BioBricks [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] (pNB-Est13) & [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025] (FsC) a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Enzyme pNP-assay]s are performed.
 +
=== CW 37 ===
 +
==== Est13 ====
 +
* a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Enzyme pNP-assay]is performed with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] (pNB-Est13)
 +
 +
[[File:lineburk_est.png|center|700px|thumb|Lineweaver-Burk plot of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] ]]
 +
===== K<sub>m</sub> and V<sub>max</sub> calculation =====
 +
To find K<sub>m</sub> the growth of the first seven data points were written down in a diagram. The slope of the regression line gave the speed of the hydrolysis for the single substrate concentrations. Now the value of the speed with the associated concentration of substrate were plotted in a Lineweaver-Burk diagram.
 +
At the point where the regression line is crossing the x-axis the x-coordinate amounts to -1/K<sub>m</sub>. So K<sub>m</sub> is about 400µM. To calculate the value of V<sub>max</sub> we used the point where the plotted line crosses the y-axis. The associated y-coordinate is 1/V<sub>max</sub>. Consequently V<sub>max</sub> for 50nM Est13 is 0,002798 1/s.
 +
===== K<sub>cat</sub> calculation =====
 +
The value K<sub>cat</sub> is calculated through dividing V<sub>max</sub> by the enzyme concentration of 50nM. K<sub>cat</sub> counts 0,055951 1/mol*s.
 +
 +
==== FsC ====
 +
 +
* a [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#pNP-Assay pNP-Assay] is performed with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025].
 +
 +
 +
[[File:lineburk_fsc.png|center|700px|thumb|Lineweaver-Burk plot of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025]]]
 +
 +
===== K<sub>m</sub> and V<sub>max</sub> calculation =====
 +
To find K<sub>m</sub> the growth of the first twelve data points were written down in another diagram. The slope of the regression line gave the speed of the hydrolysis for the single substrate concentrations. Now the value of the speed with the associated concentration of substrate were plotted in a Lineweaver-Burk diagram.
 +
At the point where the regression line is crossing the x-axis the x-coordinate amounts to -1/K<sub>m</sub>. So K<sub>m</sub> is about 400µM. To calculate the value of V<sub>max</sub> we used the point where the plotted line crosses the y-axis. The associated y-coordinate is 1/V<sub>max</sub>. Consequently V<sub>max</sub> for 5nM FsC is 0,001467 1/s.
 +
===== K<sub>cat</sub> calculation =====
 +
The K<sub>cat</sub> value is calculated through dividing V<sub>max</sub> by the enzyme concentration of 5nM. K<sub>cat</sub> counts 0,293395 1/mol*s.
 +
 +
==== FsC with ehtylenglycol ====
 +
Our [https://2012.igem.org/Team:TU_Darmstadt/Project/Simulation Simulation lab] was able to show , theoratically, a relation between an decrease of enzyme activity and an increase of ethylenglycol concentration. This could be a hint for the mysterious loss of hydrolysis when the degradation rate reaches 5% of PET foil weight as it is described in the literature (Ronkvist, Å. M., Xie, W., Lu, W., & Gross, R. a. (2009). Cutinase-Catalyzed Hydrolysis of Poly(ethylene terephthalate). Macromolecules, 42(14), 5128–5138. doi:10.1021/ma9005318).
 +
We tried to proof their theory of potentially higher ethylenglycol concentration surrounding the PET foil. An increasing amount of ehtylenglycol should hamper the hydrolytic activity of FsC in a pNP-assay.
 +
===== Procedure =====
 +
The lab test procedure was nearly equal to the normal kinetics records with only one difference. The reaction solution consisted of different composites of PBS buffer and ethylenglycol (0 - 20%). All records were done at a concentration of 1mM of 4-Nitrophenyl butyrate in the experiment.
 +
 +
===== Records of the different ethylenglycol concentrations and the associated speeds of hydrolisis in a diagram =====
 +
[[File:v_abnahme_bei_glykol.png|700px|center|thumb|Plot of enzyme activity related to an increasing ehtylenglcol concentration]]
 +
 +
===== Interpretation =====
 +
As you can see there is a stagnation of the speed of hydrolysis of the ester caused by an increasing concentration of ethylenglycol. But by that you cannot tell that ethylenglycol inhibits the FsC, because the hydrolysis of the ester rose with a higher concentration of ethylenglycol in the negative samples. So it could be that the ethylenglycol starts a concurrent reaction or blocks the 4-Nitrophenyl butyrate.
 +
 +
[[File:ethylenglykol_neg_kontrolle.png|700px|center|thumb|Plot of "activty" in the negative sample: pNPB & ethylenglycol]]
 +
=== CW 36  - 38 ===
 +
 +
==== PET degradation ====
 +
 +
===== Principle and conditions =====
 +
 +
[[File:Principle_of_pet_degradation.png|600px|center|thumb|principle of hyrolytic PET degradation. Conditions: Room temperature (~ 22°C) pH = 7.4]]<br />
 +
 +
===== Procedure =====
 +
 +
Round about 1g of PET granulate is added in each two falcon tubes to between 15 and 20 mL water of pH = 7.4 and several drops of [http://en.wikipedia.org/wiki/Bromothymol_blue bromothymol blue]. In one of these falcon tubes Est13 stock solution is added until a concentration of 2,5 µM is reached. For 15 days the solutions are incubated at room temperature. At nine specific days of these the enzymatic solutions and the negative sample are photographed, to control the shift of pH.
 +
 +
===== Results =====
 +
In all photos the degradation with Est13 is in the left falcon tube.
 +
 +
[[File:PET degradation Day 1.jpg|thumb|205px|left|Day1:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 2.jpg|thumb|205px|left|Day2:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 4.jpg|thumb|205px|left|Day3:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 7.jpg|thumb|205px|left|Day7:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 9.jpg|thumb|205px|left|Day9:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 10.jpg|thumb|205px|left|Day10:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 13.jpg|thumb|205px|left|Day13:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]
 +
[[File:PET degradation Day 15.jpg|thumb|205px|left|Day15:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control]]<br />
 +
 +
 +
 +
 +
The photos show a decrease of the pH-value over time in the sample containing Est13. The one without this enzyme remains unchanged. So it is concluded that Est13 degrades PET granulate.
 +
 +
=== CW34 - CW35 ===
 +
==== Degradation of monomethyl terephthalate over time ====
 +
 +
===== Principle and conditions =====
 +
 +
[[File:principle of degradation of monomethyl terephthalate.png]]<br />
 +
Conditions: Room temperature (~22°C)
 +
 +
===== Procedure =====
 +
 +
Three different samples of 30 mL dest. water at a pH of 7.4 are incubated for 7 days with a concentration 500µM of monomethyl terephthalate (solved in methanol) and following ingredients:
 +
 +
1. 30µL of FsC (concentration in the incubated solution: ~0,8µM)<br />
 +
2. 30µL of Est13 (concentration in the incubated solution: ~0,8µM)<br />
 +
3. Nothing<br />
 +
 +
To control the shift of the pH during the estercleavage some drops of [http://en.wikipedia.org/wiki/Bromothymol_blue bromothymol blue] are added.
 +
 +
===== Results =====
 +
 +
Following pictures show the shift of the pH over 7 days (The degaradation with Est13 is in the left falcon tube and with FSC in the middle one):
 +
 +
[[File:monomethyl terephthalate degradation at day 1.jpg|thumb|445px|left|Day1: Degradation of monomethyl terephthalate. Left: with Est13(~0,8µM) Middle: with FSC(~8µM) Right: Negativ sample]]
 +
[[File:monomethyl terephthalate degradation at day 8.jpg|thumb|445px|left|Day8: Degradation of monomethyl terephthalate. Left: with Est13(~0,8µM) Middle: with FSC(~8µM) Right: Negativ sample]]<br />
 +
 +
So you can see that both enzymes catalyzed the cleavage of the ester in a few days. In 7 days the pH-value shifted about one unit.
 +
 +
=== CW38 ===
 +
 +
==== Degradation of 4-nitrophenyl-3-phenylpropanoate and bis(4-nitrophenyl) succinate ====
 +
 +
===== Principles, conditions and method =====
 +
 +
[[File:principle of 4-Nitrophenyl-3-phenylpropanoate.png|thumb|435px|left|Principle of degradation of 4-nitrophenyl-3-phenylpropanoate]]
 +
[[File:principle of Bis(4-nitrophenyl) succinate.png|thumb|435px|left|Principle of degradation of bis(4-nitrophenyl) succinat]]
 +
 +
Conditions and method are listed by the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Enzyme pNP-assay].
 +
 +
===== Procedure =====
 +
 +
The procedure is the same like in the [https://2012.igem.org/Team:TU_Darmstadt/Protocols/pNP_Assay#Enzyme pNP-assay].
 +
Only if bis(4-nitrophenyl) succinate is added, add 900µL of reagent A to 100µL of reagent B in step 1.<br />
 +
 +
===== Results =====
 +
 +
[[File:qual degradation of 4-Nitrophenyl-3-phenylpropanoate and Bis(4-nitrophenyl) succinate.png|700px|thumb|center|Plot of enzyme activities on 4-nitrophenyl-3-phenylpropanoate and bis(4-nitrophenyl) succinate]]
 +
 +
===== Interpretation =====
 +
 +
The result shows that Est13 can catalyze the cleavage of both esters. FsC cannot do this in the given conditions. It is not clear what the reasons for the deactivation of FsC are. Maybe DMSO and/or methanol inhibit the enzyme or it is even not able to catalyze the hydrolysis.

Latest revision as of 02:51, 27 September 2012

Degradation

This page features the work carried out by the degradation team. The main objectives were the production of a BioBrick containing Fusarium solani cutinase or Est13 esterase two enzymes potentially enabling E.coli of PET degradation and over-expression stems for activity screening.

The degradation group consists of six undergraduates and two PhD student advisors. Our objective is the expression of a fusion protein on the surface of E. coli to enable a microbial polyethylenterephtalate (PET) degradation.

We identified three potential PET degradation enzymes from literature. Two of them are cutinases HiC (Humicola insolens cutinase) and FsC (Fusarium solani cutinase), the other namely pNB-Est13 beeing an esterase. After a short examination we dropped the HiC due to a temperature optimum of 80+°C. Shortly after the FsC was dropped as well, due to its toxicity for E.coli.
Enzymatical degradation of polyethylen terephtalate (PET) to terephtalic acid (TPA)

In order to maximise the activity we decided to anchor and display the cutinase/esterase directly on the surface of the producing bacterial cell. Surface-exposed enzymes are directly accessible to the respective substrates which no longer have to traverse the cellular membrane barriers. Furthermore, the enzyme reaction occurs in a chemically more defined environment as compared to the interior of a microbial cell. We use the outer membrane proteins of Pseudomonas aeruginosa (EstA) as a membrane anchor and the signaling sequence of PhoA translocators to display the enzyme on the outer surface of E. coli cells. In addition the fusion protein contains a his-tag and a myc-tag for detection via flow cytometry after antibody staining or Western blot.The degradation group consists of six undergraduates and two PhD student advisors. Our objective is the expression of a fusion protein on the surface of E. coli to enable a microbial polyethylenterephtalate (PET) degradation.

At first the signal sequence (PhoA), the catalytic domain (FsC/Est13) and EstA were assembled inline from their respective vectors. This is due to the fact, that by combining multiple parts in the standardized BioBrick vectors, scars with stop codons are generated that would effectively prevent the fusionproteins expression. In consideration of the DNA constructs length we pursued two PCR based synthesis strategies. One being the SKV (standard cloning procedure) the other being the SOE (standard overlap procedure). The first using primers and restriction sites for assembly the latter using overlapping primers. During both assembly procedures restriction sites of PstI, EcorI, SpeI or XbaI were eliminated from the coding sequence by mutagene PCR. In the end we completely changed our assembly strategy, using synthesis products and BsaI sites to put our parts together. After completion the fusionprotein and its subunits were transfered to the BioBrick standard and sent to the registry. For further characterisation the enzymes were overexpressed in E. coli strains Top10, DH5α, Mg1655, screened on tributyrin agar and detected via flow cytometry after performing an antibody staining. The material science group went even further and tried to examine them using AFM.


Contents

SOE PCR

schematic drawing of SOE PCR. the red gene has to be assembled upstream of the blue gene. Pay attention to the primer overlapps.


SOE PCR stands for Splicing by Overlapp Extension PCR. It is a standard overlapp extension procedure, enabling the assembly of genes wihtout performing any cloning, digesting or ligation inbetween. All you need to do ist running PCRs with specific primers. If gene A is the upstream part and gene B has to be assembled downstream of gene A, primer lo of gene A should have an overlapp of around 20 nucleotides complementary to the first 20 nucleotides of gene B. Primer up of gene B should haven a complementary overlapp of 20 nucleotides to the end of gene A.

We stopped using SOE PCR after a couple of weeks. It is a good method to perform mutationial PCR but to assemble genes of the length of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] it is not the best. Due to bad yields of gel extraction after the first assembly steps we stopped SOE PCR and went on with SKV. But eventually we got our chimeric genes synthesized by [http://de-de.invitrogen.com/site/de/de/home/Products-and-Services/Applications/Cloning/gene-synthesis/GeneArt-Gene-Synthesis.html GeneArt].





Week 1 / CW 17

Tuesday, 24.04.12

  • Production of electrocompetent cells [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5alpha] and [http://ecoliwiki.net/colipedia/index.php/Category:Strain:BL21 BL21]
  • Pouring of LB-Agar plates with ampecilin resistance (AMP)
  • setting of DYT media
  • Electroporation of BL21 with the following plasmids
    • pEST100, carrying a CMP-resistance, the genes of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 phoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA]
    • pET26b(+), carrying a Kan-resistance and the gene of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13]
    • pET16b, carrying an Amp-resistance , and is needed for our SKV
    • transformed Bl21 cells are incubated over night at 37°C in DYT-media and crossed out on LB-Agar plates

Wednesday, 25.04.12

Thursday, 26.04.12

Annotation: Every PCR is done in 4 assays à 50 µL, TA = 60°C, ta = 35s, tE = 25 s

  1. PCR on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SKV
    primers: SKV a1 up XbaI & SKV a1 lo NdeI
  2. PCR on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Esterase13
    primers: SOE A up & SOE a1 lo
  3. PCR on pEST100]
    gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with FsC
    primers: SOE A up & SOE a2 lo
  4. PCR on pEST100
    gene of interest: FsC for SOE PCR with Promo-LacO-RBS-Phoa and EstA part1
    primers: SOE b2 up & SOE b2 lo
  5. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
    primers: SOE b1 up & SOE Est13 mut lo
  6. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
    primers: SOE Est13 mut up & SOE b1 lo

120426 PCR 1-3 dunkel siehe Laborbuch 26.4.tif

  • 2-5 1.PCR, 6-9 2.PCR, 10-13 3.PCR

120426 PCR 4-6 siehe Laborbuch 26.4.tif

  • 2-5 4.PCR, 6-9 5.PCR, 710-13. 6.PCR

Friday, 27.04.12

Week 2 / CW 18

Monday, 30.04.12

  • SOE PCR
    • pNB-Est13 part1 & pNB-Est13 part2, primers: SOE b1 up & SOE b1 lo
    • Promo-LacO-RBS-Phoa & FsC, primers: SOE A up & SOE b2 lo
    • Annotation: Every PCR is done in 4 assays à 50 µL, TA = 60°C, ta = 35s, tE1 = 20s, tE1 = 35s
  • Agarose gel electrophoresis of SOE PCR

120430 SOE PCR1 dunkel siehe Laborbuch 30.4.png

  • SOE PCR of Promo-LacO-RBS-Phoa-FsC worked, pNB-Est13 did not due to missing clean up via Agarose gel electrophoresis, precipitation is insufficient, we do it again
  • PCRs
  1. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
    primers: SOE b1 up & SOE Est13 mut lo
  2. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
    primers: SOE Est13 mut up & SOE b1 lo
  • Agarose gel electrophoresis
    • 1. PCR worked well 2. PCR did not

120430 PCR -2 der beiden EST Fragmente 1234 est lo 5678 est up.tif

Wednesday, 02.05.12

  1. PCR on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
    primers: SOE A up & SOE a1 lo
  2. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
    primers: SOE b1 up & SOE Est13 mut lo
  3. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
    primers: SOE Est13 mut up & SOE b1 lo
TA = 57°C, ta = 35s, tE = 25 s
every PCR is performed in 3 batches à 50 µL
TA1 = 60°C, ta1 = 25 s, tE1 = 25 s
TA = 60°C, ta2 = 25 s, tE2 = 35 s

Tuesday, 03.05.12

Friday, 04.05.12

  1. PCR on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
    primers: SOE A up & SOE a1 lo
  2. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13
    primers: SOE c1 up & SOE EstA mut PstI out lo
  3. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and FsC
    primers: SOE c2 up & SOE EstA mut PstI out lo
  4. PCR on pEST100
    gene of interest: EstA part2 for SOE PCR with EstA part1
    primers: SOE EstA mut PstI out up & SOE D lo

Week 3 / CW 19

Tuesday 08.05.12

gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
primers: SOE A up & SOE b1 lo
template: pNB-Est13 from last friday & Promo-LacO-RBS-Phoa from Wednesday, 02.05.12
    • annotation: TA1 = 60°C, ta1 = 25 s, tE1 = 35 s
    • TA2 = 60°C, ta2 = 25 s, tE2 = 1 min
  • did not work

Wednesday, 09.05.12

  1. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13 part2
    primers: SOE b1 up & SOE Est13 mut lo
  2. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for SOE PCR with pNB-Est13 part1 and EstA part1
    primers: SOE Est13 mut up & SOE b1 lo
  3. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and pNB-Est13
    primers: SOE c1 up & SOE EstA mut PstI out lo
  4. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with Promo-LacO-RBS-Phoa and FsC
    primers: SOE c2 up & SOE EstA mut PstI out lo
  5. PCR on pEST100
    gene of interest: EstA part2 for SOE PCR with EstA part1
    primers: SOE EstA mut PstI out up & SOE D lo
    • annotation: TA = 60°C, ta = 25 s, tE = 35 s
    • every PCR is performed in 2 batches à 50 µL

Friday, 09.05.12

Week 4 / CW 20

Monday, 14.05.12

  • Gel extraction of remaining PCRs from Wednesday, 09.05.12
    • c(pNB-Est13 part1)=24 ng/µL
    • c(pNB-Est13 part2)=26 ng/µL
    • c(EstA part2)=13 ng/µL
  • new SOE EstA mut PstI out lo is orderd from Sigma-Aldrich
  • SOE PCR
gene of interest: pNB-Est13 for SOE PCR with EstA and Promo-LacO-RBS-Phoa
primers: SOE b1 up & SOE b1 lo
template: pNB-Est13 part1 from last friday & pNB-Est13 part2

Tuesday, 15.05.12

  1. SOE PCR
    gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
    primers: SOE A up & SOE b1 lo
    template: pNB-Est13 from yesterday & Promo-LacO-RBS-Phoa from Wednesday, 02.05.12
  2. SOE PCR
    gene of interest: Promo-LacO-RBS-Phoa-FsC for SOE PCR with EstA
    primers: SOE A up & SOE b2 lo
    template: FsC from Thursday, 26.04.12 & Promo-LacO-RBS-Phoa from Wednesday, 02.05.12
    • annotation: TA1 = 52°C, ta1 = 25 s, tE1 = 35 s
    • TA2 = 57°C, ta2 = 25 s, tE2 = 1.15 min
    • each PCR is performed in 2 batches à 50 µL

Wednesday, 16.05.12

  • SOE PCR of Promo-LacO-RBS-Phoa-pNBEst13 did not work but Promo-LacO-RBS-Phoa-FsC worked
  • Gel extraction
    • c(Promo-LacO-RBS-Phoa-FsC)=10 ng/µL

Week 5 / Kw 21

Monday, 23.05.12

  1. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with pNB-Est13 and EstA part2
    primers: SOE c1 up & SOE EstA mut PstI out lo
  2. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR with FsC and EstA part2
    primers: SOE c2 up & SOE EstA mut PstI out lo

Tuesday, 22.05.12

Wednesday, 23.05.12

  1. SOE PCR
    gene of interest: EstA for SOE PCR with FsC
    primers: SOE c2 up & SOE D lo
    template: EstA part1 from yesterday & EstA part2 from Monday, 14.05.12
    • annotation: TA1 = 52°C, ta1 = 25 s, tE1 =45 s
    • TA2 = 65°C, ta2 = 25 s, tE2 = 90 s
  • qualitative Agarose gel electrophoresis
  • Gel extraction
    • c(EstA for SOE PCR with pNB-Est13)=42 ng/µL
    • c(EstA for SOE PCR with FsC)=23 ng/µL

Thursday, 24.05.12

  1. PCR on EstA for SOE PCR with pNB-Est13 from yesterday
    gene of interest: EstA for SOE PCR with pNB-Est13
    primers: SOE c1 up & SOE D lo
  2. PCR on EstA for SOE PCR with FsC
    gene of interest: EstA for SOE PCR with FsC
    primers: SOE c2 up & SOE D lo
  3. PCR on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13
    primers: SOE A up & SOE a1 lo
  4. PCR on pEST100
    gene of interest: FsC for SOE PCR with Promo-LacO-RBS-Phoa and EstA part1
    primers: SOE b2 up & SOE b2 lo
    • annotation: TA = 60°C, ta = 25 s, tE =45 s
each PCR is performed in 3 batches à 50 µL
  • qualitative Agarose gel electrophoresis
    • both EstAs worked
    • Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13 worked
  • Gel extraction
    • c(EstA for SOE PCR with pNB-Est13)=39 ng/µL
    • c(EstA for SOE PCR with FsC)=20 ng/µL
    • c(Promo-LacO-RBS-Phoa for SOE PCR with pNB-Est13)=13 ng/µL

Week 6 / Kw 22

Tuesday, 29.05.12

  1. SOE PCR
    gene of interest: Promo-LacO-RBS-Phoa-Fsc-EstA
    primers: SOE A up & SOE D lo
    template: EstA from Thursday, 24.05.12 & Promo-LacO-RBS-Phoa-Fsc from Wednesday, 16.05.12
  2. SOE PCR
    gene of interest: Promo-LacO-RBS-Phoa-pNBEst13-EstA
    primers: SOE A up & SOE D lo
    template: EstA from Thursday, 24.05.12 & Promo-LacO-RBS-Phoa from Wednesday, 02.05.12 & pNB-Est13 from Monday, 14.05.12
  3. SOE PCR
    gene of interest: Promo-LacO-RBS-Phoa-pNBEst13 for SOE PCR with EstA
    primers: SOE A up & SOE b1 lo
    template: Promo-LacO-RBS-Phoa from Wednesday, 02.05.12 & pNB-Est13 from Monday, 14.05.12
    • annotation: each PCR is performed in 3 batches à 50 µL
    • TA1 = 52°C, ta1 = 25 s, tE1 =45 s
    • TA2 = 65°C, ta2 = 25 s, tE2 = 90 s
  • Agarose gel electrophoresis
    • Promo-LacO-RBS-Phoa-Fsc-EstA worked
    • Promo-LacO-RBS-Phoa-pNBEst13 worked

Thursday, 29.05.12

  • Gel extraction
    • c(Promo-LacO-RBS-Phoa-Fsc-EstA)= 8 ng/µL
    • c(Promo-LacO-RBS-Phoa-pNBEst13)= 13 ng/µL



Due to better results in SKV we stopped our tries in SOE PCR assembly of our chimeric protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030].

SKV

Molecular cloning.jpg

The shortcut SKV stands for "Standard Klonierungs Verfahren", in english standard molecular cloning. The team tried to build up the whole construct without usage of the BioBrick system as a second way. Here the team had to generate many primers with different restriction sites to connect the parts of the construct.







Week 1 / CW 17

Tuesday, 24.04.12

  • Production of electrocompetent cells DH5alpha and [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21]
  • Pouring of LB-Agar plates with ampecilin resistance (AMP)
  • setting of DYT media
  • Electroporation of BL21 with the following plasmids
    • pEST100, carrying a CM-resistance, the genes of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 phoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA]
    • pET26b(+), carrying a Kan-resistance and the gene of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13]
    • pET16b, carrying an Amp-resistance , and is needed for our SKV

Wednesday, 25.04.12

Thursday, 26.04.12

Annotation: Every PCR is done in 4 assays à 50 µL, TA = 60°C, ta = 35s, tE = 25 s

  1. PCR 1on pEST100
    gene of interest: Promo-LacO-RBS-Phoa for SKV
    Primers: SKV a1 up XbaI & SKV a1 lo NdeI

120426 PCR 1-3 siehe Laborbuch 26.4-1.png

  • 2-12= phoA

Friday, 27.04.12

Week 2 / CW 18

Monday, 30.04.12

  • Agarose gel electrophoresis of DNA digestion from Friday, 27.04.12
  • Only one single band on Agarose gel electrophoresis
    • For saveness two single digests are performed at 20 µL batches. One with XbaI and the other with NdeI. Incubation for 2 hours.
  • Agarose gel electrophoresis of single digests
    • Enzymes cut once each, so digest should have worked.

120430 Testrestrikt.XbaINdeI zugeschnitten.png

  • Ligation of PhoA in cut (XbaI / NdeI) pET16b
    • Annotation: 30 µL batch, 1:5 ratio, Ligation at 4°C for 2 days till Wednesday, 02.05.12

Week 4/CW 20

Monday, 07.05.

Annotation: If it does not say anything else, Ligation is always done in 20µl batches.

Tuesday, 08.05.

Wednesday, 09.05.

  • Colony-PCR
    • gene of interest: PhoA
    • primer:SKV a1 up XbaI, SKV a1 lo NdeI
  • PhoA was not inserted, but 2 colonies were picked and inoculated in 5 ml LB Amp medium to look at it again due to a test-restriction.

Thursday, 10.05.

Friday, 11.05.

  • an analytic, 1% agarose-gel proves that the amplification of FSC, Est13 and EstA was successfull.
  • But to amplify Est13 it was used the product of the SOE PCR which had not been cleaned up, so the large Fragments of the SOE-primers might have disturbed the amplification. The PCR of Est13 had to be performed again (Wednesday, 16.05.)

120511 - Kopie1.png

  • 2,3,5,6= Est13
  • 7,8,9,10= EstA
  • 11,12= FSC
  • DNA digestion of pET16b to produce template for a new ligation of PhoA
    • concentration: 76,3 ng/µl
    • enzymes: XbaI, NdeI
    • incubation: for 2 days, 37°C
  • Ligation of PhoA x pET16b cut with XbaI and NdeI is carried out using different rates of Vector and insert:
    • ratio vector/insert= 3:1, 1:1, 1:3, 1:5, 1:7, 1:10
    • PhoA= 10,6 ng/µl Monday,07.05.
    • incubation: 2 days, 4°C

Week5/CW21

Monday, 14.05.

Tuesday, 15.05.

120515 colony PCR + SkV Est13 beschriftet.png

  • PhoA is inserted, so 10 clones (2-9,11,12) are picked to be grown in 5ml DYT over night.

Wednesday, 16.05.

  • Miniprep of 10 clones, the plasmid-DNA is isolated out of 3ml culture per clone.
  • Restriction digest with NdeI and NcoI of the plasmids (phoA x pET16b) 1-4, so FSC and Est13 can be added to the construct.
  • FSC is cut with NdeI and NcoI
  • PCR1 of EST13
    • template: product of SOE-PCR, cleaned up by the Promega-Kit
    • primer: SKV b1 up NdeI, SKV b1 lo NcoI
    • an analytical Agarose gel electrophoresis is performed

120516 SOE PCR PhoA Est13 + SkV Est13 FsC2.png

Friday, 18.05.

  • Ligation of FSC x (phoA x pET16b)
    • ratio vector/insert: 3:1, 1:1, 1:3
    • concentration:
  • (phoA x pET16b)= 3,72 ng/µl
  • FSC= 12,22 ng/µl

Week 6/CW 22

Monday, 21.05.

120523 pET16b Verdau pET16b NN1.png

Tuesday, 22.05.

Wednesday, 23.05.

Thursday, 24.05.

  • Colony-PCR proves, that Est13 has been inserted into (phoA x pET16b)
    • plates are covered with colonies, 8 colonies are chosen for colony-PCR
    • colony No.5 is chosen to be inoculated in 5µ DYT/Amp medium

120524 o Est13 FsC u Kolonie PCR Est131.png

Friday, 25.05.

Week 7/CW 23

Tuesday, 29.05.

  • 120529 EstASKVund SOEXXX1.png

Wednesday, 30.05.

  • Restriction digest of EstA (product of PCR, 80 µl) and Plasmid: (Est13 x phoA x pET16b)
    • enzymes: EcoRI, NcoI
    • incubation: 1,5h, 37°C
    • The Agarose gel electrophoresis shows, that two DNA fragments are cut out of the vector (Est13 x phoA x pET16b). This might be a hint that Est13 is not inserted.

120530 VPE + EstA Reinigung Verdau1.png

    • 1-3 = (Est13 x phoA x pET16b)
    • 4-5 = EstA
    • c(EstA) = 6,7 ng/µl
    • c(Est13 x phoA x pET16b)= 23 ng/µl
  • Electroporation of (FSC x phoA x pET16b) worked well, plates are covered with colonies which are picked to be grown in 5ml DYT/Amp medium over night.

Thursday, 31.05.

  • Miniprep of the amplified (FSC x phoA x pET16b)
  • to be sure that the plasmid (Est13 x phoA x pET16b) really carries Est13 and PhoA, an analytic PCR is performed. Also pEt16b is used as template with different primers.
  • templates:
  • Primers, used on each template:
    • SKV b1 up NdeI, SKV b1 lo NcoI
    • SKV a1 up XbaI, SKV a1 lo NdeI
  • conditions:
    • TA = 66°C, ta = 35s, tE = 90s
  • the Agarose gel electrophoresis shows, that there is no binding-specifity concerning the genes of interest and the primers, but primers have been checked on mistakes.
  • to solve the problem, the Ligation of FSC and Est13 shall be repeated from the beginning.

120531ae Est131.png

  • Additionally,the decision was to go on with the Ligation of EstA into the Plasmids (Est13 x phoA x pET16b) and (FSC x phoA x pET16b), in case that the PCR was proceeded under wrong conditions.

Friday, 01.06.

  • Restriction digest of (phoA x pET16b)
    • enzymes: NcoI, NdeI
    • incubation: 1,5 h, 37°C
  • Ligation of Est13 and FSC x (PhoA x pET16b)
    • ratio vector/insert: 1:3, 1:5
    • c([[Est13)= 3 ng/µl
    • c(FSC)= 11 ng/µl
    • c(phoA x pET16b)= 29 ng/µl
    • incubation: over night, 25°C
  • Restriction digest of (FSC x (PhoA x pET16b)
  • enzymes: NcoI, EcoRI
  • incubation: 1,5h, 37°C

Week 8/CW 24

Monday, 04.06.

Tuesday, 05.06.

Wednesday, 06.06.

  • Electroporation of DH5alpha with Ligation-assays from 01.06.
  • Ligation of EstA Wednesday,30.05 and the Plasmids (Est13 x phoA x pET16b),(FSC x phoA x pET16b) from Monday,04.06.
    • ratio vector/insert: 1:3,1:5
    • incubation: 2h, 25°C
    • Electroporation of DH5alpha with (EstA x Est13 x phoA x pET16b) and (EstA x FSC x phoA x pET16b)

Friday, 08.06.

  • No cells are grown on plates, so the plates are incubated for another two days at RT.

Week8/ CW24

Monday, 11.06.

  • all plates are covered with cells, so a colony-PCR is performed on either Est13,FSC or EstA
  • Primer:
    • SKV b1 up NdeI, SKV b1 lo NcoI
    • SKV b2 up NdeI, SKV b2 lo NCOI
    • SKV c1 up NcoI, SKV c1 lo EcoRI
    • Every PCR is done in 8 assays à 50 µL, TA = 57°C, ta = 35s, tE = 90 s

Tuesday, 12.06.

  • colonies No.3,4 (EstA x FSC x phoA x pET16b) and No.15,16 (EstA x Est13 x phoA x pET16b) seem to be positive on EstA and are picked to be grown in 5ml DYT/Amp medium.
  • Colony-PCR on Est13 and FSC shows a lot of unspecific bands, so cloning of the genes from the beginning has to be dropped.

120612 SKVcolony-PCR,VPFE,VPEE.png

Wednesday, 13.06.

  • Miniprep of the clones No. 3,4,15 and 16. Tuesday, 12.06.
    • c(EstA x FSC x PhoA x pET16b)=
    • No.3=65,17 ng/µl
    • No.4=63,8 ng/µl
    • c(EstA x Est13 x PhoA x pET16b)=
    • No.15=66,3 ng/µl
    • No.16=59,7 ng/µl
  • for gene-expression, it is performed a elektroporation of [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21]-cells with 1µl of the PLasmid-DNA which has just been isolated.

Friday, 15.06.

  • Transformation of [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli BL21] worked well
  • Tributyrinagar plates with 1mM IPTG were generated, to induce the Lac-Promotor of pET16b, and to demonstrate the esterase-activity by the lysis of Tributyrin.
  • afterwards Tributyrinagar plates are inoculated with cells which were transformed by Miniprep No.3,4,15,16 on Wednesday, 13.06.
    • incubation: 37°C, 2 days

Week9/CW25

Monday, 18.06.

  • Tributyrinagar plates are covered with cells, but no lysis is visible.
    • plates are incubated for another day at 25°C.

Tuesday, 19.06.

  • no lysis, plates stay incubated at 25°C.

Wednesday, 20.06.

  • no lysis

Friday, 22.06.

  • The plasmids No.3,4 (EstA x FSC x phoA x pET16b) and No.15,16 (EstA x Est13 x phoA x pET16b) are prepared for sequencing.
  • Primer:
  • (EstA x FSC x phoA x pET16b):
    • T7 up
    • T7 lo
    • SOE EstA mut up lo
    • [[SOE EstA mut up lo
  • (EstA x Est13 x phoA x pET16b):
    • T7 up
    • T7 lo
    • SOE Est13 mut up lo
    • SOE Est13 mut up lo

Sequencing was not successfull. It was discovered later, that there was a contamination of the DH5alpha cells with other plasmid-DNA, probably caused by Electroporation. SOE-PCR
Due to this fact, the isolated plasmids were always mixed up with other plasmids, and sequencing had to fail. The contamination of the cells may have also caused false-positive results of the colony-PCRs.

We suggest that the cutinase FSC has an additional lipase-activity, which causes a lysis of the cell-membrane and may have an selective effect on FSC-negative mutants while cultivating the cells.

BioBricks

[http://partsregistry.org/Help:An_Introduction_to_BioBricks BioBricks] are standardized parts of synthetic biology. For more information visit the [http://partsregistry.org/Help:An_Introduction_to_BioBricks BioBrick registry]. As a contribution to iGEM it is necessary to submit the isolated enzymes and proteins in the [http://partsregistry.org/Part:pSB1C3 pSB1C3] vector.

Week 1 / CW 21

  • PCR of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA], [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 FsC] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 Est13]: 3 assays à 50 µl TAnneal = 57°C @ 20s
  • Agarose gel electrohporesis of the PCR products yields no result due to too short annealing time
  • PCR of PhoA, FsC and Est13: 3 assays à 50 µl TAnneal = 57/62/67°C @ 120s
  • 1% Agarose gel electrohporesis and PCR clean-up using the Wizard SV Gel and PCR Clean-Up System
M Est13 PhoA+RBSx2 PhoAx3 PhoA+RBS Est13x2 FsCx3
Pcr ae 03.JPG
Note: Accidental exchange of PhoA+RBS (57°C) and Est13 (57°C)

Week 2 / CW 22

  • PCR of FsC: 3 assays à 50 µl TAnneal = 57/58,6/60°C @ 120s
Marker FsC x 3
Pcr ae 01.JPG
  • PCR of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] and Est13: 2 assays à 50 µl TAnneal = 57/62°C @ 120s
M Est13x2 EstAx2
Pcr ae 02.JPG
Note: PCR of Est13 did fail [only primer band]
  • Electroporation of electrocompetent [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] @ 2,5kV/2mm cuvette using 1µl of [http://partsregistry.org/Part:pSB1C3 pSB1C3] insert cultivation on chlor LB plates overnight at 37°C -> no colonies -> growth over weekend at ~25°C

Week 3 / CW 23

  • Purity Plate of [http://partsregistry.org/Part:pSB1C3 pSB1C3] cultures 1d at 37°C
  • DYT culture of pSB1C3 [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] at 500 Hz / 37°C overnight
  • Miniprep of the pSB1C3 cutures and determination of the concentration via NanoDrop yields of ~120ng/µl at 100µl
  • Restriction digest of PhoA, EstA, Est13 and FsC (200 ng each) with PstI & EcoRI (à 20 µl)
  • Clean-up of the restriction digest via ammonium sulfate precipitation utterly fails

Week 4 / CW 24

Week 5 / CW 25

M PhoA EstA EstA Est13 Est13 FsC Fsc Kol.1 Kol.2
Pcr ae 04.JPG
  • PCR of EstA, Est13 and PhoA (Templates: PhoA = pEst100; EstA,Est13 = komp. Est13 mutated): 3 assays à 50 µl TAnneal = 57/62°C @ 120s
  • 1% Agarose gel electrohporesis and PCR clean-up using the Wizard SV Gel and PCR Clean-Up System

Week 6 / CW 26

  • Cultivation of [http://partsregistry.org/Part:pSB1C3 pSB1C3] in DYT (3ml) @ 37°C
  • Miniprep of the pSB1C3 cutures and determination of the concentration via NanoDrop yields of ~47,02/52,11 ng/ml @ 30 µl each
  • Restriction digest of EstA, Est13, PhoA and pSB1C3 (200 ng each) with PstI & EcoRI (à 20 µl) @ 37°C for 1:55h
  • Heat inactivation of the restriction digest @ 55°C for 25min

Week 7 / CW 27

Gelelectrophoresis of the restriction digest.

M PhoA EstA Est13 - pSB1C3
Pcr ae 05.JPG

Extraction of the PhoA, EstA, Est13 and pSB1C3 from the agarose gel. Ligation and transformation of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α].

Week 8 / CW 28

Colony PCR of the cultures.

M PhoA PhoA PhoA PhoA EstA EstA Est13 Est13
Pcr ae 06.JPG

Gel was run too long. Therefore no conclusion in regard of the transformation success was possible.

Week 9 / CW 29

Tuesday, 17.07.12

each PCR is performed in 5 batches à 50 µL.
TA = 57°C, tA = 30 s, tE = 2 min
  1. PCR on pEST100
    gene of interest: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] for designing part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 BBa_K808028]
    primers: BBa PhoA up & BBa PhoA down
  2. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for designing part BBa_K808026 via SOE PCR
    primers: BBa Est13 up & SOE Est13 mut lo
  3. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for designing part BBa_K808026 via SOE PCR
    primers: BBa Est13 down & SOE Est13 mut up
gene of interest: pNB-Est13 for designing part BBa_K808028
primers: BBa Est13 up & BBa Est13 down
    • Annotation: SOE PCR is performed in 5 batches à 50 µL
    • TA1 = 52°C, tA1 = 25 s, tE1 = 75 s
    • TA2 = 57°C, tA2 = 30 s, tE2 = 2 min
    • stored over night at 10°C

Wednesday, 18.07.12

120718 SOE PCR Est13.jpg

gene of interest: EstA from SKV Date for designing part BBa_K808027
primers: BBa EstA up and BBa EstA down
    • Annotation: PCR is performed in 5 batches à 50 µL
    • TA = 57°C, tA = 25 s, tE = 75 s
    • GC Buffer is used
  • preparative Agarose gel electrophoresis
  • Gel extraction of PCR product
    • gene of interest: EstA: c(pNB-Est13 part2)=119 ng/µL
    • stored in freezer

Thursday, 19.07.12

    1. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] from Tuesday, 17.07.12
    2. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] fromTuesday, 17.07.12
    3. [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] from Wednesday, 18.07.12
    4. [http://partsregistry.org/Part:pSB1C3 pSB1C3] 1
    5. pSB1C3 2

Friday, 20.07.12

  • the following Electroporation from Thursday, 19.07.12 worked
  • inoculation of 5 mL DYT-media with 5 µL Cmp and two positive colonies from each transformation (from pNB-Est13 3 colonies are taken) .
    • in addition FsC is already on plate, but to controle it, 2 colony PCRs are performed
  • Ligation of EstA into digested and 5' dephosphorylated [http://partsregistry.org/Part:pSB1C3 pSB1C3]
  • Electroporation of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α]
  • Miniprep of inoculated FsC in pSB1C3 (BBa_K808025) from Thursday, 19.07.12 failed
  • inoculation of 5 mL DYT-media with 5 µL Cmp and [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] carrying pSB1C3 with part BBa_K808025 (FsC)
    • incubation at 37°C over weekend of transformations and picked colonies

Week 10 / CW 30

Monday, 23.07.12

120723 BBaPhoA BBa PhoA BBa FsC BBa FsC BBa Est13 BBa Est13 BBa Est13.jpg

  • 2-3 PhoA colonies, 4-5 FsC colonies, 6-8 pNB-Est13 colonies
  • Miniprep of one inoculated colony in DYT-media with CAM from Friday, 20.07.12
    • c(PhoA in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=220 ng/µL
    • c(pNB-Est13 in pSB1C3)=50 ng/µL
  • inoculation of 2 x 5 mL DYT-media-Cmp with pSB1C3 carrying FsC
  • second transformation of EstA from Friday, 20.07.12 worked, but too many colonies!
    • purity plate is done

Tuesday, 24.07.12

  • Miniprep of the 2 FsC DYT-media-Cmp cultures with [http://partsregistry.org/Part:pSB1C3 pSB1C3] carrying FsC from yesterday
    • c(FsC in pSB1C3)=168 ng/µL
  • purity plate of EstA in pSB1c3 is positive
    • colonies picked
    • Colony PCR with positive control by amplfifying an EstA from SKV
    • Annotation: TA = 57°C, tA = 25 s, tE = 2 min, done with NEB- Phusion so its similiar to PCR 1
    • GC Buffer is used

Wednesday, 25.07.12

120725 Colony BBaEstA positiv probe auf SKV EstA.jpg

  • 2 EstA colony, 4 EstA from SKV as a control
  • Miniprep of inoculated 5 ml DYT-media-Cmp
    • c(EstA in pSB1C3)=350 ng/µL

Thursday, 26.07.12

  • Sequencing is ordered. The following premixes are used :
    • 10 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808028 PhoA] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=220 ng/µL, 1µL VR, 9 µL ddH2O
    • 10 µL of c(PhoA in pSB1C3)=220 ng/µL, 1µL VF2, 9 µL ddH2O
    • 7 µL of c(FsC in pSB1C3)=168 ng/µL, 1µL VR, 7 µL ddH2O
    • 7 µL of c(FsC in pSB1C3)=168 ng/µL, 1µL VF2, 7 µL ddH2O
    • 5 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808027 EstA] in pSB1C3)=350 ng/µL, 1µL VR, 9 µL ddH2O
    • 5 µL of c(EstA in pSB1C3)=350 ng/µL, 1µL VF2, 9 µL ddH2O
    • 5 µL of c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in pSB1C3)=50 ng/µL, 1µL VR, 9 µL ddH2O
    • 5 µL of c(pNB-Est13 in pSB1C3)=50 ng/µL, 1µL VF2, 9 µL ddH2O
  • in order to prepare DMSO stocks and Minipreps 5 mL DYT-media-Cmp are inoculated with following colonies containing
    • pNB-Est13 in pSB1C3
    • PhoA in pSB1C3
    • FsC in pSB1C3
    • EstA in pSB1C3
    • Annotation: incubation is done at 37°C over night

Friday, 27.07.12

  • inoculated pNB-Est13 in [http://partsregistry.org/Part:pSB1C3 pSB1C3] from Thursday, 26.07.12 has not grown over night
    • new colony pcked from plate and incubated in 5 mL DYT-media-Cmp at 37°C over night
  • Miniprep of 3 mL from the following over night DYT-media cultures from Thursday, 26.07.12
    • c(PhoA in pSB1C3)=440 ng/µL
    • c(pNB-Est13 in pSB1C3)=450 ng/µL
    • c(FsC in pSB1C3)=90 ng/µL

Week 11 / CW 31

Monday, 30.07.12

Tuesday, 31.07.12

Trouble shooting

  • Symptoms
    • very much transformants on crossed out plates after bacterial transformation by Electroporation
    • at first Colony PCR is positive
    • Minipreps result in very high yields (exceeding >200 ng/µL)
    • second Colony PCR is negative
    • sequencing failed
    • BUT FsC in [http://partsregistry.org/Part:pSB1C3 pSB1C3]
      • has had not very much transformants
      • has had a seuqencing result
      • its Minipreps resulted in medium concentrations, settling around 90 ng/µL
  • Diagnosis:
    • our bacterial transformation is done by Electroporation
    • therefor we use electroporation cuvettes, stored in DNA precipitating liquids like isopropanol or ethanol after being washed out.
    • long before we started these electroporation cuvettes were in use.
    • if not washed out carefully, DNA debris (like vectors and Inserts) accumulates in these storage liquids, due to precipitation
    • when an Electroporation is performed with one of these cuvettes, probably containing only little DNA debris, the cells get transformed with numbers of different precipitated plasmids
    • these plasmids contain a variety of resistances, reaching from CAM over KAN to Amp, allowing even "wrong" transformants to grow on selective media
    • after a short period of time, bacterial colonies start to seperate and repel their plasmids, selecting only the most "comfortables"
    • probably our plasmids, containing big genes on ligated vectors, are pushed out during this phase of selection
    • this slow decrease of plasmid could explain the missing second positive signal of Colony PCR

Wednesday, 01.08.12

  • due to change of strategy the following PCR 1s are performed
  1. PCR on pEST100
    gene of interest: PhoA BioBrick for assembly of part BBa_K808028
    primers: BBa PhoA up & BBa PhoA down
  2. PCR on pEST100
    gene of interest: EstA part1 for SOE PCR of EstA (BBa_K808027)
    primers: BBa Est A up & SOE EstA mut PstI out lo
  3. PCR on pEST100
    gene of interest: EstA part2 for SOE PCR of EstA (BBa_K808027)
    primers: BBa EstA mut up & BBa EstA down
  4. PCR on pET26b(+)
    gene of interest: pNB-Est13 part1 for SOE PCR of pNB-Est13 (BBa_K808026)
    primers: BBa Est13 up & BBa Est13 mut lo
  5. PCR on pET26b(+)
    gene of interest: pNB-Est13 part2 for SOE PCR of pNB-Est13 (BBa_K808026)
    primers: BBa Est13 lo & BBa Est13 mut up
  1. SOE PCR
    gene of interest: EstA
    primers: EstA part1 & EstA part2
  2. SOE PCR
    gene of interest: pNB-Est13
    primers: pNB-Est13 part1 & pNB-Est13 part2

120801 SOE PCR Est13 EstA EstApart2 kontrolle.jpg

    1. PhoA
    2. pNB-Est13
    3. EstA

Thursday, 02.08.12

Friday, 03.08.12

  • transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]

Saturday, 04.08.12

TA = 60°C, ta = 35s, tE = 25 s

120804 Verdau PhoA, EstA, Est13, PCR auf EstA, Est 13, PhoA, Kontrolle auf Insert und Vektor.jpg

Week 12 / CW 32

Assembly of our composite part RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808030) is reached by synthesis (from GENEART) of 2 different gene parts:

Monday, 06.08.12

Tuesday, 07.08.12

Wednesday, 08.08.12

Thursday, 09.08.12

  • Heatshock transformation of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] with 10 µL of each ligation batch from yesterday

Friday, 10.08.12

  • transformation from yesterday suceeded
    • one colony per plate (1:5:5 & 1:10:10 at room temperature and 1:5:5 & 1:10:10 at room 4°C)is picked for inoculation of 5 mL DYT-media-CAM

Saturday, 11.08.12

  • Miniprep of picked colonies from yesterday
  • Colony PCR on picked colonies
    • Annotation: TA = 55°C, tA = 25 s, tE = 2 min, done with house-taq so its similiar to PCR 2
    • primers: VR & VF2
  • Ligation and transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]

120811 PCR (VR,VF2) und Verdau (EcoRI,PstI) auf BBa Gesamt von Geneart.jpg

Week 13 / CW 33

Monday, 13.08.12

  1. PCR 1 on bba prefix-PhoA-His6tag-pNBEst13-BsaI site, as a template the pure synthesis product is used
    TA = 57°C, tA = 25 s, tE = 2 min
    primers: XbaI Rbs Phoa up & Est13 Bsa1 lo
  2. PCR 1 on BsaI-Myctag-EstA- bba suffix, as a template the pure synthesis product is used
    TA = 57°C, tA = 25 s, tE = 2 min
    primers: EstA Bsa1 lo & BBa EstA down
  3. PCR 3 on preped colony (1:5:5 room temperature from Friday, 10.08.12)
    TA = 57°C, tA = 25 s, tE = 2 min
    primers: XbaI Rbs Phoa up & BBa EstA down

120813 PCR 1-4 RBSPE 5-8 EXN-Myc-Est 9-12.jpg

120813 PCR Q5 auf bba gesamt konstrukt.jpg

  1. 1.PCR & 2.PCR in pSB1C3 carrying RFP
  2. 3.PCR in pSB1C3 carrying RFP
  3. 1.PCR & 2. PCR in BBa_K808000 possibility 1
  4. 3.PCR in BBa_K808000 possibility 1
  5. 1.PCR & 2. PCR in BBa_K808000 possibility 2
  6. 3.PCR in BBa_K808000 possibility 2

Tuesday, 14.08.12

Wednesday, 15.08.12

  • transformation [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
  • inoculation of 5 mL DYT-media-Cmp of the following colonies
    • colony 1.1
    • colony 2.1
    • colony 2.2
    • colony 3.1
    • colony 4.1
    • colony 4.2
    • colony 5.1
    • colony 5.2
    • colony 6.1
    • colony 6.2
      • incubation over night at 37°C
  • Colony PCR on colonies 1.1-6.2 with house-taq
    • primers: VR & VF2

Thursday 16.08.12

120816 Testrestriktion der pSB1C3 mit e und p colony platten 1 - 6.jpg

  • 2 colony 1.1, 3 colony 2.1, 3 colony 2.2, 4 colony 3.1, 5 colony 4.1, 6 colony 4.2, 7 colony 5.1, 8 colony 5.2
  • for further information see discussion below
  • new inoculation of 5 mL DYT-media-Cmp of Colonies 1.1 - 5.2

Trouble shooting

What should have been transformed:

  • colony 1.1: 1.PCR & 2.PCR in [http://partsregistry.org/Part:pSB1C3 pSB1C3]
    • should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808030) in pSB1C3 (length: ~ 3.1 kb)
  • colony 2.1: 3.PCR in pSB1C3 upstream of part BBa_K808000 (Arabinose inducible promotor) possibility 1
    • should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808032) in pSB1C3 (length: ~ 4.3kb)
  • colony 2.2: similar to colony 2.1
  • colony 3.1: 3.PCR in pSB1C3 upstream of part BBa_K808000 (Arabinose inducible promotor) possibility 2
    • should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808032) in pSB1C3 (length: ~ 4.3kb) like colony 2.1
  • colony 4.1: 3.PCR in pSB1C3
    • should be RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808030) in pSB1C3 (length: ~ 3.1 kb)
  • colony 4.2: similiar to colony 4.1
  • colony 5.1: 1.PCR & 2.PCR in pSB1C3 upstream of part BBa_K808000 (Arabinose inducible promotor) possibility 1
    • should be Arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA (BBa_K808032) in pSB1C3 (length: ~ 4.3kb)
  • colony 5.2: similar to colony 5.1

Conclusion:

120816 Colony 1.1 3.1 4.1 4.2 Colony Pcr 1-8.tif

  • 2-5 colonies 1.1, 3.1, 4.1, 4.2, 6 - 13 colony 1.1, 2.1, 2.2, 3.1, 4.1, 4.2, 5.1, 5.2

Friday, 17.08.12

Week 14 / CW 34

Monday 20.08.12

Tuesday 21.08.12

  • Ligation of BBa_K808000 upstream of BBa_K808032 in pSB1C3 ( to design BBa_K808032) from Friday, 17.08.12 worked well
  • 6 colonies are picked in order to perform a Colony PCR and for inoculation of 5 mL DYT-media-Cmp
    • colony A 4.1/2.1 ligated at 4°C
    • colony B 4.1/2.1 ligated at 37°C
    • colony C 1.1/5.1 ligated at 4°C
    • colony D 1.1/5.1 ligated at 37°c
    • colony E 4.2/2.2 ligated at 4°C
    • colony F 4.2/2.2 ligated at 37°C
  • Colony PCR
TA = 55°C, tA = 25 s, tE = 5 min
primers: VF2 & VR

Wednesday, 22.08.12

  • Miniprep of inoculated 5 mL DYT-media-Cmp with colony E,F,C,D
    • c(colony C 1.1/5.1 ligated at 4°C)=46 ng/µL
    • c(colony D 1.1/5.1 ligated at 37°c)=46 ng/µL
    • c(colony E 4.2/2.2 ligated at 4°C)=60 ng/µL
    • c(colony F 4.2/2.2 ligated at 37°C)=58 ng/µL
  • DNA Digestion of 15 µL of preped plasmids with EcoRI-HF & PstI-HF
  • Agarose gel electrophoresis with 0.8% agarose
    • ligation worked well, bands are in estimated length
    • lane 2-5: colony 4.2/2.2, lane 6-9: colony 5.1/1.1

Verdau vom Gesamtkonstrukt 4.2 2.2 und 5.1 1.1 beide temperaturen.tif

Thursday, 23.09.12

  • Miniprep of colonies from
    • c(colony C 1.1/5.1 ligated at 4°C)=147 ng/µL
    • c(colony D 1.1/5.1 ligated at 37°c)=131ng/µL
    • c(colony E 4.2/2.2 ligated at 4°C)=85 ng/µL
    • c(colony F 4.2/2.2 ligated at 37°C)=128 ng/µL
  • preparative Agarose gel electrophoresis of digested pNB-Est13 from yesterday
  • Gel extraction leads to c(pNB-Est13- cut E/P)=25 ng/µL
  • Ligation of digested pNB-Est13 in digested pSB1C3
    • 1:5 ratio is used
  • Heatshock transformation] of [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] with 10 µL of ligation batch
  • incubation of transformed cells at 37°C over night

Friday, 24.08.12

Week 15 / CW 35

Monday, 27.08.12

  • Miniprep of picked colony from [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])
    • c([http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3])=116 ng/µL
  • sequencing of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 pNB-Est13] in [http://partsregistry.org/Part:pSB1C3 pSB1C3]
  • test expression of BBa_K808032 (colony C 1.1/5.1 ligated at 4°C) in [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α]
    • BBa_K808032 is an arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA
    • inoculation of 50 mL DYT-media-Cmp with [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5α] carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
      • stop incubation at at OD600=0.7
      • storaging cultures on ice for 15mins
      • inducing with ~ 1.5% L-arabinose (using 3.75 mL of 20% mw L-arobinose solution)
      • incubation at 20°C, 25°C and 30°C over night

Tuesday, 28.08.12

  • antibody staining
  • detection of surface expression of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] by using FACS
  • positive signal increases with higher temperature, staining [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 BBa_K808000]
  • protein purification of test expression without running IMAC afterwards, just using supernatant and cell debris pellet
    • 32 µL of supernatant is used
    • 3 mL pellet of each testexpression is treated with more SDS as a detergent, in order to solve membrane proteins
  • running two SDS-tris gels with an myc positive probe
  • one of these gels is used for performing a Westernblot
    • using mouse-antimyc antibody as first antibody and goat-antimouse-AP as second antibody
    • lane 2-4: supernatant of induced and disrupted cells. Level of induction decreases from lane 2 (1.5% arabinose) to lane 4 (0.5% arabinose)
    • lane 6-8: Pellet of induced and disrupted cells, treated with high SDS concentrations. Level of induction decreases from lane 6 (1.5% arabinose) to lane 8 (0.5% arabinose).
    • Lane 9-10 show myc positive probes.
    • The blot shows that our expression worked of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] and proofs the membrane intercalation of our chimeric protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808030] because the blot only gives positive signals when high concentrations of detergent where used to treat the cell debris pellet.

120831 Westermblot auf Gesamt konstrukt aus DH5 alpha 5111.tif

  • both are not very good in their solution, we do it again with Laemmli gels

Wednesday, 29.08.12

  • evalutation of sequencing from last week:
    • PhoA worked
    • EstA worked
    • pNB-Est13 worked
    • RBS-PhoA-His6tag-pNBEst13-Myctag-EstA worked
    • arabinose regulated RBS-PhoA-His6tag-pNBEst13-Myctag-EstA

Thursday, 30.08.12

  • running 2 SDS-Laemmli gels
    • pellet is treated with n-Dodecyl-ß-maltoside (DDM) in order to solve membrane proteins
  • one gel is used to perform a second Western blot with a myc positive probe

120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111.png

  • 2 supernatant 30°C, 3 pellet (treated with detergent) 30°C, 4 supernatant 25°C, 5 pellet (treated with detergent) 25°C, 6 supernatant 20°C, 7 pellet (treated with detergent) 20°C, 8 myc positive probe
  • as we can see, only the treated 120831 Westermblot 2 auf Gesamt konstrukt aus DH5 alpha 5111pellets show positive signals when treated with antibodies, so we have expressed our membrane protein [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
  • now our lab can start with quantification of enzymatic activites of BBa_K808032 on PET or model substrates

Activity tests of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]

We were able to generate our BioBricks [http://partsregistry.org/Part:BBa_K808030 BBa_K808030] (chimeric, membrane bound, hydrolytic protein) and [http://partsregistry.org/Part:BBa_K808032 BBa_K808032] ( arabinose inducible operon, regulating the expression of BBa_K808030). Funcionality of both parts will be described by a bunch of tests:


  • As hosts we will use E.coli strains [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10], [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5alpha] or [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655]

Week 1 / CW 35

Friday, 31.08.12

  • Activity assay in DYT with DH5α containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
Component test tube 1 test tube 2 test tube 3 test tube 4
DYT-medium 8 mL 8 mL 8 mL 8 mL
PET particle yes yes yes yes
bacteria yes yes yes no
induced 1.5% L-arabinose 1.5% L-arabinose no no
  • test seemed to have worked: but an induced test tube without PET-granula was missing

Week 2 / CW 36

Tuesday, 04.09.12

  • Activity assay in DYT with DH5α containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
Component test tube 1 test tube 2 test tube 3 test tube 4 test tube 5
DYT-medium 8 mL 8 mL 8 mL 8 mL 8 mL
PET particle yes yes no yes yes
bacteria yes yes yes no yes
induced 1.5% L-arabinose 1.5% L-arabinose 1.5% L-arabinose no no
  • test tube 3: DYT without bacteria contains Cmp, Kan, Amp
  • looks good but test tube 2 shows no significant change of colour

Wednesday, 05.09.12

  • Activity assay in DYT with DH5α containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
Component tube 1 tube 2 tube 3 tube 4 tube 5 tube 6 tube 7 tube 8 tube 9
DYT-medium 8 mL 8 mL 8 mL 8 mL 8 mL 8 mL 8 mL 8 mL 8 mL
PET particle yes yes yes yes no no yes yes yes
bacteria yes yes yes yes yes yes yes yes no
induced 1.5% L-arabinose 1.5% L-arabinose 1.5% L-arabinose 1.5% L-arabinose 1.5% L-arabinose 1.5% L-arabinose no no no
  • test tube 9: DYT without bacteria contains Cmp, Kan, Amp
  • all induced tubes turned yellow, even without PET-granula as a substrate
  • no more avtivity tests, we are awaiting the evaluation of test expression series of the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter] conjugated to GFP

Trouble shooting

  • evaluation shows a very high sensisty of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808000 arabinose inducible promoter [BBa_K808000]] even to low concentrations of L-arabinose (expression starts at around 0.01%)
  • induction of the DH5α with 1.5% arabinose ended fatal due to extrem expression of the transmembrane construct [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 RBS-PhoA-His6tag-pNBEst13-Myctag-EstA]
  • starting test expressions with lower L-arabinose concentrations ranging from 0.05% - 1%

Thursday, 06.09.12

  • Activity assay in DYT with DH5α containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 [BBa_K808032]] (arabinose inducable RBS-PhoA-His6tag-pNBEst13-Myctag-EstA)
Component tube 1 tube 2 tube 3 tube 4 tube 5 tube 6 tube 7 tube 8 tube 9 tube 10 tube 11
DYT-medium 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL 5 mL
PET particle yes yes yes yes yes yes no no no no no
bacteria yes yes yes yes yes yes yes yes yes yes no
induced 1% L-arabinose 1% L-arabinose 0.75% L-arabinose 0.75% L-arabinose no no 1% L-arabinose 1% L-arabinose 0.75% L-arabinose 0.75% L-arabinose no
  • test tube 11: DYT without bacteria contains Cmp, Kan, Amp
  • all induced tubes turned yellow, even without PET-granula as a substrate

Week 3 / CW 37

we stopped the trial of quantification via PET-substrates because in terms of color the change of pH value (due to acid groups that are released by degradtion) is not very exactly. In order to get reproducible data, we are using other activity assays:

Monday, 10.09.12

  • Heatshock transformation of [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
  • activity assay on LB-Tributyrin-CAM-plates with L-arabinose concentrations: 0.1%, 0.2%, 0.4%
    • colony 1-5 are [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5 alpha] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] but colony 6 is just DH5 alpha carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
    • incubated over night at 37°C

Tuesday, 11.09.12

  • inoculation of 5 mL DYT-media-Cmp with K1 and K2 of transformed [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655] from yesterday
  • acticity tests on LB-Tributyrin-Cmp-plates shows good results
    • from now on incubation at room temperature

120911 dh5alpha k808032 0.1 ara.jpg 120911 dh5alpha k808032 0.2 ara.jpg 120911 dh5alpha k808032 0.4 ara.jpg

Wednesday, 12.09.12

120912 Testrestriktion K808032 im ethylenglycol stamm K1 und K2 mit ecori und psti.tif

Thursday, 13.09.12

120913 dh5alpha k808032 0.1 ara.jpg 120913 dh5alpha k808032 0.2 ara.jpg 120913 dh5alpha k808032 0.4 ara.jpg

  • to perform a better expression of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030] we will use [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] as a host for [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]. Its unability to metabolize L-arabinose is crucial for our decision. We hope to generate good expression levels.
  • Electroporation (after washing ecletroporation cuvettes very carefully) of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]

Friday, 14.09.12

  • yesterdays electroporation worked well
  • inoculation of 50 mL DYT-media-Cmp with colony from plate of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]

Saturday, 15.09.12

  • making 10% DMSO stocks from 50 mL [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] culture

Week 4/ KW 38

Monday, 17.09.12

  • inoculation of 4 x 50 mL DYT-media-Cmp with [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] stocks
  • at OD600=0,5 the cultures are incduced with:
    • 0.02% mw L-arabinose
    • 0.2% mw L-arabinose
    • 0.5% mw L-arabinose
    • one culture is not induced and will serve as a negative control
  • after 3 hours an antibody staining is performed on our expressed [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] containing a myc-epitope
  • checking surface expression levels via [http://en.wikipedia.org/wiki/Flow_cytometry#Labels flow cytometry]
    • inducing worked well, we can go on with screening the enzymatic activity
E.coli Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.02% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.
E.coli Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.2% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.
E.coli Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.5% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.
E.coli Top10 carrying BBa_K808032 and induced at an OD600=0.5 with an arabinose concentration of 0.02%, 0.2%, 0.5% and no arabinose at all. The relative absorbance of 50000 cells was meassured and is shown in this plot. The induced cells show a significant difference in their absorption due to the binding of a fluorescent labeled antibody. Fot the antibody staining we used an anti-myc antibody.

Tuesday, 18.09.12

  • Electroporation of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030], serving as a negative (directly used after 1h of incubation at 37°C in pure DYT-medium)
  • activity assay of [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10] containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] on LB Tributyrin agar with L-arabinose concentrations: 0.02%, 0.2%, 0.5%
    • colonies 1-3 containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032] but colony 4 containing [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]
  • Protein purification from induced cultures and negative control
    • cell debris pellets are treated with [http://www.sigmaaldrich.com/catalog/product/sigma/d4641?lang=en&region=US n-Dodecyl ß-D-maltoside] as a detergent
  • SDS PAGE (Laemmli) of pellets and supernatants
2: supernatant 0.5% arabinose, 3: treated pellet 0.5% arabinose, 4: supernatant 0.2% arabinose, 5: treated pellet 0.2% arabinose, 7: supernatant 0.02% arabinose, 8: treated pellet 0.02% arabinose, 9: supernatant no arabinose, 10: treated pellet no arabinose
















We use our induced cells (Top10) with an OD600=0.1-0.025 (resuspended in PBS-buffer) as catalysts and para-Nitrophenylbutyrate as a substrate. Induced cells have the [http://partsregistry.org/Part:BBa_K808030 fusion protein (BBa_K808030)] expressed on their surface. The catalytical domain, formed by pNB-Esterase 13 will show hydrolytic activity we can screen for by performing a pNP-assay. The substrate will be hydrolysed, and one degradation construct is para-Nitrophenylbutyrate. If released by hydrolysis, a characeristic absorption at 405 nm can be detected and plotted against the time, resulting in straight lines. The hydrolytic activity is quantified by the slope of the respective straight line.

Plot of the bacterial pNP-Assay using induced cells (Top10) with an OD600=0.1-0.025 (in PBS-buffer) as catalysts and para-Nitrophenylbutyrate as a substrate. The hydrolytic activity is quantified by the slope of the respective straight.
Plot shows relation of the slopes from Figure 6, representing the hydrolytic activity, in coherence with the level of arabinose concentration in % used for induction.

Wednesday, 19.09.12

  • activity assays on LB Tributyrin agar worked well (incubation occured just for the night at 30°C)

120919 top10 k808032 0.02 ara.jpg 120919 top10 k808032 0.2 ara.jpg 120919 top10 k808032 0.5 ara.jpg

  • activity assays on LB Tributyrin agar with 0.5% mw L-arabinose for inducing
    • colonies 1-4 [http://ecoliwiki.net/colipedia/index.php/DH5_alpha DH5 alpha], 5-8 [http://ecoliwiki.net/colipedia/index.php/TOP10 Top10], 9-12 [http://ecoliwiki.net/colipedia/index.php/MG1655 Mg1655]
    • colonies 1,2,5,6,9,10 are carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]
    • colonies 3,4,7,8,11,12 are carrying [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808030 BBa_K808030]

Tuesday, 18.09.12

120920 k808032 k808030 dh5a top10 mg1655.tif.jpg

Protein Expression

CW 20

Monday 14.05.2012

Tuesday 15.06.2012

  • one coclony of the retransformation was picked and transfered into 50 mL LB-Medium containing Cmp
  • the culture was stirred at 180 rpm at 30°C

Wednesday 16.06.12

  • centrifugation of the culture and resolving the pellet in 2 mL LB-Medium and 15% glycerine
  • seperate the cell suspension into 100 µL aliquots
  • store the stocks at -80°C

CW 24

Thursday, 14.06.2012

  • PCR for protein expression of FsC
    • each PCR is performed in 5 batches à 50 µL.
    • Parameter: TA = 57°C, tA = 35 s, tE = 65 s
  • PCR on pEST100 vector for expression with pEX vector gene of interest: FsC for designed part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808032 BBa_K808032]

primers: pEX FsC His SfiI up and pEX FsC Stop SfiI lo

Friday, 15.06.2012

CW 25

Wednesday, 20.06.2012

Thursday, 21.06.2012

Friday, 22.06.2012

CW 26

Monday, 25.06.2012

Component 1:3 1:5
FsC sequence 1.12 µL 2.2 µL
pEX 0.64 µL 0.64 µL
Ligase buffer 4 µL 4 µL
T4 DNA ligase 1 µL 1 µL
H2O 33 µL 30 µL
  • Ligation time: over night

Tuesday, 26.06.2012

Wednesday, 27.06.2012

  • Two positive clones on LB Cmp plates picked for liquid culture
    50 mL DYT Cmp cultures at 180 rmp and 37°C, over night

Thursday, 28.06.2012

  • Miniprep of pEX-Fsc in TOP10
    Concentration: 45 ng/µL and 405 ng/µL
  • Bacterial transformation by Electroporation of [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strains-bmh-71_18-muts-and-es1301-muts/ BmH7118] with the Miniprep product pEX-FsC

CW 27

Monday, 02.07.2012

Tuesday, 03.07.2012

Wednesday, 04.07.2012

Expression at 16°C/25°C
120711 FsC 16 25.jpeg
Expression at 30°C/37°C
120711 FsC 30 37.jpeg
  • The best results were maintained at an expression temperature of 30°C

Friday, 06.07.2012

  • Inoculation of 5 ml DYT Cmp with [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/bacterial-strains-bmh-71_18-muts-and-es1301-muts/ BmH7118] containing pEX-FsC
  • Incubation for 3 days at 20°C

CW 28

Monday, 09.07.2012

Wednesday, 11.07.2012

Thursday, 12.07.2012

120713 FsC 30.jpeg

CW 29

Monday, 16.07.2012

Tuesday, 17.07.2012

120719 Est13.jpeg

CW 31

Monday, 30.07.2012

Tuesday, 31.07.2012

120801 FsC 30.jpeg

CW 33

Friday, 17.08.2012

Saturday, 18.08.2012

120819 FsC 30.jpeg

CW 34

Wednesday, 22.08.2012

Thursday, 23.08.2012

120824 FsC 30.jpeg

Enzyme Activity Assays

To characterise our BioBricks [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] (pNB-Est13) & [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025] (FsC) a pNP-assays are performed.

CW 37

Est13

  • a pNP-assayis performed with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026] (pNB-Est13)
Lineweaver-Burk plot of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808026 BBa_K808026]
Km and Vmax calculation

To find Km the growth of the first seven data points were written down in a diagram. The slope of the regression line gave the speed of the hydrolysis for the single substrate concentrations. Now the value of the speed with the associated concentration of substrate were plotted in a Lineweaver-Burk diagram. At the point where the regression line is crossing the x-axis the x-coordinate amounts to -1/Km. So Km is about 400µM. To calculate the value of Vmax we used the point where the plotted line crosses the y-axis. The associated y-coordinate is 1/Vmax. Consequently Vmax for 50nM Est13 is 0,002798 1/s.

Kcat calculation

The value Kcat is calculated through dividing Vmax by the enzyme concentration of 50nM. Kcat counts 0,055951 1/mol*s.

FsC

  • a pNP-Assay is performed with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025].


Lineweaver-Burk plot of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K808025 BBa_K808025]
Km and Vmax calculation

To find Km the growth of the first twelve data points were written down in another diagram. The slope of the regression line gave the speed of the hydrolysis for the single substrate concentrations. Now the value of the speed with the associated concentration of substrate were plotted in a Lineweaver-Burk diagram. At the point where the regression line is crossing the x-axis the x-coordinate amounts to -1/Km. So Km is about 400µM. To calculate the value of Vmax we used the point where the plotted line crosses the y-axis. The associated y-coordinate is 1/Vmax. Consequently Vmax for 5nM FsC is 0,001467 1/s.

Kcat calculation

The Kcat value is calculated through dividing Vmax by the enzyme concentration of 5nM. Kcat counts 0,293395 1/mol*s.

FsC with ehtylenglycol

Our Simulation lab was able to show , theoratically, a relation between an decrease of enzyme activity and an increase of ethylenglycol concentration. This could be a hint for the mysterious loss of hydrolysis when the degradation rate reaches 5% of PET foil weight as it is described in the literature (Ronkvist, Å. M., Xie, W., Lu, W., & Gross, R. a. (2009). Cutinase-Catalyzed Hydrolysis of Poly(ethylene terephthalate). Macromolecules, 42(14), 5128–5138. doi:10.1021/ma9005318). We tried to proof their theory of potentially higher ethylenglycol concentration surrounding the PET foil. An increasing amount of ehtylenglycol should hamper the hydrolytic activity of FsC in a pNP-assay.

Procedure

The lab test procedure was nearly equal to the normal kinetics records with only one difference. The reaction solution consisted of different composites of PBS buffer and ethylenglycol (0 - 20%). All records were done at a concentration of 1mM of 4-Nitrophenyl butyrate in the experiment.

Records of the different ethylenglycol concentrations and the associated speeds of hydrolisis in a diagram
Plot of enzyme activity related to an increasing ehtylenglcol concentration
Interpretation

As you can see there is a stagnation of the speed of hydrolysis of the ester caused by an increasing concentration of ethylenglycol. But by that you cannot tell that ethylenglycol inhibits the FsC, because the hydrolysis of the ester rose with a higher concentration of ethylenglycol in the negative samples. So it could be that the ethylenglycol starts a concurrent reaction or blocks the 4-Nitrophenyl butyrate.

Plot of "activty" in the negative sample: pNPB & ethylenglycol

CW 36 - 38

PET degradation

Principle and conditions
principle of hyrolytic PET degradation. Conditions: Room temperature (~ 22°C) pH = 7.4

Procedure

Round about 1g of PET granulate is added in each two falcon tubes to between 15 and 20 mL water of pH = 7.4 and several drops of [http://en.wikipedia.org/wiki/Bromothymol_blue bromothymol blue]. In one of these falcon tubes Est13 stock solution is added until a concentration of 2,5 µM is reached. For 15 days the solutions are incubated at room temperature. At nine specific days of these the enzymatic solutions and the negative sample are photographed, to control the shift of pH.

Results

In all photos the degradation with Est13 is in the left falcon tube.

Day1:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day2:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day3:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day7:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day9:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day10:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day13:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control
Day15:Degradation of PET. Left: With Est13(2,5µM) Right: Negative control



The photos show a decrease of the pH-value over time in the sample containing Est13. The one without this enzyme remains unchanged. So it is concluded that Est13 degrades PET granulate.

CW34 - CW35

Degradation of monomethyl terephthalate over time

Principle and conditions

Principle of degradation of monomethyl terephthalate.png
Conditions: Room temperature (~22°C)

Procedure

Three different samples of 30 mL dest. water at a pH of 7.4 are incubated for 7 days with a concentration 500µM of monomethyl terephthalate (solved in methanol) and following ingredients:

1. 30µL of FsC (concentration in the incubated solution: ~0,8µM)
2. 30µL of Est13 (concentration in the incubated solution: ~0,8µM)
3. Nothing

To control the shift of the pH during the estercleavage some drops of [http://en.wikipedia.org/wiki/Bromothymol_blue bromothymol blue] are added.

Results

Following pictures show the shift of the pH over 7 days (The degaradation with Est13 is in the left falcon tube and with FSC in the middle one):

Day1: Degradation of monomethyl terephthalate. Left: with Est13(~0,8µM) Middle: with FSC(~8µM) Right: Negativ sample
Day8: Degradation of monomethyl terephthalate. Left: with Est13(~0,8µM) Middle: with FSC(~8µM) Right: Negativ sample

So you can see that both enzymes catalyzed the cleavage of the ester in a few days. In 7 days the pH-value shifted about one unit.

CW38

Degradation of 4-nitrophenyl-3-phenylpropanoate and bis(4-nitrophenyl) succinate

Principles, conditions and method
Principle of degradation of 4-nitrophenyl-3-phenylpropanoate
Principle of degradation of bis(4-nitrophenyl) succinat

Conditions and method are listed by the pNP-assay.

Procedure

The procedure is the same like in the pNP-assay. Only if bis(4-nitrophenyl) succinate is added, add 900µL of reagent A to 100µL of reagent B in step 1.

Results
Plot of enzyme activities on 4-nitrophenyl-3-phenylpropanoate and bis(4-nitrophenyl) succinate
Interpretation

The result shows that Est13 can catalyze the cleavage of both esters. FsC cannot do this in the given conditions. It is not clear what the reasons for the deactivation of FsC are. Maybe DMSO and/or methanol inhibit the enzyme or it is even not able to catalyze the hydrolysis.

Retrieved from "http://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation"