Team:Potsdam Bioware/Biobricks/Overview

From 2012.igem.org

(Difference between revisions)

Latest revision as of 17:08, 26 October 2012

Biobricks

Overview (click on a label to see the Bricks)

Selection Parts

Antibody Parts

Mutation Parts

RFC Potsdam Standard Parts

Favorite Biobricks

[http://partsregistry.org/Part:BBa_K929107 BBa_K929107] Anti-GFP, IgG1 Fc with TEV site, TMD, mCherry, framed by LoxP	This part was derived by de novo synthesis based on sequence information provided by GenBank and UniProt and by one already existing Biobrick part. The antibody construct consists of two major building blocks represented by the actual antibody unit (BBa_K929102) and the switchable membrane anchoring region (BBa_K929103). Both elements guarantee the eligibility and the easy handling of the construct and are optimized for expression in CHO cells. The antibody unit is represented by the human Ig kappa chain V-I region signal peptide (UniProt: P01601), the anti-GFP Nanobody (PDB: 3OGO) and the Fc region (UniProt: P01857). TEV protease recognition site, 2 LoxP sites, the B-cell receptor transmembrane domain (modified BBa_K157010) and the mCherry reporter display the switchable membrane anchoring region. The TEV recognition site on protein level and the LoxP sites on the genetically level allow the shift from surface presentation to secretion of the antibody unit. For detailed information see the [http://partsregistry.org/Part:BBa_K929107 partsregistry], for experimental experience also see All Biobricks.
[http://partsregistry.org/Part:BBa_K929003 BBa_K929003] modified AID with CMV, hGH-polyA and eGFP	This part is an improved version of wildtype AID, the enzyme that randomly mutates predominantly in the immunoglobulin genes. It is designed for strong expression of the fusion protein modified AID+eGFP. Modified AID has an additional Nuclear Localization Sequence (NLS)and the naturally occurring Nuclear Export Sequence (NES)is deleted. Due to the fact that AID mutates the actively transcribed single stranded DNA, it is supposed that the direction of the enzyme to the inside of the nucleus would improve the mutation rate.The fusion with the green fluorescent reporter eGFP allows 1.)to check the transfection success 2.)select transfected cells via FACS and 3.)to check the cellular localization of the fusion protein. For detailed information see the [http://partsregistry.org/Part:BBa_K929003 partsregistry], for experimental experience also see All Biobricks.
[http://partsregistry.org/Part:BBa_K929301 BBa_K929301] Potsdam Standard Backbone	This part is the new backbone of the Potsdam Standard. It contains two new restriction sites, Apa I and Sph I, and a RFP expression cassette which can be used as a ligation control. For the cloning process, the backbone has to be digested with Apa I and Sph I. The insert is amplified with primers which contains thiophosphates at the 5' end. After knocking out the thiophosphates with iodine/ethanol solution, the insert can be ligated into the digested backbone. The ligation success can be controlled by the red fluorescent protein. If the ligation faild, you would see red fluorescent colonies. For detailed information see the [http://partsregistry.org/Part:BBa_K929301 partsregistry], for experimental experience also see All Biobricks.

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 ==Biobricks==
-===Overview===
+===Overview (click on a label to see the Bricks)===
 <br>
-[[File:UP12biobricks.png|600px|left]]
+[[File:UP12biobricks.png|link=https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks|600px|left]]
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+<div style="position:absolute; top:600px; left:730px;">
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@@ Line 26: / Line 29: @@
-<a href="https://2012.igem.org/wiki/"
+<a href="https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks#Potsdam_Standard_BioBricks"
 onmouseover="button04.src=image2.src"
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 <div style="position:absolute; top:834px; left:575px;">
-<span style="color:#00C000; font-weight:bold; font-size: 20px;">[http://syntbio.net/iGEM/wiki2011/index.php/TESTWIKI#antibody_module_parts Selection Parts]</span>
+<span style="color:#00C000; font-weight:bold; font-size: 20px;">[https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks#Selection_BioBricks Selection Parts]</span>
 </div>
 <div style="position:absolute; top:493px; left:142px;">
-<span style="color:#00C000; font-weight:bold; font-size: 20px;">[http://syntbio.net/iGEM/wiki2011/index.php/TESTWIKI#antibody_module_parts Antibody Parts]</span>
+<span style="color:#00C000; font-weight:bold; font-size: 20px;">[https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks#Antibody_BioBricks Antibody Parts]</span>
 </div>
-<div style="position:absolute; top:683px; left:238px;">
+<div style="position:absolute; top:683px; left:168px;">
-<span style="color:#00C000; font-weight:bold; font-size: 20px;">[http://syntbio.net/iGEM/wiki2011/index.php/TESTWIKI#antibody_module_parts Mutation Parts]</span>
+<span style="color:#00C000; font-weight:bold; font-size: 20px;">[https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks#Mutation_BioBricks Mutation Parts]</span>
+</div>
+<div style="position:absolute; top:575px; left:680px;">
+<span style="color:#00C000; font-weight:bold; font-size: 20px;">[https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks#Potsdam_Standard_BioBricks RFC Potsdam Standard Parts]</span>
 </div>
 ----
 ===Favorite Biobricks===
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 <tr>
-    <td>[http://partsregistry.org/Part:BBa_929107 BBa_929107]<br>
+    <td>[http://partsregistry.org/Part:BBa_K929107 BBa_K929107]<br>
-'''Anti-GFP, IgG1 Fc with TEV site, TMR, mCherry, framed by LoxP'''<br>
+'''Anti-GFP, IgG1 Fc with TEV site, TMD, mCherry, framed by LoxP'''<br>
-Antibody Module
     </td>
-    <td> [[Image:UP12_BBa_K929107.png|right|400px]]This part is an improved version of wildtype AID, the enzyme that randomly mutates predominantly in the immunoglobulin genes. It is designed for strong expression of the fusion protein modified AID+eGFP. Modified AID has an additional Nuclear Localization Sequence (NLS)and the naturally occurring Nuclear Export Sequence (NES)is deleted. Due to the fact that AID mutates the actively transcribed single stranded DNA, it is supposed that the direction of the enzyme to the inside of the nucleus would improve the mutation rate.The fusion with the green fluorescent reporter eGFP allows 1.)to check the transfection success 2.)select transfected cells via FACS and 3.)to check the cellular localization of the fusion protein. For detailed information see the [http://partsregistry.org/Part:BBa_K929003 partsregistry], for experimental experience also see [https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks All Biobricks].
+    <td> [[Image:UP12_BBa_K929107.png|right|400px]]This part was derived by de novo synthesis based on sequence information provided by GenBank and UniProt and by one already existing Biobrick part. The antibody construct consists of two major building blocks represented by the actual antibody unit (BBa_K929102) and the switchable membrane anchoring region (BBa_K929103). Both elements guarantee the eligibility and the easy handling of the construct and are optimized for expression in CHO cells. The antibody unit is represented by the human Ig kappa chain V-I region signal peptide (UniProt: P01601), the anti-GFP Nanobody (PDB: 3OGO) and the Fc region (UniProt: P01857). TEV protease recognition site, 2 LoxP sites, the B-cell receptor transmembrane domain (modified BBa_K157010) and the mCherry reporter display the switchable membrane anchoring region. The TEV recognition site on protein level and the LoxP sites on the genetically level allow the shift from surface presentation to secretion of the antibody unit.  For detailed information see the [http://partsregistry.org/Part:BBa_K929107 partsregistry], for experimental experience also see [https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks All Biobricks].
     </td>
 </tr>
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     <td>[http://partsregistry.org/Part:BBa_K929003 BBa_K929003]<br>
 '''modified AID with CMV, hGH-polyA and eGFP'''<br>
-Mutation Module
     </td>
     <td> [[Image:UP12_BBa_K929003_smaloverview.png|right|400px]] This part is an improved version of wildtype AID, the enzyme that randomly mutates predominantly in the immunoglobulin genes. It is designed for strong expression of the fusion protein modified AID+eGFP. Modified AID has an additional Nuclear Localization Sequence (NLS)and the naturally occurring Nuclear Export Sequence (NES)is deleted. Due to the fact that AID mutates the actively transcribed single stranded DNA, it is supposed that the direction of the enzyme to the inside of the nucleus would improve the mutation rate.The fusion with the green fluorescent reporter eGFP allows 1.)to check the transfection success 2.)select transfected cells via FACS and 3.)to check the cellular localization of the fusion protein. For detailed information see the [http://partsregistry.org/Part:BBa_K929003 partsregistry], for experimental experience also see [https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks All Biobricks].
@@ Line 76: / Line 82: @@
     <td>[http://partsregistry.org/Part:BBa_K929301 BBa_K929301]<br>
 '''Potsdam Standard Backbone'''<br>
-Potsdam Standard
     </td>
-    <td> [[Image:UP12_BBa_K929301_smaloverview.png|right|400px]] This part is an improved version of wildtype AID, the enzyme that randomly mutates predominantly in the immunoglobulin genes. It is designed for strong expression of the fusion protein modified AID+eGFP. Modified AID has an additional Nuclear Localization Sequence (NLS)and the naturally occurring Nuclear Export Sequence (NES)is deleted. Due to the fact that AID mutates the actively transcribed single stranded DNA, it is supposed that the direction of the enzyme to the inside of the nucleus would improve the mutation rate.The fusion with the green fluorescent reporter eGFP allows 1.)to check the transfection success 2.)select transfected cells via FACS and 3.)to check the cellular localization of the fusion protein. For detailed information see the [http://partsregistry.org/Part:BBa_K929003 partsregistry], for experimental experience also see [https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks All Biobricks].
+    <td> [[Image:UP12_BBa_K929301_smaloverview.png|right|400px]] This part is the new backbone of the Potsdam Standard. It contains two new restriction sites, Apa I and Sph I, and a RFP expression cassette which can be used as a ligation control. For the cloning process, the backbone has to be digested with Apa I and Sph I. The insert is amplified with primers which contains thiophosphates at the 5' end. After knocking out the thiophosphates with iodine/ethanol solution, the insert can be ligated into the digested backbone. The ligation success can be controlled by the red fluorescent protein. If the ligation faild, you would see red fluorescent colonies. For detailed information see the [http://partsregistry.org/Part:BBa_K929301 partsregistry], for experimental experience also see [https://2012.igem.org/Team:Potsdam_Bioware/Biobricks/All_Biobricks All Biobricks].
     </td>
 </tr>