Team:TU Darmstadt/Materials/Metabolism

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Materials


Contents

Primers

No. Name 5´-->3´
1 tphA2-l-F TCATGCTTGCATCTCCTGTC
2 tphA2-l-Prefix GAATTCGCGGCCGCTTCTAGATGCAAGAATCCATCATCCAGTGGC
3 tphA1-Suffix_R CTGCAGCGGCCGCTACTAGTACTAATGGTTGCCAGTCGGGTCTG
4 tphA3-Suffix_R CTGCAGCGGCCGCTACTAGTATCATAGCGGCAATGACATCAGCGTG
5 tphA3-Prefix_F GAATTCGCGGCCGCTTCTAGATGATCCATGAAATTCAAATCGCGG
6 tphA1-l-R CTAATGGTTGCCAGTCGGGT
7 tphA1-l-PstI(99)-F CATGGTCTCCTCCAGGCCGGCATCGAGCT
8 tphA1-l-Prefix GAATTCGCGGCCGCTTCTAGATGAACCACCAGATCCATATCCACG
9 tphA3-l-F TCATAGCGGCAATGACATCA
10 tphA3-l-Prefix GAATTCGCGGCCGCTTCTAGAGATGATCCATGAAATTCAAATCGC
11 Prefix GAATTCGCGGCCGCTTCTAGAG
12 tphB-l-F TCAGACCGGTTGGGCTCCGA
13 tphB-l-Prefix GAATTCGCGGCCGCTTCTAGAGATGACAATAGTGCACCGTAGATT
14 tphA2-l-R ATGCAAGAATCCATCATCCAG
15 tphA1-l-R ATGAACCACCAGATCCATATC
16 tphA1-l-PstI(99)-R CATGGTCTCCTGGAGGGCTGCATCCAGTAC
17 tphA3-l-R ATGATCCATGAAATTCAAAT
18 Suffix CTGCAGCGGCCGCTACTAGTA
19 tphB-l-Suffix-R CTGCAGCGGCCGCTACTAGTATCAGACCGGTTGGGCTCCGAGTA
20 EcoRIGFxa-tphA1 TTCTGGAATTCGGGTATTGAAGGAAGAATGAACCACCAGATCCATAT
21 EcoRIGFxa-tphA2 TTCTGGAATTCGGGTATTGAAGGAAGAATGCAAGAATCCATCATCCA
22 EcoRIGFxa-tphA3 TTCTGGAATTCGGGTATTGAAGGAAGAATGATCCATGAAATTCAAAT
23 EcoRIGFxa-tphB TTCTGGAATTCGGGTATTGAAGGAAGAATGACAATAGTGCACCGTAG
24 EcoRIGFxa-aroY TTCTGGAATTCGGGTATTGAAGGAAGAATGACAGCGCCTATCCAG
25 RBS-tphA1 TTCTGGAATTCGCGGCCGCTTCTAGAGAAAGACAGGACCTACTAGATGAACCACCAGATCCATAT
26 RBS-tphA2 TTCTGGAATTCGCGGCCGCTTCTAGAGAAAGACAGGACCTACTAGATGCAAGAATCCATCATCCA
27 RBS-tphA3 TTCTGGAATTCGCGGCCGCTTCTAGAGAAAGACAGGACCTACTAGATGATCCATGAAATTCAAAT
28 RBS-tphB TTCTGGAATTCGCGGCCGCTTCTAGAGAAAGACAGGACCTACTAGATGACAATAGTGCACCGTAG
29 RBS-aroY TTCTGGAATTCGCGGCCGCTTCTAGAGAAAGACAGGACCTACTAGATGACAGCGCCTATCCAG
30 VF2 TGCCACCTGACGTCTAAGAA
31 VR ATTACCGCCTTTGAGTGAGC
32 pPR-IBA2 rev TAGTTATTGCTCAGCGGTGG
33 pPR-IBA2 for TAATACGACTCACTATAGGG

Plasmids

No. Name Sequence
1 pSB1C3 [http://partsregistry.org/Part:pSB1C3 Get]
2 pSB1AK3 [http://partsregistry.org/Part:pSB1AK3 Get]
3 BBa_J61002 [http://partsregistry.org/Part:BBa_J61002 Get]
4 pSB1A2 [http://partsregistry.org/Part:pSB1A2 Get]
5 pPR-IBA2 [http://www.iba-lifesciences.com/isotope/2/2-1391-000-Sequence-pPR-IBA2.txt Get]

Biobricks from the registry

No. Name Platte Well Resistence Plasmid backbone
1 BBa_K316003 4 15C C pSB1C3
2 BBa_J23100 1 18C A BBa_J61002
3 BBa_B0015 1 23L A und K pSB1AK3
4 BBa_J61101 1 5L A pSB1A2


Bacteria

Species Strain Genotype DSM-No.
Escherichia coli DH5α F- endA1 glnV44 thi-1 recA1 relA1 gyrA96 deoR nupG Φ80dlacZΔM15 Δ(lacZYA-argF)U169, hsdR17(rK- mK+), λ– 6897
Escherichia coli MG1655 F- λ- ilvG- rfb-50 rph-1 18039
Escherichia coli BL21(DE3)pLysS F- ompT gal dcm lon hsdSB(rB- mB-) λ(DE3) pLysS(cmR) none
Comamonas testosteroni Kf-1 - 14576

Enzymes

No. Enzyme Supplier
1 Antarctic Phosphatase NEB
2 BsaI NEB
3 EcoRI-HF NEB
4 Phusion® High-Fidelity DNA Polymerase NEB
5 PstI-HF NEB
6 SpeI-HF NEB
7 T4 DNA Ligase NEB
8 Taq DNA Polymerase with ThermoPol Buffer NEB
9 XbaI NEB

Chemicals

No. Name Firma Order-ID
1 Terephthalat Sigma-Aldrich 185361-500G
2 Acetic acid Roth 6755.1
3 Methanol Roth CP43.1
4 Coomassie Brilliant Blue R-250 Roth 9598.1
5 Trypton Roth 8952.1
6 Ethylene glycol Roth 9516.1
7 3,4-Dihydroxybenzoic acid Sigma-Aldrich 37580-25G-F
8 Catechol Sigma-Aldrich C9510-100G
9 Isopropyl β-D-1-thiogalactopyranoside Roth CN08.1
10 Tetramethylethylenediamine Roth 2367.3
11 Ammonium persulfate Roth 9592.3
12 Bromophenol blue Roth A512.1
13 Glucose Roth X997.1
14 Calcium chloride Roth CN92.1
15 Dithiothreitol Roth 6908.1
16 Sodium carbonate Roth 8563.1
17 Phenylmethanesulfonylfluoride Roth 6367.1
18 NADH-Disodium Roth AE12.1
19 Nicotinamide adenine dinucleotide Roth AE11.1
20 orthophosphoric acid 85% Roth 9079.1
21 Trichloroacetic acid Roth 8789.2
22 Quick-Load® 100 bp DNA Ladder NEB Biolabs N0467S
23 Phenol AppliChem A4458.0250
24 Dimethyl sulfoxide AppliChem A1584.0100
25 Methylene blue AppliChem A4084.0025
26 Magnesium sulfate AppliChem A6287.0250
27 Cetrimonium bromide AppliChem A0805.0100
28 Tetramethylethylenediamine AppliChem A1148.0025
29 Urea AppliChem A5470.0500
30 Tween20 AppliChem A1389.0500
31 Protein Marker III (6,5-200) AppliChem A4402.0001
32 Thiamine hydrochloride AppliChem A09955.0050
33 Triton X-100 AppliChem A1388.0500
34 DNA-Dye NonTox AppliChem A9555.1000
35 Agarose Roth 3810.2
36 Ethanol 96 % Roth T171.4
37 Ethylenediaminetetraacetic acid Roth X986.2
38 Ethanol Roth P076.1
39 Tetracycline hydrochloride Roth 237.1
40 D-Desthiobiotin 10x Buffer E iba 2-1000-025
41 2-(4-Hydroxyphenylazo)benzoic acid Sigma-Aldrich H5126-5G
42 10 mM dNTP-Mix Roth L785.2
43 Hydrochloric acid Roth 9277.1
44 Acrylamid - Bis (37,5:1) Roth 3029.1
45 Ammonium acetate Roth 7869.2
46 Agar-Agar Roth 5210.3
47 Chloroform Roth 4423.1
48 Glycine Roth 3790.2
49 Dipotassium phosphate Roth T875.1
50 Sodium chloride Roth 9265.1
51 Yeast extract Roth 2363.2
52 Monopotassium phosphate Roth P018.1
53 Glycerine Roth 3783.1
54 Sodium hydroxide Roth P031.1
55 Tris-Base Roth AE15.2
56 Isopropyl alcohol Roth CP41.3
57 Isoamyl alcohol Roth T870.1
58 Acetonitrile Roth 7330.2
59 Acetone Roth 5025.5
60 Chloramphenicol Roth 3886.2
61 Ampicillin Roth K029.1
62 Kanamycin Roth T832.1
63 Sodium dodecyl sulfate Roth 5136.1


Kits

No. Kit Supplier
1 PureYield™ Plasmid Miniprep System Promega
2 PureYield™ Plasmid Midiprep System Promega
3 Wizard® SV Gel and PCR Clean-Up System Promega

Consumabels

No. Article Supplier
1 epT.I.P.S.® Box pipette tips 0.1–20 µL Eppendorf
2 epT.I.P.S.® Box pipette tips 10–200 µL Eppendorf
3 epT.I.P.S.® Box pipette tips 100–1000 µL Eppendorf
4 epT.I.P.S.® Bulk pipette tips 0.1–20 µL Eppendorf
5 epT.I.P.S.® Bulk pipette tips 10–200 µL Eppendorf
6 epT.I.P.S.® Bulk pipette tips 100–1000 µL Eppendorf
7 PCR Tubes 0.2 mL Eppendorf
8 PCR Tube Strips 0.2 mL Eppendorf
9 Safe-Lock Tubes (1.5 mL) Eppendorf
10 Safe-Lock Tubes (2 mL) Eppendorf
11 Rotilabo®-syringe filters Carl Roth GmbH
12 NORM-Ject Syringes Henke/Sass/Wolf
13 Multiply®-PCR-tubes 0.2 mL Sarstedt
14 VWR® Pipet Tips (Standard Tips, 0.1–20 µL) VWR
15 VWR® Pipet Tips (Standard Tips, 10–200 µL) VWR
16 VWR® Pipet Tips (Standard Tips, 100-1000 µL) VWR
17 VWR® Powder-Free Nitrile Examination Gloves VWR
18 Eco-friendly centrifuge tubes (15 mL, unsterile) Carl Roth GmbH
19 50 mL Centrifuge tubes, sterile Greiner bio-one
20 Sekuroka®-disposal bags Carl Roth GmbH
21 Rotiprotect®-nitrile gloves, unpowdered Carl Roth GmbH
22 UV-cuvettes PLASTIBRAND® (Micro z = 8,5 mm) Brand GmbH & Co. KG
23 Parafilm® M Pechiney Plastic Packaging

Equipment

No. Equipment Supplier
1 Mastercycler personal (Thermocycler) Eppendorf
2 Heraeus Pico Microcentrifuge Thermo Scientific
3 Multifuge® 1S-R Thermo Scientific
4 VX-150 Autoclave Systec
5 Uni-Drybath Thermoshaker Universal Labortechnik
6 Vortex Genie 2 Scientific Industries
7 Universal Centrifuge Sigma Laborzentrifugen
8 Dark Hood DH-40 with control panel and display Biostep
9 BioMate 3S Spectrophotometer Thermo Scientific
10 GENESYS 10S UV-Vis Thermo Scientific
11 Heraeus LaminAir HA 2448 GS Heraeus
12 Signature™ Ergonomic High Performance Single-Channel Variable Volume Pipettors 10 µL VWR
13 Signature™ Ergonomic High Performance Single-Channel Variable Volume Pipettors 100 µL VWR
14 Signature™ Ergonomic High Performance Single-Channel Variable Volume Pipettors 1000 µL VWR
15 Research® plus, adjustable pipette 0.5 - 10 µL Eppendorf
16 Research® plus, adjustable pipette 10 - 100 µL Eppendorf
17 Research® plus, adjustable pipette 100 – 1000 µL Eppendorf
18 Research® plus, adjustable pipette 10 - 200 µL Eppendorf
19 Research® plus, adjustable pipette 0.5 - 20 µL Eppendorf
20 Reference, adjustable pipette 0.5 – 10 µL Eppendorf
21 M-Prove Balances Sartorius
22 M-Power Balances Sartorius
23 Owl Series EasyCast™ Horizontal Mini-Gel Systems VWR
24 Owl Series Horizontal Gel Systems VWR
25 Owl Series Dual Gel Vertical Electrophoresis System VWR
26 Power Supplies 250V VWR
27 Incubation/Inactivation Water Bath 1008 Gesellschaft für Labortechnik
28 Lab-Shaker LSR-V Adolf Kühner AG
29 MR Hei-Mix S Heidolph
30 FE20 – FiveEasy™ pH Mettler Toledo
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