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Team:ETH Zurich/lab/protocols
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Revision as of 09:07, 25 August 2014
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Materials
LB medium
Preparation of antibiotics stock (1000x)
| Ampicillin (200 mg/mL) in H2O, sterile filtered |
| Kanamycin (50 mg/mL) in H2O, sterile filtered |
| Chloramphenicol (34 mg/mL) in ethanol |
| Tetracycline (10 mg/mL) in ethanol |
| Streptamycin (25 mg/mL) in H2O, sterile filtered |
SOC
| Tryptone | 20 g |
| Yeast extract | 5 g |
| NaCl | 0.5 g |
| Dissolve, then add | |
| KCl (250 mM) | 10 mL |
| MgCl2 | 5 mL |
| Autoclave, then add | |
| sterile glucose (1 M) | 20 mL |
According to [http://www.qiagen.com/resources/molecular-biology-methods/dna/ QIAGEN DNA protocols and applications]
Transformation buffer 1 (TFB1)
| RbCl (100 mM) | 12.1 g |
| MnCl2·4H2O (50 mM) | 9.9 g |
| Potassium acetate (30 mM) | 2.9 g |
| CaCl2·2H2O (10 mM) | 1.4 g |
| Glycerol (15%) | 150 mL |
| Adjust pH to 5.8 with KOH | |
| Sterilize by filtration |
According to [http://www.qiagen.com/resources/molecular-biology-methods/dna/ QIAGEN DNA protocols and applications]
Transformation buffer 2 (TFB2)
| RbCl (10 mM) | 1.2 g |
| MOPS (10 mM) | 2.1 g |
| CaCl2·2H2O (75 mM) | 11.0 g |
| Glycerol (15%) | 150 mL |
| Adjust pH to 6.8 with KOH | |
| Sterilize by filtration |
According to [http://www.qiagen.com/resources/molecular-biology-methods/dna/ QIAGEN DNA protocols and applications]
Gibson Assembly reaction mixture
5x isothermal reaction buffer
| Tris-HCl pH 7.5 (1 M) | 3 mL |
| MgCl2 (2 M) | 150 μL |
| dGTP (100 mM) | 60 μL |
| dATP (100 mM) | 60 μL |
| dTTP (100 mM) | 60 μL |
| dCTP (100 mM) | 60 μL |
| DTT (1 M) | 300 mL |
| PEG-8000 | 1.5 g |
| NAD (100 mM) | 300 μL |
Aliquots can be stored at -20 °C
Assembly master mixture
| Isothermal reactio buffer (5x) | 320 μL |
| T5 exonuclease (10 U/μL) | 0.64 μL |
| Phusion DNA polymerase (2 U/μL) | 20 μL |
| Taq DNA ligase (40 U/μL) | 160 μL |
| H2O | 1.2 mL |
Aliquots of 15 μL can be stored at -20 °C
Methods
Preparation of competent E. coli
Day before: Preparation of a Top10 cells preculture in LB-medium containing streptomycin (25 μg/mL)
- Addition of 1 mL overnight preculture to 100 mL LB-medium + streptomycin (25 μg/mL)
- Cultivate culture at 37 °C, 220 rpm until it reaches an OD600 of 0.5
- Cool culture for 5 min on ice and centrifuge it for 5 min at 4 °C, 4000 g
- Discard the supernatant and resuspend the cells in cold TFB1 buffer (30 mL, 4 °C)
- Keep the suspension on ice for 90 min
- Centrifuge the suspension for 5 min at 4 °C, 4000 g and discard the supernatant
- Resuspend the cells in 4 mL cold TFB2 buffer
- Make aliquots of 100 μL and freeze the aliquots in dry ice in ethanol
- Store aliquots at -80 °C
According to [http://www.qiagen.com/resources/molecular-biology-methods/dna/ QIAGEN DNA protocols and applications]
Preparation of DNA from iGEM kit
- Add 10 μL H2O to appropriate well, wait for 5 min, transfer into sterile tube
- Use 2 μL to transform competent cells
Biological parts used from iGEM kit:
| Part-ID | Function |
| BBa_F2620 | tetR-luxR-pLuxR |
| BBa_K084007 | pLacI-lasI |
| BBa_C0070 | rhlI-LVA |
| BBa_C0171 | rhlR |
| BBa_J23100 | constitutive promoter |
| BBa_K553003 | promoter-RBS-lasR-Term |
| BBa_C0161 | luxI |
For confirmation all plasmids used from the iGEM kit were sequenced
Transformation of competent E. coli
- Thaw the competent cells on ice
- Add 1 μL DNA (0.2 - 200 ng) to 50-100 μL competent cells
- Leave sample on ice for approximately 20 min
- Heat shock the cells for 90 s at 42 °C
- Add 500 μL of SOC to the sample
- Let the cells recover for 60 min at 37 °C, 220 rpm
- Plate appropriate amount of cell suspension (50 - 200 μL) on LB-agar-plates containing the appropriate antibiotic
- Let bacteria grow overnight at 37 °C
According to [http://www.qiagen.com/resources/molecular-biology-methods/dna/ QIAGEN DNA protocols and applications]
Plasmid preparation
Day before: Preparation of a preculture in LB-medium containing the appropriate antibiotics. The amount of cell culture required for plasmid preparation depends on the copy number of the plasmid (between 5 and 20 mL)
- Centrifuge the preculture in appropriate tubes for 10 min at 4000 g
- Carefully remove the supernatant
- Resuspend pellet in 200 μL resuspension solution
- Add 200 μL lysis solution and invert the tube gently 1 to 2 times
- Lysis should not exceed 5 min
- Add 350 μL neutralization solution and invert the tube 4 to 6 times
- Centrifuge the suspension for 10 min at 12 000 rcf
- Prepare the columns by adding 500 μL of column preparation solution and centrifuging it for 1 min at 12 000 rcf. Discard the flow-through
- Transfer the supernatant of the centrifuged samples onto columns
- Spin for 1 min at 12 000 rcf and subsequently discard the flow-through
- Add 750 μL wash solution and spin the loaded column for 1 min at 12 000 rcf. Discard the flow-through
- Dry the columns by centrifuging them for 1 min at 12 000 rcf
- Place columns in new collection tubes
- Elute the plasmid DNA with 50 μL ddH2O to increase the plasmid concentration
The [http://www.sigmaaldrich.com/life-science/molecular-biology/dna-and-rna-purification/plasmid-miniprep-kit.html Sigma-Aldrich GenElute™ Plasmid Miniprep Kit] was used
Preparation of samples for sequencing at Microsynth
Add 12 μL DNA (60-100 ng/μL) to 3 μL of the corresponding primer (10 μM).
PCR procol for phusion DNA polymerase
| Components | 20 μL total reaction volume | 50 μL total reaction volume |
|---|---|---|
| 5x Phusion HF buffer | 4 μL | 10 μL |
| 10 mM dNTPs | 2 μL | 5 μL |
| Forward Primer (10 μM) | 1 μL | 2.5 μL |
| Reverse Primer (10 μM) | 1 μL | 2.5 μL |
| DMSO | 0.6 μL | 1.5 μL |
| Phusion DNA polymerase | 0.2 μL | 0.5 μL |
| DNA | 40-200 ng | 40-200 ng |
| H2O | add to reach a total volume of 20 μL | add to reach a total volume of 50 μL |
Restriction Endonuclease Reaction (double digestion)
| 1-2.5 μL restriction endonuclease 1 |
| 1-2.5 μL restriction endonuclease 2 |
| 5 μL Cut Smart Buffer |
| 1-3 μg template DNA |
| add H2O to reach a total volume of 50 μL |
Enzymes, buffers and protocol are from New England BioLabs
Dephosphorylation of 5’-ends of DNA using CIP
Add 1 unit of CIP for every 1 pmol of DNA ends (about 1 μg of a 3 kb plasmid) and incubate at 37 °C for 30–60 min.
Enzymes, buffers and protocol are from New England BioLabs
DNA Purification by Centrifugation
A. Dissolving the Gel Slice
Following electrophoresis, excise DNA band from gel and place gel slice in a 1.5 ml microcentrifuge tube. Add 10 µl Membrane Binding Solution per 10 mg of gel slice. Vortex and incubate at 50–65 °C until gel slice is completely dissolved.
or
B. Processing PCR Amplifications
Add an equal volume of Membrane Binding Solution to the PCR mix.
- Insert SV Minicolumn into Collection Tube.
- Transfer dissolved gel mixture or prepared PCR product to the Minicolumn assembly. Incubate at room temperature for 1 min.
- Centrifuge at 16 000 rcf for 1 min. Discard flowthrough and reinsert Minicolumn into Collection Tube.
- Add 700 µL Membrane Wash Solution (ethanol added). Centrifuge at 16 000 rcf for 1 min. Discard flowthrough and reinsert Minicolumn into Collection Tube.
- Repeat the step before with 500 µL Membrane Wash Solution. Centrifuge at 16 000 rcf for 5 min.
- Empty the Collection Tube and recentrifuge the column assembly for 1 min with the microcentrifuge lid off to allow evaporation of any residual ethanol.
- Carefully transfer Minicolumn to a clean 1.5 mL microcentrifuge tube.
- Add 50 µL of Nuclease-Free Water to the Minicolumn. Incubate at room temperature for 1 min. Centrifuge at 16 000 rcf for 1 min.
- Discard Minicolumn and store DNA at 4 °C or –20 °C.
According to Promega Wizard SV Gel and PCR Clean-Up System, Quick protocol
Agarose gel electrophoresis
- For a 5 cm x 6 cm gel add 0.25 g Agarose to 25 mL TAE (0.5x) and heat up in microwave to dissolve it
- Let the solution cool down to approximately 50 °C
- Add nucleic acid dye (e.g. 2.5 μL peqGREEN) and mix
- Pour the solution in a tray using an appropriate comb
- Add loading dye (e.g. NEB purple loading dye) to the samples
- Fill the samples and ladder in the wells
- Run the gel at 135 V
Preparation of cryostocks
- Cultivate bacteria (37 °C) in medium with antibiotic (e.g. 5 mL LB, 5 μL amp + 500 μL preculture) until they are in log phase (OD=0.8-1.2)
- Add 750 μL sterile glycerol (30%) to 750 μL bacteria culture in a screw top tube
- Freeze the glycerol stock tube at -80 °C
Site-directed mutagenesis
| 14 μL H2O |
| 2 μL HF buffer |
| 1.6 μL dNTPs |
| 0.5 μL of primer 1 |
| 0.5 μL of primer 2 |
| 0.4 μL Phusion polymerase |
| 1 μL template DNA (2-20 ng) |
- Run PCR
- Digestion of template DNA: Addition of 1 μL DpnI, 1h at 37 °C
- Heat inactivation of DpnI: 20 min at 80 °C
Protocol based on QuikChange Site-Directed Mutagenesis
Gibson Assembly
One-step isothermal DNA assembly protocol: the exonuclease amount is ideal for the assembly of DNA molecules with 20–150 bp overlaps
- Mix the backbone and PCR fragments in 5 µL total volume in equimolar amounts
- Thaw the Gibson assembly reaction mixture on ice
- Add DNA mixture (5 µL) to the reaction mixture (15 µL)
- Run the reaction for 30-60 min at 50 °C
- Subsequently the reaction mixture (5 uL are enough) can be used directly to transform competent cells (75 uL)
Preparation of alginate beads
- Harvest bacteria in exponential phase (OD between 1.5 and 2.0)
- Centrifuge the culture for 10 min at 4000 rcf
- Resuspend and dilute the pellet in sterile NaCl solution (0.9%)
- Add bacteria-NaCl-suspension to sterile alginate (2.5%) so as to reach an alginate concentration of 2%
- Fill the suspension into a sterile syringe
blablabla
1 bead: approximatly 14.5 µl alginate-NaCl
