Team:ETH Zurich/Experiments
Experimental: Protocols, Methods and Material
Polymerase Chain Reaction - for Construction
New England Biolabs Phusion High-Fidelity DNA Polymerase
Composition:
| Component | 50 µl Reaction |
| Phusion HF Buffer (5x) | 10 µl |
| dNTPs (10 mM) | 1 µl |
| Forward Primer (10 µM) | 2.5 µl |
| Reverse Primer (10 µM) | 2.5 µl |
| Template DNA | variable |
| DMSO (optional) | up to 3% |
| Nuclease-free water | up to 50 µl |
| Phusion Polymerase | 0.5 µl |
Thermocycling Conditions:
| Temperature |
Time |
| 98°C | 30 seconds |
| 98°C 45-72°C 72°C |
5-10 seconds 10-30 seconds 15-30 seconds per kb |
| 72°C | 5-10 minutes |
The appropriate annealing temperature was calculated from NEB's Tm Calculator
Kapa Biosystems Hifi Hotstart Ready Mix
| Component | 50 µl Reaction |
| Master Mix (2x) | 25 µl |
| Forward Primer (10 µM) | 2.5 µl |
| Reverse Primer (10 µM) | 2.5 µl |
| Template DNA | variable |
| Nuclease-free water | up to 50 µl |
Thermocycling Conditions:
| Temperature |
Time |
| 95°C | 3 minutes |
| 98°C 55-75°C 72°C |
20 seconds 15 seconds 15-60 seconds per kb |
| 72°C | 1 minute per kb |
Kapa Hifi Hotstart has similar annealing temperatures as Phusion DNA polymerase, even slightly higher. Only in very few cases a lower annealing temperature was found to be better.
Polymerase Chain Reaction - Colony PCR
For screening a large number of clones, single colonies were resuspended in 20 µl LB medium of which 1 µl was used as template for the PCR.
Solis BioDyne FirePol DNA Polymerase
Composition:
| Component | 8 x 20 µl Reaction (+ 10 µl excess) |
| FIREPol DNA Polymerase | 0.85 µl |
| MgCl2 (25 mM) | 10.2 µl |
| Reaction Buffer B (10x) | 17 µl |
| dNTPs (10 mM) | 3.4 µl |
| Forward Primer (10 µM) | 3.4 µl |
| Reverse Primer (10 µM) | 3.4 µl |
| Template DNA | 1 µl per 20 µl reaction |
| Nuclease-free water | 123.25 µl |
Thermocycling Conditions:
| Temperature |
Time |
| 98°C | 3-5 minutes |
| 95°C 50-72°C 72°C |
30-60 seconds 30-60 seconds 1 minute per kb |
| 72°C | 5-10 minutes |
New England Biolabs Taq DNA Polymerase
Composition:
| Component | 8 x 20 µl Reaction (+ 10 µl excess) |
| Taq Reaction Buffer (10x) | 17 µl |
| dNTPs (10 mM) | 3.4 µl |
| Forward Primer (10 µM) | 3.4 µl |
| Reverse Primer (10 µM) | 3.4 µl |
| Template DNA | 1 µl per 20 µl reaction |
| Taq DNA Polymerase | 0.85 µl |
| Nuclease-free water | 133.45 µl |
Thermocycling Conditions:
| Temperature |
Time |
| 95°C | 5 minutes |
| 95°C 45-68°C 68°C |
30 seconds 20 seconds 1 minute per kb |
| 72°C | 5 minutes |
The appropriate annealing temperature was calculated from NEB's Tm Calculator
Site-Directed Mutagenesis (QuickChange)
| Component | 50 µl Reaction |
| Kapa Hifi Hotstart Master Mix (2x) | 25 µl |
| Forward Primer (10 µM) | 2.5 µl |
| Reverse Primer (10 µM) | 2.5 µl |
| Template DNA | variable |
| Nuclease-free water | up to 50 µl |
Thermocycling Conditions:
| Temperature |
Time |
| 95°C | 3 minutes |
| 98°C 65°C 72°C |
20 seconds 15 seconds 15-60 seconds per kb |
| 72°C | 1 minute per kb |
The resulting PCR product has to be purified (e.x. Agencourt AMPure XP) and digested with DpnI (NEB) for 4 hours and gel-purified. In case Phusion polymerase is used, DpnI can directly be added to the PCR. The product can then immediately be used for transformation. In order to obtain high base exchange efficiency, the template need to be removed from the reaction thoroughly.
Primers were designed according to the guidlines of The Richard Lab 1
Isothermal "Gibson" Assembly
Recipe for Ready-to-Use Isothermal Assembly Mixes
5x Isothermal Reaction Buffer (6ml)
- 3 ml of 1 M Tris-HCl pH 7.5
- 150 µl of 2 M MgCl2
- 60 µl of 100 mM dGTP
- 60 µl of 100 mM dATP
- 60 µl of 100 mM dTTP
- 60 µl of 100 mM dCTP
- 300 µl of 1 M DTT
- 1.5 g PEG-8000
- 300 µl of 100 mM NAD
This buffer can be aliquoted and stored at -20 °C.
Isothermal Assembly Master Mix
- 320 µl 5x isothermal reaction buffer
- 0.64 µl of 10 U/µl T5 exonuclease
- 20 µl of 2 U/µl Phusion DNA polymerase
- 160 µl of 40 U/µl Taq DNA ligase
- Fill up with water to a final volume of 1.2 ml
The master mix is devided into aliquots of 15 µl and stored at -20 °C.
Protocol for Isothermal Assembly
- 15 µl aliquot of master mix
- 0.02-0.5 pmol DNA in total for 2-3 fragments
- or
- 0.2-1 pmol DNA in total for 4-6 fragments
- Fill up with water to 20 µl
- 2-3 times more insert than backbone (molar ratio)
- 5 times more insert for fragments < 200 bp (molar ratio)
The assembled mix is then incubated for 60 minutes at 50 °C. It can be directly transformed with chemically competent cell (volume of assembly reaction not exceeding 10% of the volume of the competent cells). Otherwise, the reaction mix is purified and desalted (e.x. Agencourt AMPure XP) and a fraction of it transformed with electrocompetent cells.
Preparation of Competent Cells
Preparation of Chemically Competent Cells
- Inoculate 100 ml of prewarmed LB medium with 1 ml overnight culture and grow the bacteria to an OD600 of 0.5.
- Cool the culture on ice, transfer the cells into cetrifugation tubes and harvest them by centrifugation for 5 min (4000xg, 4°C)
- Carfully discard supernatant, keep cells always on ice.
- Resuspend cells in 30 ml cold TFB1 and incubate on ice for 90 minutes.
- Centrifuge for 5 min (4000xg, 4°C)
- Carfully discard supernatant, keep cells always on ice.
- Resuspend the cells in 4 ml ice-cold TFB2 buffer.
- Prepare aliquots of 100 µl in pre-cooled, sterile microcentrifuge tubes and freeze in liquid nitrogen. Store the competent cells at -80° C
Transformation Protocol for Chemically Competent Cells
- Thaw the competent cells on ice
- Use 50 ul of the competent cells for one transformation, do not add more than 5 ul of DNA to the cells (10% of the volume of the competent cells)
- Incubate them for 20 min on ice
- Incubate them for 90 s at 42° C and add afterwards 500 µl of SOC
- Let them regenerate for 1 h at 37° C with shaking
- Plate a part of the culture according to your expectations on LB-agar plates with the approbriate antibiotic.
Preparation of Electrocompetent Cells
- Inoculate 600 ml of prewarmed LB medium with 6 ml overnight culture and grow the bacteria to an OD600 of 0.4.
- Cool the culture on ice fpr 30 min, transfer 300 ml of the culture into 50 ml tubes and centrifuge them for 10 min (3000xg, 4°C). Discard supernatant and add the rest of the culture. Again discard supernatant.
- Carfully resuspend cells in ice-cold, autoclaved and deionized water and fill up to 50 ml
- Centrifuge again for 10 min (3000xg, 4°C) and repeat wash step from above
- Carfully resuspend cells in ice-cold 10% glycerol (working always on ice)
- Centrifuge for 10 min (3000xg, 4°C)
- Discard supernatant
- Resuspend the cells in the remaining glycerol solution.
- Prepare aliquots of 35 µl in pre-cooled, sterile microcentrifuge tubes and freeze in liquid nitrogen. Store the competent cells at -80° C
Transformation Protocol for Electrocompetent Cells
- Thaw the electrocompetent cells on ice. Pre-chill also the electroporation cuvette.
- Add DNA to the cells. Attention: the DNA should contain as little ions as possible. Purify or dilute reactions containing salt.
- Transfer the bacteria/DNA mix into a pre-chilled electroporation cuvette and electroporate them.
- Add IMMEDIATELY 500 µl of SOC and transfer them back into the microcentrifuge tube.
- Let them regenerate for 1 h at 37° C with sufficient shaking.
- Plate a part of the transformation mix according to your expectations on LB-agar plates with the approbriate antibiotic.
Buffer and Medium
TFB1
| Component | Concentration | Amount per 100 ml |
| RbCl | 100 mM | 1.21 g |
| MnCl2 · 4 H2O | 50 mM | 0.99 g |
| Potassium acetate · 4 H2O | 30 mM | 0.29 g |
| CaCl2 · 2 H2O | 10 mM | 0.147 g |
| Glycerol | 15 % | 11.9 g |
Adjust pH to 5.5 and sterilize by filtration
References:
- [1] Tom Richard, Department of Agricultural and Biological Engineering, Penn State University.
- [1] Scaldaferri, F., et al. "Gut microbiota molecular spectrum in healthy controls, diverticular disease, IBS and IBD patients: Time for microbial marker of gastrointestinal disorders?." Journal of Crohns & Colitis. Vol. 9. Oxford Univ Press, 2015.
