Team:Toulouse/Notebook/Protocols

Day 0

- Make an Escherichia coli cell culture in LB medium overnight

Day 1

- Freeze 0.1 M CaCl2 and 4 Falcon tubes of 50mL at 4°C
- Streak 2% culture in LB to get an OD of 0.3 to 0.4 (it takes approximately 1h30)
- Centrifuge 10 minutes at 4500 RPM
- Remove the supernatant
- Resuspend the pellet in 7.5 mL of 0.1 M frozen CaCl2
 Freeze the glycerol
 Prepare 20 Eppendorfs tubes and put them in ice
- Centrifuge 10 minutes at 4 500 RPM
- Resuspend the pellet in 500µL of 0.1 M CaCl2
- Add glycerol for a final concentration of 15%
- Keep the tubes at -80°C

- Let the LB agar medium plates dry in a sterile area
- Thaw out the competent cell aliquotes for about 10 to 20 minutes
- Add 20 to 100 ng of plasmid or 3µL of kit plate DNA

NB: for kit plate, resuspend the well in 10µL of sterile water - Put the tubes 20minutes in the ice
- Put the tubes 2 minutes at 42°C in the water bath
- Put the tubes back in ice immediately to create the thermic shock
- Add 1mL of LB medium
- Put the tube 2 hours in the 37°C water bath (1hour if it concerns an ampicillin resistant strain) to allow the phenotypic expression
- Centrifuge for 1 minute at 13 000 RPM
- Remove the supernatant
- Resuspend in 250 µL of LB medium
- Streak the final mix on LB agar selective medium: 200 µL on one plate, 50µL on the second plate.

Day 0

- Resuspend 4 to 12 colonies from the plate and name each colony taken on the tubes and on the plate (A, B, C…)
- Resuspend one colony/culture tube in 5mL of LB medium with antibiotic
- Leave the culture shakes overnight at 37°C

Day 1

- Use the QIAprep spin Miniprep Kit for each culture tube. The last step consisting in the elution of the DNA is made with a hot elution buffer or water at 55°C.
- Keep the tubes at -20°C

NB: It is possible to purify the plasmid with an alcaline lysis without any purification column. For 2 mL of culture, 200µL of buffer 1 is added to resuspend the pellet, 400µL of buffer 2 to allow the lysis of the cells and the denaturation of the protein and 300µL of buffer 3 to precipitate the DNA and the proteins. The solution is then centrifuged 10 minutes at 13 000 RPM. 60µL of isopropanol is added to the supernatant and the solution is centrifuged again. The pellet is then resuspended in 100µL of pH 7.4 TE buffer. A part of the contamination by the RNA can avoid by the addition of pH 7.4 TE buffer + 0.2 µL of RNAse.
Buffer 1: Tris 10 mM pH 8 + EDTA 1mM
Buffer 2: NaOH 2mM + SDS 1%
Bufer 3: A COOK 3M + A COOH 15%

After taking the competent cells, transforming the Biobricks and making the miniprep, make the digestion mix.

First Step BOTH PARTS HAVE THE SAME ANTIBIOTIC RESISTANCE
1) Digestion mix
For the vector :
- 5 µL of miniprep plasmid
- 2 µL of each restriction enzymes
- 2 µL of Green Buffer
- 9 µL of Milli-Q water

For the insert :
- 10 µL of miniprep plasmid
- 2 µL of each restriction enzymes
- 2 µL of Green Buffer
- 4 µL of Milli-Q water
 Incubate 15 minutes at 37°C

2) Gel extraction
- Prepare a 1% of 2% electrophoresis agarose gel with 0.5x TAE buffer
- Put 20µL of sample + 6µL of marker (1kb for 1% gel and 100pb for 2%) into the well
- Migration for 30 min at 100V or 1hour at 50V.
- The revelation is made in BET (10minutes) and then 5minutes in water.
- The gel extraction is realized thanks to the THERMO SCIENTIFIC GeneJET Gel Extraction and DNA Clean Up Microkit.

3) Inactivation of the enzymes for the vector
There are two ways to inactivate the enzymes :
- Use of DNA Clean up kit for the DNA fragment above 200 pb
- Heat inactivation at 95°C for 10 minutes.

THE TWO PARTS HAVE A DIFFERENT ANTIBIOTIC RESISTANCE
1) Digestion mix
For each part, add :
- 5 µL of miniprep plasmid
- 1 µL of each restriction enzymes
- 2 µL of Green Buffer
- 9 µL of Milli-Q water
 Incubate 15 minutes at 37°C

2) Inactivation of the enzymes for the vector
There are two ways to inactivate the enzymes :
- Use of DNA Clean up kit for the DNA fragment above 200 pb
- Heat inactivation at 95°C for 10 minutes.

Second step

Ligation
- Mix 10 µL of insert + 4µL of vector + 2µL of 10x T4 buffer + 0.5µL of T4 ligase + 3.5µL of Milli-Q water
A control without insert must be made
- Incubate the ligation mix 15 minutes at room temperature (22°C) and keep the tubes in ice or at -20°C to prepare the transformation

2) Transformation
- Take 5µL of the ligation mix for 50µL of competent cells and use the Toulouse iGEM Team 2014 transformation protocol.
- Plate the solution on selective medium overnight at 37°C.