Team:Glasgow/Notebook/Protocols

Protocols

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This page shows our protocols for various lab procedures.

Creating Chemically Competent Cells

1. Pipette 400μl of culture into 20ml of fresh broth
2. Incubate the cultures in shaking 37⁰C water bath for 90 min
3. Calcium chloride and centrifuge tubes must be cooled on ice.
4. Pour culture into centrifuge tubes, return to ice.
5. Centrifuge in a cold rotor for 2 min at 7000rpm (6000 G)
6. Pour out the supernatant, being careful about the pellet
7. Add 10μl of calcium chloride, immediately return to ice and leave for 1 hour (or longer)
8. Repeat the centrifuge step, pour out supernatant
9. Store on ice, add 1ml of calcium chloride. Resuspend and return to ice.

Transformation of Competent Cells

1. Add 100μl of competent cells to cooled Eppendorfs
2. Add 1μl of DNA
3. Incubate on ice for 20 min
4. Heat shock at 37⁰C for 5 min
5. Place immediately on ice and leave for 5 min.
6. Add 200μl of L-Broth and incubate at 37⁰C for 90 min. Expression step.
7. Spread 100-200μl on full dried medias. On half plates use 40μl.
8. Incubate plates

DNA Clean-up

1. Transfer supernatant to a mini-column
2. Spin for 1 min on full and pour out flowthrough
3. Add 500μl of PB, spin for 1 min and discard flowthrough
4. Add 800μl of PE, spin for 1 min and discard flowthrough
5. Spin again and discard flowthrough.
6. Add 50μl of EB to the centre of the white disc and stand for 1 min.
7. Move column to a 1.5ml Eppendorf (leaving behind the collection tube) and spin for 1 min.
8. Keep supernatant. DNA is in the liquid.

PCR

50μl reaction volume –

• 10μl 5 x HF Buffer
• 5μl 5mM dNTPs
• 1μl 50mM MgCl2
• 1.5μl DMSO
• 5μl 5μM F primer
• 5μl 5μM R Primer
• 22μl ddH2O
• 1μl (1/100 dilution) template DNA
• 0.5μl polymerase

Programme Settings

1. 98⁰C – 1 min
2. 98⁰C – 20 sec
3. 55⁰C – 30 sec
4. 55⁰C – 30 sec (Back to step 2. x30)
5. 72⁰C – 10 min
6. 4⁰C – Hold

Restriction Digests

1. Add
   a. For a 20μl sample
   1. 2μl 10 x buffer
   2. 4μl DNA sample
   3. 14μl ddH20
   4. 0.5μl restriction enzyme
   b. For a 30μl sample
   1. 3μl 10 x buffer
   2. 10μl DNA sample
   3. 17μl ddH20
   4. 0.75μl restriction enzyme
2. Mix thoroughly
3. Incubate at 37⁰C for at least an hour

Gel Extraction

1. Place gel slice into a microfuge tube
2. Weigh microfuge tube, add 3 volumes of Buffer QG to volume of gel (100μg = ~100μl)
3. Incubate at 50⁰C for 10 min (until gel has dissolved) mix by vortex every 2-3 min in incubation
4. Add 1 gel volume of isopropanol to sample and mix.
5. Apply sample to spin column, centrifuge 1 min and discard flowthrough.
6. Add 500μl Buffer QG and centrifuge for 1 min.
7. Add 750μl Buffer PE, stand for 2-5 min and centrifuge for 1 min.
8. Discard flowthrough and centrifuge again for 1 min.
9. Move spin column to microfuge tube
10. Add 30μl Buffer EB to centre of white disc stand for 1 min and centrifuge for 1 min.
11. Keep supernatant.

Annealing Top and Bottom Strand Oligos

Mix-

• 10μl top strand 100μM
• 10μl bottom strand 100μM
• 80μl ddH2O

To Anneal-

1. Heat in 85⁰C metal heating block for 5 min
2. Then turn off heat block leaving tube in block to cool down slowly (1-2 hours) to ~30⁰C
3. Dilute ‘annealed’ (cold) oligos - 1μl oligo and 99μl ddH2O