PrbbBB:colony pcr v1
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Overview
A colony PCR protocol for screening up to 8 clones each for up to 12 different assembly reactions in parallel. Colonies are picked into a 96-well plate with water. The PCR reactions are set up in another 96 well plate and the template DNA is copied over with a multi-channel pipette. During the colony picking, a copy of each clone is put into a deepwell plate with liquid medium which is later used to inoculate over-night cultures for miniprep and cell stock.
Materials
- two sterile 96-well PCR plates
- two sterile 96-deepwell plates (preferably 2 ml volume/square well)
- adhesive tape for plate sealing
- gas-transmissible adhesive tape for deepwell plate sealing
- 12-channel 1-10µl pipette
- multi-dispensing pipette (2 µl minimum) + sterile tips
- AmpliTaq DNA Polymerase 5 U/µl (Roche)
- AmpliTaq Buffer 10 x
- dNTP mix 10mM each nucleotide
- sterile ddH2O
- primers:
- liquid LB or 2xTY medium with appropriate antibiotic (Chloramphenicol, Kanamycin, or Tetracycline depending on target plasmid)
Procedure
I PCR reaction
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- prepare 96-well "Lysis" (PCR) plate:
- sterilize plate and pipette tips
- multi-dispense 50 µl H2O into each well
- prepare 96-deepwell "Copy" plate:
- sterilize plate and pipette tips
- multi-dispense 100-200 µl sterile LB + appropriate antibiotic into each well
- colony picking:
- pick colonies of one assembly with sterile 10 µl tips into...
- ... the wells of one column (like A1-H1 or A2-H2) on the Lysis plate
- pipette up and down
- eject each tip into the same position on the "Copy" deepwell plate
- proceed to next column for next assembly
- seal the "Copy" deepwell plate, shake vigorously for 1 min and let it stand at room temperature
- prepare PCR plate:
- multi-dispense 10 µl PCR mastermix into each well
- copy 1 µl per well from lysis plate to PCR plate (using multi-channel pipette)
- seal PCR plate with adhesive tape
- run PCR program
II Agarose Gel
- prepare a large 0.7 - 1.5 % Agarose gel (depending on fragment size)
- multi-dispense 2 µl loading buffer into each well of the PCR plate
- load gel with multi-channel pipette
- run, analyze, enjoy!
III Rescue positive clones
- inoculate positive clones from "Copy" plate for miniprep (and cell-stock) into a fresh sterile deepwell plate (preferably using a rich medium like 2xTY or 2xLB)
- seal plate with gas-transmissible adhesive tape
- grow over night with vigorous shaking (700 r.p.m.) at 37°C
Notes
Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!
raik: no comment
References
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