Colony PCR - 5’ RACE Colonies

Two light blue colonies (there were no white colonies) were picked, restreaked on a new Kan50 plate (no X-gal) and PCR’d.

Master Mix:

2x Apex Red Master Mix - 37.5uL

10uM M13 Forward - 3uL

10uM M13 Reverse - 3uL

H2O - 46.5

Added 25uL to each PCR tube.

Cycling Params:

  • 95C - 10mins

40 cycles of:

  • 95C - 30s

  • 55C - 30s

  • 72C - 2mins

1 cycle:

  • 72C - 10mins


The two pale blue colonies do NOT contain our desired insert. Despite the presence of a larger, faint band (~950bp), that is far smaller than our 5’RACE insert size (~1500bp). And, clearly, the primary amplicon produced is ~250bp, which is the expected size for empty vector… Ladder is Hyperladder I (Bioline).

Will need to re-do ligation reaction and will do so at the recommended volumes in the TOP TA (Invitrogen) protocol.