5’/3′ RACE – C.gigas COX2/PGS2 RACE PCR

Additional RACE using gene specific primers (SR IDs: 1347 & 1348) for C.gigas COX2/PGS2 according to Clontech’s SMARTer cDNA RACE Kit protocol. 3’/5′ RACE cDNA libraries are from 20080619. Master mix calcs and set up is here. Cycling params followed “Program 2″ of the Clontech protocol and are as follows:

25 cycles:

  • 94°C 30 sec
  • 68°C 30 sec
  • 72°C 3 min

Reactions were run with both primers on both libraries, just to ensure that in case there was any confusion in primer design. When finished, I will remove 2uL of the PCR reaction for use in a nested PCR reaction. Will run a gel with both sets of products, once the nested PCR is completed.


Gel Layout:

Lane 1 – Hyperladder 1

Lanes 2-6 = 5′ RACE Library

Lane 2 – GSP1 (5′ RACE primer)

Lane 3 – GSP2 (3′ RACE primer)

Lane 4 – Neg. Control (no RACE primers)

Lane 5 – Neg. Control (GSP1, no Universal primer)

Lane 6 – Neg. Control (GSP2, no Universal primer)

Lane 7 – Empty

Lanes 8-12 = 3′ RACE Library

Lane 8 – GSP1 (5′ RACE primer)

Lane 9 – GSP2 (3′ RACE primer)

Lane 10 – Neg. Control (no RACE primers)

Lane 11 – Neg. Control (GSP1, no Universal primer)

Lane 12 – Neg. Control (GSP2, no Universal primer)

As has generally been the case, our primary RACE PCRs failed to produce any products. This is why I performed the nested PCR (described above) before viewing the results of this primary PCR.

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