I am trying to amplify lemon shark microsatellite loci using the PCR but
haven't had much luck. The DNA I am using was extracted from fin clips
(stored in ethanol), by standard phenol-chloform extractions. The
primers being used are specific for lemon sharks (were developed from a
lemon shark gDNA library).
We are getting plenty of DNA from the extractions, so I don't think lack
of DNA is a problem.
I have tried many different PCR "recipes" (using DMSO, spermidine,
varying molarity of dNTPs, varying volumes of PCR reaction, etc.) with
no luck. Does anyone have any suggestions? Could something be
co-amplifying with the DNA that is inhibiting the PCR?
Thank you in advance,