I have to amplify an exon which is 84% rich in GC contents.
I have tried it with formamide, DMSO and et-glycol along with increased Magnasium concenteration but always got dimers and smear. Please tell me if anybody knows.....
if there is no pcr product: lower the annealing temperature to 2 deg. celcius below the lowest primer annealing temperature. as a rule of thumb AT adds 2 degree and GC 4 deg t o the temp of the sequence. then add 1.5M betaine and 5%betaine and 5% DMSO to the pcr amplification
if no effect is seen increase the betaine concentration to 2.5M add 10%DMSO and double the amount of taq polymerase. the annealing temperature can be further decreased.
if you are seeing many unspecific pcr product: increase the annealing tempand add 1.5M betaine and 5% DMSO. if no effect is seen increase the betaine and DMSO concentration...