methylation primers - problems with primers (Aug/19/2004 )
I have just statrted a project to look at methylation of a candidate gene. I have used the methprimer program to design 12 M and U primers. However, none of the primers seems to work on my genomic DNA. The DNA is quite pure (OD ratio 1.7), and intact and other primers amplify OK. I have tried different taq systems and temp/Mg.
Is this normal for so many primers not to work?
May I ask if or not you have modified your DNA with sodium bisulfite because you said "work on your genomic DNA"?
You said none of the 12 primer sets do not work on your DNA. Although sometimes primers may fail, other factors such as DNA template and PCR conditions may also contribute to PCR failure.