start a methylation study - (Jul/06/2006 )
PCR on bisulfite modified DNA is very tricky. First make sure your template DNA is good. You can try your DNA using some primers known to work. Hot-start your PCR is necessary and using some hotstart taq such JumpStart Red Taq from Sigma helps a lot.
As I said above, have you tried hotstarting your PCR? For me I cannot do without using JumpStart Taq from sigma.