Problems with PCR following bisulfite treatment - (Aug/30/2006 )

Naniko,

try using a restriction restriction enzyme before you convert your DNA. It should improve the specificity of your PCR.

Bram

Further to Bram's comments,

you could also shear your DNA by passing it through a 19G syringe needle or sonicating it. I tend to find this easier if you are intending to analyse many loci within the genome for methylation.

Good luck

Nick