Restriction Endonuclease Enzymes to Study DNA Methylation and Epigenetic Changes
A few restriction enzymes are known to differential cleave methylated versus non-methylated DNA. These enzymes can be used to help you. When selecting these restriction enzymes, it is crucial to that they leave staggered ends, have a cut site that is different from the recognition site, and cannot be affected through potentially methylated target sequences.
C. Laird et al. Hairpin-bisulfite PCR: Assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc Nat Acad Sci (2004) 101: 204-209.