Rapid Partial Digestion of DNA Fragments by PCR

In this report, a method is described for generation of a partial digestion pattern for any fragment that can be amplified by PCR. Using a mixture of 5-methyl-dCTP (5mC) and dCTP in PCR protects some of the restriction sites from digestion with 5-methyl-cytosine-sensitive restriction enzymes. After PCR amplification with 5mC, restriction digestion of the modified PCR products with a 5-methyl-cytosine-sensitive enzyme rapidly produces an array of fragments similar to a partial digestion of unmethylated DNA.

Promega Notes 73, 12.