The methylase encoded by the dam gene (Dam methylase) transfers a methyl group to the N6 position of the adenine residues in the sequence GATC (1,2). The Dcm methylase, encoded by the dcm gene, methylates the internal cytosine residues in the sequences CCAGG and CCTGG (1,3) at the C5 position. The EcoKI methylase, M.EcoKI, modifies adenine residues in the sequences AAC(N6)GTGC and GCAC(N6)GTT.
Not all DNA isolated from E.coli is methylated to the same extent. While pBR322 DNA is fully modified, only about 50% of Lambda DNA Dam sites are methylated, presumably because the methylase does not have the opportunity to methylate the DNA fully before it is packaged into the phage head.