DNA methyltransferases. Three DNMTs (DNMT1, DNMT3a, and DNMT3b) function to
mediate the methyl transfer from S-adenosyl methionine (SAM) to the 5 position of cytosine (9).
A fourth (DNMT3l) is catalytically inactive yet is required for DNA methylation–dependent ge-
nomic imprinting through its recruitment of DNMT3a and b (16, 17). All three active DNMTs
are capable of de novo methylation, but the structurally distinct DNMT1 is predominately re-
sponsible for maintenance methylation (18). The mechanism by which DNMT1 recognizes
hemimethylation and facilitates the methyl transfer was recently solved through the clever ap-
plication of a synthetic 5-fluorocytosine to trap the otherwise unstable tetrahedral intermediate
(Figure 2) (19). DNMT1 flips out the target cytosine, activates the aromatic system of the base with
electron-donating contacts, and delivers the electrophilic methyl group. The fidelity of DNMT1
for hemimethylated DNA is mediated by a hydrophobic pocket that detects the contiguous mCpG
base pair through pi-stacking and hydrogen bond contacts as well as a pair of hydrophobic Leu
residues. This small, hydrophobic pocket is ideal for accepting a methyl group and may explain