By using a purified fraction of mouse DNA methyltransferase we have sh
own, by gel-retardation analysis, that the enzyme forms a low-affinity
complex preferentially with hemimethylated DNA; the complexes formed
with unmethylated or with fully methylated DNA are of even lower affin
ity, and only very weak interaction occurs with DNA lacking CG dinucle
otides. Interaction is inhibited by N-ethylmaleimide. Methyl transfer
from S-adenosylmethionine is associated with the release of the fully
methylated product from the complex. Complexes formed with the intact
enzyme are extremely large, but limited trypsin treatment allows a maj
or complex to enter the gel. DNA binding is not inhibited by this limi
ted proteolysis of the native enzyme.