The effect of the structure of recognition site GATC in a substrate du
plex on its complexation with DNA-[N6-adenine]-methyltransferase of T4
phage (T4 MTase) was studied. The pel retardation method was employed
to reveal the complexes. As compared with the native duplexes, the ma
jority of defective duplexes had the same or even better affinity to T
4 MTase; however, no correlation was found between the complex stabili
ty and effectiveness of the duplexes as substrates for methylation. Ap
parently, formation of a stable enzyme-DNA complex does not require co
ntinuity of the two strands of the duplex and perfect base pairing in
the recognition site. A half of the constituents of the recognition si
te suffices for stable complexes with T4 MTase to form. Deoxyguanosine
residues in both strands of the modified GATC are shown to be indispe
nsable for complex formation.