A two‐dimensional 1 H‐NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence

We report two‐dimensional NOE (NOESY) spectra on the sequence d(GCGATCATGG) d(CCATGATCGC) which contains the unmethylated dam site. As expected the DNA adopts a B‐form conformation but appears to be distorted at the TG step of the second strand. This distorsion, probably bending, is not seen on the opposite strand. When the first strand is methylated on adenine in the GATC or CATG sequence the NOESY spectra indicate little or no change in the conformation. However the single strand‐duplex exchange is slowed down to the slow‐exchange region on a proton NMR time scale. We have assigned the exchangeable imino and cytidine amino resonances of the three duplexes. From the imino linewidths as a function of temperature, we observe that the unmethylated and the hemimethylated Gm 6 ATC duplexes melt normally from the ends. However, this is not so for the hemimethylated Cm 6 ATG duplex which, apart from the terminal base pairs, melts cooperatively and at higher temperature. In spectra recorded in H 2 O a second duplex is observed, for the Gm 6 ATC sequence, which we have not been able to identify. It is however unlikely to be a hairpin structure. Ultravioletmelting curves also indicate the presence of two transitions for this duplex. The effect of methylation upon base‐pair lifetimes has been studied by comparing the above three duplexes. Little effect is observed upon methylation in the GATC sequence but a drastic increase in the lifetimes of all base pairs is observed upon methylation in the CATG sequence.