Dynamic impact of methylation at the M. HhaI target site: A solid-state deuterium NMR study

Base methylation plays an important role in numerous biological functions o f DNA, from inhibition of cleavage by endonucleases to inhibition of transc ription factor binding. Studies of nucleic acid structure have shown little differences in unmethylated DNAs and the identical sequence containing met hylated analogues. We have investigated changes in the local dynamics of DN A upon substitution of a methylated cytosine analogue for cytosine using so lid-state deuterium NMR. In particular, we have observed changes in the loc al dynamics at the target site of the M. HhaI restriction system. These stu dies observe changes in the amplitudes of the local backbone dynamics at th e actual target site of the HhaI methyltransferase. This conclusion is anot her indication that the significant result of base methylation is to pertur b the local dynamics, and therefore the local conformational flexibility, o f the DNA helix, inhibiting or restricting the protein's ability to manipul ate the DNA helix in order to perform its chemical alterations.