Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs

The effects of the addition of one (hemimethylation) or two (methylation) methyl groups on the 10 different couples of base pairs of DNA (three dimers of A-T, three of C-G, and four mixed A-T and C-G complexes) has been studied. Changes in the main static properties (energy, structure, atomic charges) and dynamics (movement of hydrogen atoms from one base to the other) have been considered and analyzed. The results of this study support the idea that the quantitative effects of the methylation of these complexes depend on the specific system under consideration and on the H-bridge studied. In any case, some general behavior can be highlighted. In particular, the relationship between the transfer of hydrogen atoms between the bases (with the possible generation of mutation points) and the methylation can be schematized in the two most important methylated bases: adenine and cytosine. A different behavior has been found in these two cases, and we suggest that this could be related to the different amounts of these methylated systems in prokaryotes and eukaryotes. In particular, this different behavior could explain why adenine methylation is present mainly in the bacteria and cytosine methylation is present in more complex organisms.