Theoretical investigation of the coupling between hydrogen atoms transfer and stacking interaction in guanine–cytosine dimers

Abstract

The effect of the stacking interaction on some properties of the guanine–cytosine (G–C) base pair has been studied. In particular, the strength of the hydrogen bonds, the mechanism of hydrogen transfer and the charge redistribution intra- and inter-base pair have been analyzed in the three canonical dimers. The inclusion of both the stacking interaction and of the hydrogen bond interaction between the bases allows us to study both the local and the long-range phenomena of DNA. The comparison of these results with those of the G–C monomeric system supports the idea that the variations of these properties depend from the exact dimer considered and are different for one or another hydrogen bond. Also the different mechanisms of two hydrogen transfer (step to step and concerted) can be modified by the stacking interaction between the base pairs. The comparison with previous data shows that some generalizations found in literature must be analyzed in detail.