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Relationship between stacking and hydrogen bonding in watson-crick base pairs

The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of uracil and thymine in RNA and DNA, and of cytosine and 5-methylcytosine in DNA have been studied through complete DFT optimization of different structures of dimers, using five different functionals. The results clearly show that stacking and hydrogen bonding are deeply connected. In particular, in guanine-cytosine and in guanine-5methylcytosine, our results permit to show that stacking leads to an increase of the O6...H-N4 hydrogen bond length and to a simultaneous decrease of the N2- H...O2 one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results permit to suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. The different behavior of RNA and DNA when replacing uracil by thymine can be interpreted through the formation of a stabilizing CH/π interaction between the methyl group of thymine and the five-member ring of adenine. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA ​
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