Abstract

The results of a Monte Carlo study of the hydration of two stacked thymine dimers are presented. In water the stack in which the methyl groups are separated from each other is energetically less favourable than that in which these groups are close to each other. This difference is already found when considering the nearest water molecules only. The nature of approaching of thymine methyl groups in the case of base stacking is discussed. Monte Carlo study Nucleotide base stacking Stacked associate Water structure Hydrophobic group

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