Nature of the stacking of nucleic acid bases in water: a Monte Carlo study

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simultaions have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting...

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Bibliographic Details
Published in:Journal of molecular structure. Theochem 1985-01, Vol.24 (1), p.109-119
Main Authors: Danilov, Victor I., Tolokh, Igor S.
Format: Article
Language:English
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Summary:The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simultaions have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water—water interaction during the transition from monomers to dimer. It has been found that stacked base associates are more favourable than base pairs in water. This is mainly due to the energetically more preferable structure of water around stacks.
ISSN:0166-1280
1872-7999
DOI:10.1016/0166-1280(85)85187-3