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

Journal of Biomolecular Structure & Dynamics
V I Danilov, I S Tolokh

Abstract

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. Simulations 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 the 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 out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.

References

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Citations

Mar 1, 2012·The Journal of Physical Chemistry. B·Salem JafilanJan Florián
Dec 17, 1997·Journal of Biomolecular Structure & Dynamics·V I DanilovJ L Alderfer
Feb 2, 2006·Nucleic Acids Research·Peter YakovchukMaxim D Frank-Kamenetskii
Sep 3, 2004·Journal of Molecular Biology·Ekaterina ProtozanovaMaxim D Frank-Kamenetskii
Apr 6, 2016·The Journal of Physical Chemistry. B·Chi H Mak
Aug 1, 1989·Journal of Biomolecular Structure & Dynamics·A V TeplukhinG G Malenkov
Jun 1, 1992·Journal of Biomolecular Structure & Dynamics·V I DanilovP Lautenschlager
Sep 13, 2012·The Journal of Physical Chemistry. B·Akshaya ShankarJeetain Mittal

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