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Journal
2011 | 9 | 4 | 720-727
Article title

A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach

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EN
Abstracts
EN
The adenine-thymine (AT), adenine-uracil (AU) and guanine-cytosine (GC) base associates in clusters containing 400 water molecules were studied using a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. Starting from the hydrogen-bonded Watson-Crick geometries, all three base pairs are transformed into more favorable stacked configurations during the simulation. The obtained results show, for the first time, the transition from planar base pairs to stacked base associates in the Monte Carlo framework. Analysis of the interaction energies shows that, in the water cluster, the stacked dimers are energetically preferable compared to the corresponding Watson-Crick base pairs. This is due to the larger base-water interaction in the stacked structures. The water-water interaction is one of the main factors promoting the formation of stacked dimers, and the obtained data confirm the crucial role of the water-water interactions in base stacking.
Publisher

Journal
Year
Volume
9
Issue
4
Pages
720-727
Physical description
Dates
published
1 - 8 - 2011
online
4 - 6 - 2011
Contributors
  • Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv-680, Ukraine, 03680, vid@ipnet.kiev.ua
  • Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, Kyiv-680, Ukraine, 03680
author
  • EaStCHEM School of Chemistry, University of St Andrews, North Haugh, KY16 9ST, Fife, Scotland, UK
  • EaStCHEM School of Chemistry, University of St Andrews, North Haugh, KY16 9ST, Fife, Scotland, UK
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Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.-psjd-doi-10_2478_s11532-011-0056-0
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