A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach |
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| Authors: | Victor I. Danilov Vladimir V. Dailidonis Tanja van Mourik Herbert A. Früchtl |
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| Affiliation: | (1) Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, 14b Metrologicheskaya Street, Kyiv-143, 03143, Ukraine;(2) Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine;(3) School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, UK; |
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| Abstract: | 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. |
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