The nature of base stacking: a Monte Carlo study |
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Authors: | Vladimir V Dailidonis Victor I Danilov Herbert A Fr??chtl Tanja van Mourik |
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Institution: | 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: | To elucidate the physical origin of the preference of nucleic acid bases for stacking over hydrogen bonding in water, Monte Carlo simulations were performed starting from Watson?CCrick structures of the adenine?Cthymine, adenine?Curacil and guanine?Ccytosine base pairs, as well as from the Hoogsteen adenine?Cthymine base pair, in clusters comprising 400 and 800 water molecules. The simulations employed a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. All simulations reached stacked structures, confirming that such structures are preferred over the hydrogen-bonded Watson?CCrick and Hoogsteen base pairs. The Monte Carlo simulations show the complete transition from hydrogen-bonded base pairs to stacked structures in the Monte Carlo framework. Analysis of the average energies shows that the preference of stacked over hydrogen-bonded structures is due to the increased water?Cbase interaction in these structures. This is corroborated by the increased number of water?Cbase hydrogen bonds in the stacked structures. |
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