Hydration of nucleic acid bases studied using novel atom-atom potential functions

Journal of Biomolecular Structure & Dynamics
V I PoltevG G Malenkov

Abstract

New simple atom-atom potential functions for simulating behavior of nucleic acids and their fragments in aqueous solutions are suggested. These functions contains terms which are inversely proportional to the first (electrostatics), sixth (or tenth for the atoms, forming hydrogen bonds) and twelfth (repulsion of all the atoms) powers of interatomic distance. For the refinement of the potential function parameters calculations of ice lattice energy, potential energy and configuration of small clusters consisting of water and nucleic acid base molecules as well as Monte Carlo simulation of liquid water were performed. Calculations using new potential functions give rise to more linear hydrogen bonds between water and base molecules than using other potentials. Sites of preferential hydration of five nucleic bases - uracil, thymine, cytosine, guanine and adenine as well as of 6,6,9-trimethyladenine were found. In the most energetically favourable sites water molecular interacts with two adjacent hydrophilic centres of the base. Studies of interaction of the bases with several water molecules showed that water-water interactions play an important role in the arrangement of the nearest to the base water molecules. Hydrophilic centre...Continue Reading

References

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Citations

Feb 1, 1996·Journal of Biomolecular Structure & Dynamics·V I PoltevJ H Miller
Jul 24, 1987·Nucleic Acids Research·A A Lipanov, V P Chuprina
Jun 1, 1995·International Journal of Radiation Biology·A O Colson, M D Sevilla
Jun 7, 2011·The Journal of Chemical Physics·M CogoniD W M Hofmann
Jan 15, 1991·Biochemistry·V P ChuprinaB R Reid
Aug 1, 1989·Journal of Biomolecular Structure & Dynamics·A V TeplukhinG G Malenkov
Feb 16, 2007·Physical Chemistry Chemical Physics : PCCP·Martin Kabelác, Pavel Hobza
Oct 1, 1987·Journal of Biomolecular Structure & Dynamics·V I Poltev, S V Steinberg
Feb 1, 1986·Journal of Biomolecular Structure & Dynamics·V I Poltev, N V Shulyupina

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