8th Liquid Matter Conference September 6-10, 2011 Wien, Austria ...

P4.46Fri 911:10-14:00Monte Carlo simulation of the fine structures of liquidwater around DNA base associatesValeri Poltev, 1 Victor Danilov, 2 Vladimir Dailidonis, 3 Alexandra Deriabina, 1 andEduardo Gonzalez 11 Autonomous University of Puebla, Av. San Claudio y 18 Sur, Ciudad Universitaria,72570, Puebla, Mexico2 Institute of Molecular Biology and Genetics, Kiev, Ukraine3 Bogolyubov Institute for Theoretical Physics, Kiev, UkraineNucleic acid bases in water-deficient media can form hydrogen-bonded (H-bonded) pairs (includingWatson-Crick A:T, A:U, and G:C pairs) while in water solutions stacking associates occurs.Both base arrangements are important for DNA structure and functions. To understand the detailsof water influence on the base interactions we analyze water shells of the base associates. We haveperformed Monte Carlo (MC) simulations (via extended cluster approach, canonic NVT ensemble,298K) of the systems containing two bases and 800 water molecules. Starting MC sampling fromWatson-Crick pairs, we observed gradual base displacements resulted after 2 millions of completeMC steps in nearly parallel base stacking with more favorable mean energy (in accord with[1]). The weakening of base-base interactions is followed by more pronounced enhancement ofthe water-base interactions. The changes of mutual base positions during MC sampling originatefrom water rearrangement around the bases. We characterize the first water shells of a molecularassociate by mean number of water molecules H-bonded to each of hydrophilic atoms and bysingle-water, two-water, and three-water bridges connecting these atoms. The breakage of basebaseH-bonds during MC sampling is followed by the formation of greater number of base-waterH-bonds. The single-water bridges correspond to H-bond formations by the same water moleculewith two atoms of bases. No such bridges have been detected between the bases in the H-bondedpairs, while various such bridges exist for stacked complexes with the total mean probability up to1.1 (for G-C stacks). The probability of the two-water bridges (i.e. the formation of H bond betweentwo water molecules H-bonded to two bases) for stacks is many times greater as comparedto H-bonded pairs. The bridges contribute to the system state advantage and to the stability of thespecific base arrangements. [1] V. I. Danilov et al. , J. Biomol. Struct. Dyn. 28, 1140 (2011)46