Computer study of the role of hydration in the accuracy of nucleic acid biosynthesis

To approach the quantitative understanding of hydration contribution to the accuracy of nucleic acid biosynthesis, a computer simulation has been perf ormed to study the hydration characteristics for individual atoms of DNA ba ses and various AT and GC base pairs. Both Watson-Crick pairs and other typ es of pairs with two hydrogen bonds are considered. Monte Carlo simulation of individual bases demonstrates good concord of calculated hydration energ ies with experimentally determined hydration enthalpies. Computations for b ase pairs allow us to account for the experimental fact that formation of s uch pairs in water solution is disadvantageous. The correlations between hy dration indices of hydrophilic atoms and their accessible volumes to hydrog en bonding with water were followed. These correlations will allow us to de velop a semi-quantitative method of rapid estimation of hydration changes u nder DNA conformational transitions and binding to other molecules. The mai n hydration characteristics of mispairs important for their formation in DN A biosynthesis are discussed. (C) 1999 Elsevier Science B.V. All rights res erved.