MONTE-CARLO MODELING OF DNA HYDRATION

Monte Carlo simulation of a system consisting of six complementary base pairs (in A- and B-conformations) and 180 water molecules was performed. The hydration shell structures in the major and minor grooves have been determined for stacks of repeating AU and GC pairs and for alternating (AU, UA) and (GC, CG) pairs. Probabilities of the formation of water bridges consisting of one, two, or three water molecules have been estimated. A water molecule forms H-bonds with two hydrophilic centers of bases most frequently if the distance (N...N, N...O, or O...O) between them is close to 4.3 angstrom. It was found that the hydration shell structure depends on the stack conformation and base sequence, even though for the global hydration characteristics (average energy, the number of water-base and water-water H-bonds) this dependence is weak. It was shown that during the B --> A transition the number of water molecules forming two or more H-bonds with bases increases. This result is discussed in connection with the concept of "hydration enconomy" during the B --> A transition.