Monte Carlo simulation of DNA fragment hydration in the presence of alkaline cations using novel atom-atom potential functions.

The set of atom-atom potential functions specially adjusted to simulation of nucleic acid fragment hydration (Poltev, Grokhlina & Malenkov, J. Biomol. Struct. Dyn. 2, 413, 1984) is extended by including alkaline cation interactions. The choice of new potential functions was realized using experimental data on crystal hydrates of nucleotides and related compounds as well as thermodynamic data on ion solutions. The extended set of potential functions allows to reproduce many features of interactions between alkaline cations and nucleic acid fragments in water solutions. The sites of preferential cation localization near bases and phosphate groups were obtained and examined. The potential functions reproduce the dissociation tendency of cation-phosphate group and cation-base complexes in aqueous medium. Pathways of cation dissociations from nucleic acid components have been studied, and metastable water-bridged positions of cations near bases and phosphate group have been revealed.