Monte carlo simulations of nucleotide crystal hydrates and their counter-ions

Abstract

A knowledge of structural and energetic aspects of water- and ion-nucleic acid interactions is essential for the understanding of the role of solvent and counterions in stabilising the various helical forms of nucleic acids. In this study, Monte Carlo computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates containing the ions sodium, ammonium and calcium. Appropriate parameters to describe the interaction potentials of the ions are added to those previously developed for water and nucleic acid atoms. A comparison is made between the predicted and experimental results and it is concluded that the potential functions used lead to simulated solvent structure in reasonable agreement with experimental data, at least in the cases of sodium and calcium. It is now feasible to use these functions in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.