Eur. Phys. J. D 20, 331-337 (2002)
https://doi.org/10.1140/epjd/e2002-00145-8

Hydration of nucleic acid components in dependence on nucleotide composition and relative humidity: a Monte Carlo simulation

Institute for Radiophysics and Electronics National Academy of Sciences of Ukraine, 12, Acad. Proscura str., 61085 Kharkov, Ukraine

Corresponding author: ^a shestop@ire.kharkov.ua

Received: 25 December 2001
Revised: 22 March 2002
Published online: 13 September 2002

Abstract

What role does the nucleotide composition play in the process of formation of hydrated environment of nucleic acids? Can one estimate the hydration of nucleic acids on the level of their components? In order to resolve these questions we have completed an extensive computer simulation of the hydration of nucleic acids components – deoxynucleoside monophosphates distinguished by nucleotide composition. The energetic characteristics of systems containing deoxynucleoside monophosphates and water clusters of various dimensions are received. Our results demonstrate that deoxynucleoside monophosphates containing guanine and/or cytosine residues hydrated more strongly because of formation of more hydrogen bonds with water molecules in small water clusters, i.e. at low values of relative humidity. With increasing of number of water molecules in a water cluster the energetic preference of deoxynucleoside monophosphates containing guanine and/or cytosine residues decreases, and for water clusters corresponding to a state of a dilute aqueous solution the hydration of all types of deoxynucleoside monophosphates does not differ in a great degree. Deoxynucleoside monophosphates containing guanine and/or cytosine residues cause the greater destruction of the water structure compensated by the greater interaction with the nearest water molecules for all levels of relative humidity.