Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation.

Abstract

A theoretical description of aqueous hydration in the minor groove of a B-form DNA is presented on the basis of a liquid-state Monte Carlo compute simulation on a system consisting of the oligonucleotide duplex d(CGCGAATTCGCG).cntdot.d(GCGCTTAAGCGC) in a canonical B-form together with 1777 water molecules contained in a hexagonal prism cell and treated under periodic boundary conditions. The results are analyzed in terms of solvent density distributions. The calculated minor-groove solvent density shows considerable localization, indictive of discrete solvation sites and providing theoretical evidence for a well-defined ordered water structure. In the AATT sequence, this corresponds to the "spine of hydration" described by H. R. Drew and R. E. Dickerson [(1981) J. Mol. Biol. 151, 535-556] based on the x-ray crystal structure of the dodecamer hydrate. We find, however, that the calculated ordered water structure also extends into the CGCG flanking sequences, supported by the N2 hydrogen bond donors of the guanine residues and indicating that the spine of hydration could thus extend throughout the minor groove of a B-form DNA. This provides a possible explanation of the positive binding entropies observed by L. A. Marky and K. J. Breslauer [(1984) Proc. Natl. Acad. Sci. USA 84, 4359-4363] for both A .cntdot. T and C .cntdot. G sequences on the complexation of netropsin to the minor groove of DNAs. Implications of these results with regard to the thermodynamic stability of DNA in water and the sequence specificity of the minor groove hydration are discussed.