Solvent accessibilities in the dimeric subunits of RNA and DNA

Abstract

AbstractTo obtain information on the solvent‐solute interactions in the dinucleoside monophosphates pertaining to the dimeric subunits of RNA and DNA, we have computed the accessibility of a water molecule to the oxygen atoms of the subunits following the method of Lee and Richards [J. Mol. Biol. 55, 379–400 (1971)]. The solute molecules (dimeric unit) is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the total surface accessible to the solvent molecule—and hence the solvent accessibility of various atoms of the solute molecule for different conformations—are computed. From the calculated atomic accessibilities, solvation maps in the (ω′,ω) space have been constructed, keeping ψ at 60°, 180°, and −60°. The C(3′)‐endo sugar system in the case of DNA subunit have been considered. The solvation maps describing the solvatability of single and groups of atoms give significant information on the backbone conformational domains that are preferred for solvent interaction, thus adding knowledge to the relative stability of the various possible conformations. The B‐DNA‐type conformer exposes three polar atoms—namely, PO1, O(3′), and O(1′)—to external solvent, whereas the A‐DNA‐ and C‐DNA‐type conformers expose only one polar atom—O(3′) and O(1′), respectively—to the solvent. The O(2′) atom of the furanose ring system in the RNA subunit could give added stability via solvent association or interunit hydrogen bonding with or without a bridging water. The superposition solvation maps describing the accessibility of a group of polar atoms help to interpret a good number of phosphodiester conformations observed in a energetically less favored conformational domains in the tRNAPhe crystal. Another intresting fact that results from this study is the prediction that the trans oriented of ω is the most favorable conformations of random‐coil polynucleotides in solution.