Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base-sugar units

Abstract

In this paper, the preferred conformations of the bases with respect to the sugar in various base-sugar units are worked out using criteria of potential energy. The van der Waals type of intercations between nonbonded atoms is represented by a 6-12 function and the electrostatic interactions have been calculated in the monopole approximation using Coulomb's law. The torsional contributions to the total energy have been neglected. It is found that in general the pyrimidines have preferred anti contributions (as described by Donohue and Trueblood) and purines have both syn and anti and conformations. Certain differences between differently puckered riboses in regard to the above general tendency are discussed. The conclusions, in general, conform with the results obtained by us earlier with the use of hard-sphere potential and are also supported by observations on conformations of nucleotides and nucleotides in crystal structure.