Stereochemistry of Nucleic Acids and Polynucleotides: I. Theoretical Determination of the Allowed Conformations of the Monomer Unit

Abstract

The approach through the hard-sphere model, based on certain stereochemical criteria for non-bonded distances, developed in this laboratory for determining the allowed conformations of proteins and polypeptide chains, has now been extended to nucleic acids and polynucleotides. In this paper, notations have been developed for representing the monomer nucleotide unit and for characterizing the conformation of this unit. This is done by means of a set of parameters θ1, θ2 and θ3 denoting the rotation about the 05'— C5′, C5'— C4′ and C3′ — O3′ bonds, respectively, and another parameter x giving the rotation of the base about the glycosidic bond. As a first step, the allowed conformations for the monomer unit have been determined. It is shown that the theoretically predicted values for the above parameters agree remarkably well with the values obtained from the data on the available crystal structures of nucleosides and nucleotides. The most interesting result that comes out of the present study is that the number of possible conformations for the nucleotide unit is limited to 3, or at most 6, from out of the 300 different possible conformations it might take up according to the usual ideas on restricted rotation about single bonds. This has simplified the study on the conformation of the polynucleotide chain, the details of which will be published in a series of later papers.