A self-consistent formulation for analysis and generation of non-uniform DNA structures

Abstract

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters"are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.