Principal component analysis of nucleosome DNA conformational data

Abstract

The deformation mechanism of double helical DNA can be elucidated by the correlations between various conformational properties of its constituent dinucleotides. In this paper, we study the structural features of nucleosomes by performing principle component analysis on structural parameters within three categories: sugar-phosphate backbone, base pairs and base steps. The aim of this study is to find out the coupling modes of these conformational properties which are probably responsible for the special conformational settings of dinucleotides in nucleosomes. For comparison, a number of B-form oligomers are selected and subjected to PCA. Analysis of similarity and difference between nucleosomes and oligomers is implemented. The result shows that nucleosomes have a series of unique coupling patterns and reveals the multidimension-coordinated deformation mechanisms.