Title

Authors

Affiliation

¹Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong; ²School of Electrical and Information Engineering, University of Sydney, NSW 2006, Australia

Email

yangxi_anne@yahoo.com.cn; *Corresponding author

Article Type

Hypothesis

Date

Received September 06, 2011; Accepted September 11, 2011; Published September 28, 2011

The histone octamer induced bending of DNA into the super-helix structure in nucleosome core particle, is very unique and vital for DNA packing into chromatin. We collected 48 nucleosome crystal structures from PDB and applied a multivariate analysis on the nucleosome structural data. Based on the anisotropic nature of DNA structure, a principal conformational subspace (PCS) is derived from multiple properties to represent the most significant variances of nucleosome DNA structures. The coupling of base pair-oriented parameters with sugar phosphate backbone parameters presented in principal dimensionalities reveals two main deformation modes that have supplemented the existing physical model. By using sequence alignment-based statistics, a position-dependent conformational map for the super-helical DNA path is established. The result shows that the crystal structures of nucleosome DNA have much consistency in position-specific structural variations and certain periodicity is found to exist in these variations. Thus, the positions with obvious deformation patterns along the DNA path in nucleosome core particle are relatively conservative from the perspective of statistics.

Citation

Yang & Yan. Bioinformation 7(3): 120-124 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.