Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

Tadasu Nozaki; Nozomu Yachie; Ryu Ogawa; Rintaro Saito; Masaru Tomita

doi:10.1016/j.gene.2011.02.004

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA

Gene. 2011 May 1;476(1-2):10-4. doi: 10.1016/j.gene.2011.02.004. Epub 2011 Feb 19.

Authors

Tadasu Nozaki¹, Nozomu Yachie, Ryu Ogawa, Rintaro Saito, Masaru Tomita

Affiliation

¹ Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.

PMID: 21338662
DOI: 10.1016/j.gene.2011.02.004

Abstract

Eukaryotic chromosomal DNA coils around histones to form nucleosomes. Although histone affinity for DNA depends on DNA sequence patterns, how nucleosome positioning is determined by them remains unknown. Here, we show relationships between nucleosome positioning and two structural characteristics of DNA conferred by DNA sequence. Analysis of bendability and hydroxyl radical cleavage intensity of nucleosomal DNA sequences indicated that nucleosomal DNA is bendable and fragile and that nucleosome positional stability was correlated with characteristics of DNA. This result explains how histone positioning is partially determined by nucleosomal DNA structure, illuminating the optimization of chromosomal DNA packaging that controls cellular dynamics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Composition
Computer Simulation
DNA / chemistry*
DNA / genetics
DNA Packaging
Databases, Nucleic Acid
Histones / chemistry
Humans
Nucleic Acid Conformation*
Nucleosomes / chemistry*
Nucleosomes / genetics

Substances

Histones
Nucleosomes
DNA