ニシモリ　ヒラク   NISHIMORI HIRAKU   西森　拓    所属   明治大学研究・知財戦略機構・農場  研究・知財戦略機構    職種   特任教授
言語種別	英語
発行・発表の年月	2015
形態種別	学術雑誌
査読	査読あり
標題	Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.
執筆形態	共著(筆頭者以外)
掲載誌名	PloS one
掲載区分	国外
巻・号・頁	10(12),pp.e0143760
著者・共著者	Isami Shuhei, Sakamoto Naoaki, Nishimori Hiraku, Awazu Akinori
概要	This study develops simple elastic network models to explore the relationship between DNA structure and dynamics across various nucleotide sequences. First, an all-atom elastic network model is introduced that accurately reproduces temperature factor profiles observed in several DNA crystal structures. Next, a coarse-grained model is proposed, representing each nucleotide with a single node. This simplified model effectively captures detailed sequence-dependent dynamics similar to the all-atom model. Using normal-mode analysis on the coarse-grained model, the dynamics of many long DNA sequences (~150 base pairs) were extensively studied. The analysis revealed a positive correlation between the DNA’s nucleosome-forming ability and the strength of inter-strand fluctuations, providing insight into how dynamic properties influence DNA’s biological function.
DOI	10.1371/journal.pone.0143760
ISSN	1932-6203
PMID	26624614