title: Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.
abstract: Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Isami
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.|Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Naoaki
authors.initials: N
authors.lastname: Sakamoto
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.|Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Hiraku
authors.initials: H
authors.lastname: Nishimori
authors.affiliation: Department of Mathematical and Life Sciences, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.|Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagami-yama 1-3-1, Higashi-Hiroshima 739-8526, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Awazu
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009707:Nucleosomes / Q000378:metabolism; D013696:Temperature
chemical_list: D009707:Nucleosomes; D004247:DNA