Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

PLoS One. 2015 Dec 1;10(12):e0143760. doi: 10.1371/journal.pone.0143760. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • DNA / metabolism
  • Molecular Dynamics Simulation*
  • Molecular Structure
  • Nucleosomes / metabolism
  • Temperature

Substances

  • Nucleosomes
  • DNA

Grants and funding

This work was supported by Platform Project for Supporting in Drug Discovery and Life Science Research (Platform for Dynamic Approaches to Living System) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and Japan Agency for Medical Research and Development (AMED). Grant-in-Aid for Scientific Research on Innovative Areas "Spying minority in biological phenomena” (No. 3306) (24115515) and "Initiative for High-Dimensional Data-Driven Science through Deepening of Sparse Modeling” (No. 4503) (26120525) of MEXT of Japan (A. A) Grants-in-Aid for Scientific Research (C) (No. 25430169) of MEXT of Japan (N. S).