Molecular dynamics simulations and normal-mode analysis of these models have identified the flexibilities, nucleosome-forming abilities, and zip-unzip transitions of the double helices of some specific DNA sequences from tens to a few hundred base pairs in length. Some of these describe the detailed shape of each nucleotide using three or more particles, whereas others describe each base pair by simply one or two particles. Several coarse-grained models of DNA (and RNA) have also been proposed. Since the last century, much progress has been made in revealing the physical aspects of DNA using all-atom normal-mode analysis and molecular dynamics simulations. However, comprehensive understanding of the physical properties of nucleotide sequences lags far behind the knowledge accumulated of their biochemical aspects. The functional behavior of each strand of DNA is determined not only by chemical aspects of the nucleotides and base pairs but also by its physical characteristics such as the structure and dynamics of the nucleotide sequences in each functional region. Therefore DNA is no longer considered to have the sole function in the storage of genetic information, but is now known to be actively involved in gene regulation, insulator activity, and in the construction of chromosomal architectures such as heterochromatins and topologically associated domains through nucleosome formation and protein bindings. Recent developments in molecular biology have revealed that DNA contains several functional regions. These models can thus demonstrate the large and slow deformations of proteins that are essential for protein functions, but remain difficult to demonstrate via all-atom molecular dynamics simulations.ДЄlong with proteins, DNA is the most important biomolecule for the activities of all living organisms. Such models have also been widely employed to accurately reproduce the temperature factors on the crystal structure of a protein via normal-mode analysis. S).Д¬ompeting interests: The authors have declared that no competing interests exist.Д®lastic network models of proteins, including all-atom models and coarse-grained models represent some of the simplest and most powerful types of theoretical models that can accurately reveal structure-dynamics relationships and the mechanisms underlying a proteinвЂ™s functional activities. A) Grants-in-Aid for Scientific Research (C) (No. 3306) (24115515) and 'Initiative for High-Dimensional Data-Driven Science through Deepening of Sparse ModelingвЂќ (No.

Grant-in-Aid for Scientific Research on Innovative Areas 'Spying minority in biological phenomenaвЂќ (No. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedДata Availability: All relevant data are within the paper and its Supporting Information files.ДЇunding: 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).

Received: JAccepted: NovemPublished: December 1, 2015Д¬opyright: В© 2015 Isami et al. Citation: Isami S, Sakamoto N, Nishimori H, Awazu A (2015) Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.

Double helix server network