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A coarse grain model for DNA

J. Chem. Phys. 126, 084901 (2007); doi:10.1063/1.2431804

Published 23 February 2007

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Thomas A. Knotts, IV
Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602

Nitin Rathore
Amgen Inc., Thousand Oaks, California 91320

David C. Schwartz
Departments of Genetics and Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706

Juan J. de Pablo
Department of Chemical and Biological Engineering, University of Wisconsin—Madison, Madison, Wisconsin 53706
Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration. ©2007 American Institute of Physics
History: Received 24 July 2006; accepted 13 December 2006; published 23 February 2007
Permalink: http://link.aip.org/link/?JCPSA6/126/084901/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.14.Gg
    DNA, RNA
  • 87.15.By
    Structure and bonding of biomolecules
  • 36.20.Ey
    Macromolecular conformation (statistics and dynamics)
  • YEAR: 2007

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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