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Journal of Chemical Physics / Volume 134 / Issue 8 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 134, 085101 (2011); http://dx.doi.org/10.1063/1.3552946 (22 pages)

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Thomas E. Ouldridge1, Ard A. Louis1, and Jonathan P. K. Doye2

1Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
2Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom

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(Received 24 September 2010; accepted 17 January 2011; published online 22 February 2011)

We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson–Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an “average base” description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. METHODS
    1. The model
      1. Philosophy of the model
      2. The potential
      3. Parameterization of interactions
    2. Simulation technique
  3. RESULTS
    1. Basic structure
    2. Model thermodynamics
      1. Single-stranded stacking transition
      2. Duplex formation
      3. Free energy profile of duplex formation and fraying
      4. Effect of stacking and fraying on thermodynamics of duplex formation
    3. Mechanical properties
      1. Double-stranded persistence length
      2. Single-stranded persistence length for fully stacked strands
      3. Single-stranded persistence length for unstacked strands
      4. Double-stranded torsional and extensional stiffness
    4. Structural motifs
      1. Hairpins
      2. Mismatches, bulges, and internal bubbles
  4. DISCUSSION

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KEYWORDS and PACS

Keywords

biomechanics, DNA, elastic moduli, molecular biophysics, molecular configurations, physiological models, thermodynamic properties

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3552946

PUBLICATION DATA

ISSN

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

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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