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Journal of Chemical Physics / Volume 135 / Issue 11 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 115101 (2011); http://dx.doi.org/10.1063/1.3631564 (10 pages)

Thermodynamics of twisted DNA with solvent interaction

Marco Zoli

School of Science and Technology, CNISM, Università di Camerino, I-62032 Camerino, Italy

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(Received 20 June 2011; accepted 8 August 2011; published online 16 September 2011)

The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over ∼107 − 108 base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. HAMILTONIAN MODEL
  3. COMPUTATIONAL METHOD
  4. THERMODYNAMICAL RESULTS
    1. Fractions of open base pairs
    2. Specific heat versus twist
    3. Base pairs path ensemble versus twist
  5. CONCLUDING REMARKS

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KEYWORDS and PACS

Keywords

DNA, hydrogen bonds, specific heat, thermodynamics, torsion

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3631564

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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