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JCP: BioChemical Physics / Volume 6 / Issue 1 / ARTICLES

J. Chem. Phys. 136, 045102 (2012); http://dx.doi.org/10.1063/1.3679654 (11 pages)

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

David A. Sivak and Phillip L. Geissler

Biophysics Graduate Group, University of California, Berkeley, California 94720, USA

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(Received 13 July 2011; accepted 8 January 2012; published online 31 January 2012)

The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 1–10 basepair (bp) scale, which holds particular interest in biological contexts. Here, we examine a class of microscopic models which allow for disruption of base pairing (i.e., a “melt” or “kink”, generically an “excitation”) and consequently enhanced local flexibility. We first analyze the effect on the excitation free energy of integrating out the spatial degrees of freedom in a wormlike chain. Based on this analysis, we present a formulation of these models that ensures consistency with the well-established thermodynamics of melting in long chains. Using a new method to calculate cyclization statistics of short chains from enhanced-sampling Monte Carlo simulations, we compute J-factors of a meltable wormlike chain over a broad range of chain lengths, including very short molecules (30 bp) that have not yet been explored experimentally. For chains longer than about 120 bp, including most molecules studied to date in the laboratory, we find that melting excitations have little impact on cyclization kinetics. Strong signatures of melting, which might be resolved within typical experimental scatter, emerge only for shorter chains.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THE WORMLIKE CHAIN MODEL WITH THERMAL EXCITATIONS OF ENHANCED FLEXIBILITY
  3. CYCLIZATION KINETICS
  4. CONNECTION WITH LATTICE MODELS
  5. PARAMETERIZATION
  6. RELATING CYCLIZATION PROBABILITIES TO DISTRIBUTIONS OF END-TO-END DISTANCE AND ANGLE IN A DISCRETIZED CHAIN
  7. MONTE CARLO SIMULATIONS
  8. J -FACTORS
  9. TEMPERATURE DEPENDENCE
  10. CONCLUSION

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KEYWORDS and PACS

Keywords

DNA, free energy, molecular biophysics, Monte Carlo methods, thermodynamics

PACS

  • 87.15.Cc

    Folding: thermodynamics, statistical mechanics, models, and pathways

  • 87.14.gk

    DNA

  • 87.15.ak

    Monte Carlo simulations

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3679654

PUBLICATION DATA

ISSN

1931-9223 (online)

Publisher

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

For access to fully linked references, you need to log in.
    C. Yuan, H. Chen, X. W. Lou, and L. A. Archer, Phys. Rev. Lett. 100, 018102 (2008).

    P. A. Wiggins and P. C. Nelson, Phys. Rev. E 73, 031906 (2006).

    J. Yan and J. F. Marko, Phys. Rev. Lett. 93, 108108 (2004).

    J. Yan, R. Kawamura, and J. F. Marko, Phys. Rev. E 71, 061905 (2005).

    P. A. Wiggins, R. S. Phillips, and P. C. Nelson, Phys. Rev. E 71, 021909 (2005).

    J. Yan and J. F. Marko, Phys. Rev. E 68, 011905 (2003).

    B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959)JCPSA6000031000002000526000001.

    J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007).

    H. Yamakawa and W. Stockmayer, J. Chem. Phys. 57, 2843 (1972)JCPSA6000057000007002843000001.

    T. Dauxois, M. Peyrard, and A. R. Bishop, Phys. Rev. E 47, 684 (1993).


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