J Chem Phys. 2012 Jan 28;136(4):045102. doi: 10.1063/1.3679654.
Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA.
The Journal of chemical physics
David A Sivak, Phillip L Geissler
Affiliations
Affiliations
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.
PMID: 22299918
DOI: 10.1063/1.3679654
Abstract
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
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