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

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

2011-09-30

arxiv.org/abs/1109.6715v2

Physics

Condensed Matter

Statistical Mechanics

13 pages, 5 figures

Scientific paper

10.1063/1.3679654

The wormlike chain (WLC) 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 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 (MWLC) 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.

Affiliated with

Also associated with

No associations

Rating

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-667222