Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

Publication: Research - peer-reviewJournal article – Annual report year: 2009

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We investigate the coalescence of two DNA bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift diffusion toward coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few of the base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA in single molecule fluorescence experiments.
Original languageEnglish
JournalJournal of Chemical Physics
Publication date2009
Volume130
Issue16
Pages164117
ISSN0021-9606
DOIs
StatePublished

Bibliographical note

Copyright (2009) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

CitationsWeb of Science® Times Cited: 3
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