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

Pedersen, Jonas LU ; Hansen, Mikael Sonne; Novotný, Tomás; Ambjörnsson, Tobias and Metzler, Ralf (2009) In Journal of Chemical Physics 130(16).
Abstract
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
130
issue
16
publisher
American Institute of Physics
external identifiers
  • wos:000266885200018
  • pmid:19405571
  • scopus:65149095479
ISSN
0021-9606
DOI
10.1063/1.3117922
language
English
LU publication?
yes
id
7f6eda67-6a3b-459c-b696-8f43bc260da8 (old id 1412813)
date added to LUP
2009-06-11 12:35:33
date last changed
2017-01-01 04:30:21
@article{7f6eda67-6a3b-459c-b696-8f43bc260da8,
  abstract     = {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.},
  articleno    = {164117},
  author       = {Pedersen, Jonas and Hansen, Mikael Sonne and Novotný, Tomás and Ambjörnsson, Tobias and Metzler, Ralf},
  issn         = {0021-9606},
  language     = {eng},
  number       = {16},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Bubble merging in breathing DNA as a vicious walker problem in opposite potentials.},
  url          = {http://dx.doi.org/10.1063/1.3117922},
  volume       = {130},
  year         = {2009},
}