Bubble merging in breathing DNA as a vicious walker problem in opposite potentials release_2bvce2dtnbektb5igdcrm4a3vy

by Jonas Nyvold Pedersen, Mikael Sonne Hansen, Tomas Novotny, Tobias Ambjornsson, Ralf Metzler

Released as a article .

2009  

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 towards 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 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.
In text/plain format

Archived Files and Locations

application/pdf  800.0 kB
file_jrl6wkbxlfcrbhpbnsswebyig4
arxiv.org (repository)
web.archive.org (webarchive)
Read Archived PDF
Preserved and Accessible
Type  article
Stage   submitted
Date   2009-01-13
Version   v1
Language   en ?
arXiv  0901.1820v1
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: 69a254af-ed20-4134-ba2f-4ffb4109ce5f
API URL: JSON