Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

Tomas Novotný; Jonas Nyvold Pedersen; Tobias Ambjörnsson; Mikael Sonne Hansen; Ralf Metzler

doi:10.1209/0295-5075/77/48001

Bubble coalescence in breathing DNA

Authors:

Novotný, Tomas ;
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Charles University
Pedersen, Jonas Nyvold ;
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0000-0001-7642-8212
Department of Micro- and Nanotechnology, Technical University of Denmark
Ambjörnsson, Tobias ;
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Massachusetts Institute of Technology
Hansen, Mikael Sonne ;
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Geometry, Department of Mathematics, Technical University of Denmark
Metzler, Ralf
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University of Ottawa

Subtitle:

Two vicious walkers in opposite potentials

DOI:

10.1209/0295-5075/77/48001

Abstract:

We investigate the coalescence of two DNA bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. 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 behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.

Type:

Journal article

Language:

English

Published in:

Epl, 2007, Vol 77

Main Research Area:

Science/technology

Publication Status:

Published

Review type:

Peer Review

Submission year:

2007

Scientific Level:

Scientific

ID:

162623044

Bubble coalescence in breathing DNA

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