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Master equation approach to DNA breathing in heteropolymer DNA

Ambjörnsson, Tobias LU ; Banik, Suman K.; Lomholt, Michael A. and Metzler, Ralf (2007) In Physical Review E 75(2).
Abstract
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few kBT. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where the single strand of the denatured zone joins the still intact double strand, can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution... (More)
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few kBT. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where the single strand of the denatured zone joins the still intact double strand, can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement. (Less)
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
subject
in
Physical Review E
volume
75
issue
2
publisher
American Physical Society
external identifiers
  • scopus:33847309773
ISSN
1539-3755
DOI
10.1103/PhysRevE.75.021908
language
English
LU publication?
no
id
48cc27e6-cad9-4656-9bee-c079adf2d63e
alternative location
https://link.aps.org/doi/10.1103/PhysRevE.75.021908
date added to LUP
2019-05-03 11:39:19
date last changed
2019-07-30 08:56:52
@article{48cc27e6-cad9-4656-9bee-c079adf2d63e,
  abstract     = {After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies up to a few kBT. Thermal motion within the DNA double strand therefore causes the opening of intermittent single-stranded denaturation zones, the DNA bubbles. The unzipping and zipping dynamics of bps at the two zipper forks of a bubble, where the single strand of the denatured zone joins the still intact double strand, can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA breathing in a heteropolymer DNA with given sequence in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.},
  articleno    = {021908},
  author       = {Ambjörnsson, Tobias and Banik, Suman K. and Lomholt, Michael A. and Metzler, Ralf},
  issn         = {1539-3755},
  language     = {eng},
  number       = {2},
  publisher    = {American Physical Society},
  series       = {Physical Review E},
  title        = {Master equation approach to DNA breathing in heteropolymer DNA},
  url          = {http://dx.doi.org/10.1103/PhysRevE.75.021908},
  volume       = {75},
  year         = {2007},
}