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Dynamic Approach to DNA Breathing

Metzler, Ralf and Ambjörnsson, Tobias LU (2005) In Journal of Biological Physics 31(3-4). p.339-350
Abstract
Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its... (More)
Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description. (Less)
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author
and
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Biological Physics
volume
31
issue
3-4
pages
339 - 350
publisher
Springer
external identifiers
  • scopus:28744445820
ISSN
0092-0606
DOI
10.1007/s10867-005-2410-y
language
English
LU publication?
no
id
4b35c720-a5d9-44c7-a098-8aa416a1b877
date added to LUP
2019-05-03 11:42:23
date last changed
2022-03-31 17:20:09
@article{4b35c720-a5d9-44c7-a098-8aa416a1b877,
  abstract     = {{Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.}},
  author       = {{Metzler, Ralf and Ambjörnsson, Tobias}},
  issn         = {{0092-0606}},
  language     = {{eng}},
  month        = {{12}},
  number       = {{3-4}},
  pages        = {{339--350}},
  publisher    = {{Springer}},
  series       = {{Journal of Biological Physics}},
  title        = {{Dynamic Approach to DNA Breathing}},
  url          = {{http://dx.doi.org/10.1007/s10867-005-2410-y}},
  doi          = {{10.1007/s10867-005-2410-y}},
  volume       = {{31}},
  year         = {{2005}},
}