Dynamic Approach to DNA Breathing
(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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/4b35c720-a5d9-44c7-a098-8aa416a1b877
- author
- Metzler, Ralf and Ambjörnsson, Tobias LU
- publishing date
- 2005-12-01
- 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}}, }