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Dynamics of DNA conformations and DNA-protein interaction

Metzler, Ralf ; Ambjörnsson, Tobias LU ; Lomholt, Michael A. and Krichevsky, Oleg (2005) 2005 MRS Fall Meeting In Materials Research Society Symposium Proceedings 899. p.7-18
Abstract

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to... (More)

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.

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author
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publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
host publication
Dynamics in Small Confining Systems VI
series title
Materials Research Society Symposium Proceedings
volume
899
pages
12 pages
conference name
2005 MRS Fall Meeting
conference location
Boston, MA, United States
conference dates
2005-11-28 - 2005-12-02
external identifiers
  • scopus:34249994650
ISSN
0272-9172
language
English
LU publication?
no
id
c6a44aed-2e99-49ed-a77f-680af0e61c67
date added to LUP
2019-05-03 11:52:16
date last changed
2020-01-14 12:50:58
@inproceedings{c6a44aed-2e99-49ed-a77f-680af0e61c67,
  abstract     = {<p>Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.</p>},
  author       = {Metzler, Ralf and Ambjörnsson, Tobias and Lomholt, Michael A. and Krichevsky, Oleg},
  booktitle    = {Dynamics in Small Confining Systems VI},
  issn         = {0272-9172},
  language     = {eng},
  month        = {12},
  pages        = {7--18},
  series       = {Materials Research Society Symposium Proceedings},
  title        = {Dynamics of DNA conformations and DNA-protein interaction},
  volume       = {899},
  year         = {2005},
}