Dynamics of DNA conformations and DNA-protein interaction
(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.
(Less)
- author
- Metzler, Ralf ; Ambjörnsson, Tobias LU ; Lomholt, Michael A. and Krichevsky, Oleg
- publishing date
- 2005-12-01
- type
- Chapter in Book/Report/Conference proceeding
- publication status
- published
- subject
- 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
- 2022-03-31 17:20:40
@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}},
}