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Dynamics of DNA conformations and DNA-protein interactions

Published online by Cambridge University Press:  26 February 2011

Ralf Metzler ,
Tobias Ambjörnsson ,
Michael A. Lomholt  and
Oleg Krichevsky
Ralf Metzler
Affiliation:
metz@nordita.dk, NORDITA, Blegdamsvej 17, Copenhagen OE, N/A, 2100, Denmark, +45 353 25507
Tobias Ambjörnsson
Affiliation:
ambjorn@nordita.dk, NORDITA, Denmark
Michael A. Lomholt
Affiliation:
mlomholt@nordita.dk, NORDITA, Denmark
Oleg Krichevsky
Affiliation:
okrichev@bgumail.bgu.ac.il, Ben Gurion University, Israel
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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 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.

Keywords

diffusionpolymerbiological
Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 899: Symposium N – Dynamics in Small Confining Systems VIII , 2005 , 0899-N03-06
Copyright
Copyright © Materials Research Society 2006

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