Dynamics of DNA conformations and DNA-protein interaction

Ralf Metzler, Tobias Ambjörnsson, Michael A. Lomholt, Oleg Krichevsky

Research output: Contribution to journalConference articlepeer-review

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.

Original languageEnglish
Pages (from-to)7-18
Number of pages12
JournalMaterials Research Society Symposium Proceedings
Volume899
StatePublished - 1 Dec 2005
Event2005 MRS Fall Meeting - Boston, MA, United States
Duration: 28 Nov 20052 Dec 2005

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