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Target search on a dynamic DNA molecule

Schötz, Thomas and Neher, Richard A. and Gerland, Ulrich. (2011) Target search on a dynamic DNA molecule. Physical Review E, 84 (5). 051911.

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Official URL: http://edoc.unibas.ch/53997/

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Abstract

We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein "jumps" between sites distant along the DNA contour but close in three-dimensional space. A strongly binding protein that searches by one-dimensional sliding and jumping alone explores the search space less redundantly when the DNA dynamics is fast on the time scale of protein jumps than in the opposite "frozen DNA" limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in "islands" within random DNA configurations in solution.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Physical Society
ISSN:1063-651X
e-ISSN:1095-3787
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:18 Sep 2019 06:15
Deposited On:30 Nov 2017 09:43

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