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Title: Sequence heterogeneity accelerates protein search for targets on DNA

Abstract

The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

Authors:
;  [1]
  1. Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)
Publication Date:
OSTI Identifier:
22493436
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 143; Journal Issue: 24; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; CHEMICAL BONDS; CHEMICAL COMPOSITION; DNA; DNA SEQUENCING; PROBES; PROTEINS; STOCHASTIC PROCESSES; SYMMETRY

Citation Formats

Shvets, Alexey A., and Kolomeisky, Anatoly B., E-mail: tolya@rice.edu. Sequence heterogeneity accelerates protein search for targets on DNA. United States: N. p., 2015. Web. doi:10.1063/1.4937938.
Shvets, Alexey A., & Kolomeisky, Anatoly B., E-mail: tolya@rice.edu. Sequence heterogeneity accelerates protein search for targets on DNA. United States. doi:10.1063/1.4937938.
Shvets, Alexey A., and Kolomeisky, Anatoly B., E-mail: tolya@rice.edu. Mon . "Sequence heterogeneity accelerates protein search for targets on DNA". United States. doi:10.1063/1.4937938.
@article{osti_22493436,
title = {Sequence heterogeneity accelerates protein search for targets on DNA},
author = {Shvets, Alexey A. and Kolomeisky, Anatoly B., E-mail: tolya@rice.edu},
abstractNote = {The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.},
doi = {10.1063/1.4937938},
journal = {Journal of Chemical Physics},
number = 24,
volume = 143,
place = {United States},
year = {Mon Dec 28 00:00:00 EST 2015},
month = {Mon Dec 28 00:00:00 EST 2015}
}
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