Issue 6, 2011

Physics of protein–DNA interactions: mechanisms of facilitated target search

Abstract

One of the most critical aspects of proteinDNA interactions is the ability of protein molecules to quickly find and recognize specific target sequences on DNA. Experimental measurements indicate that the corresponding association rates to few specific sites among large number of non-specific sites are typically large. For some proteins they might be even larger than maximal allowed three-dimensional diffusion rates. Although significant progress in understanding protein search and recognition of targets on DNA has been achieved, detailed mechanisms of these processes are still strongly debated. Here we present a critical review of current theoretical approaches and some experimental observations in this area. Specifically, the role of lowering dimensionality, non-specific interactions, diffusion along the DNA molecules, protein and target sites concentrations, and electrostatic effects are critically analyzed. Possible future directions and outstanding problems are also presented and discussed.

Graphical abstract: Physics of protein–DNA interactions: mechanisms of facilitated target search

Article information

Article type
Perspective
Submitted
28 9 2010
Accepted
02 11 2010
First published
29 11 2010

Phys. Chem. Chem. Phys., 2011,13, 2088-2095

Physics of proteinDNA interactions: mechanisms of facilitated target search

A. B. Kolomeisky, Phys. Chem. Chem. Phys., 2011, 13, 2088 DOI: 10.1039/C0CP01966F

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