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Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA
Int. J. Mol. Sci. 2014, 15(9), 15090-15108; doi:10.3390/ijms150915090

What Controls DNA Looping?

1 BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA 2 Wright–Rieman Laboratories, Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
* Author to whom correspondence should be addressed.
Received: 11 July 2014 / Revised: 11 August 2014 / Accepted: 19 August 2014 / Published: 27 August 2014
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
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The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.
Keywords: DNA looping; optimization; J factor; lac operon; Monte Carlo simulations DNA looping; optimization; J factor; lac operon; Monte Carlo simulations
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Perez, P.J.; Clauvelin, N.; Grosner, M.A.; Colasanti, A.V.; Olson, W.K. What Controls DNA Looping? Int. J. Mol. Sci. 2014, 15, 15090-15108.

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