Next Article in Journal
Development and Application of Loop-Mediated Isothermal Amplification Assays for Rapid Visual Detection of cry2Ab and cry3A Genes in Genetically-Modified Crops
Next Article in Special Issue
Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea
Previous Article in Journal
Protective Effects of Hericium erinaceus Mycelium and Its Isolated Erinacine A against Ischemia-Injury-Induced Neuronal Cell Death via the Inhibition of iNOS/p38 MAPK and Nitrotyrosine
Previous Article in Special Issue
Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

What Controls DNA Looping?

BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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.
Int. J. Mol. Sci. 2014, 15(9), 15090-15108;
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)
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. View Full-Text
Keywords: DNA looping; optimization; J factor; lac operon; Monte Carlo simulations DNA looping; optimization; J factor; lac operon; Monte Carlo simulations
Show Figures

Graphical abstract

MDPI and ACS Style

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.

AMA Style

Perez PJ, Clauvelin N, Grosner MA, Colasanti AV, Olson WK. What Controls DNA Looping? International Journal of Molecular Sciences. 2014; 15(9):15090-15108.

Chicago/Turabian Style

Perez, Pamela J.; Clauvelin, Nicolas; Grosner, Michael A.; Colasanti, Andrew V.; Olson, Wilma K. 2014. "What Controls DNA Looping?" Int. J. Mol. Sci. 15, no. 9: 15090-15108.

Find Other Styles

Article Access Map by Country/Region

Only visits after 24 November 2015 are recorded.
Search more from Scilit
Back to TopTop