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Biochem Soc Trans. 2013 Apr;41(2):513-8. doi: 10.1042/BST20120324.

The thermodynamics of DNA loop formation, from J to Z.

Author information

1
Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083, U.S.A. sdlevene@utdallas.edu

Abstract

The formation of DNA loops is a ubiquitous theme in biological processes, including DNA replication, recombination and repair, and gene regulation. These loops are mediated by proteins bound at specific sites along the contour of a single DNA molecule, in some cases many thousands of base pairs apart. Loop formation incurs a thermodynamic cost that is a sensitive function of the length of looped DNA as well as the geometry and elastic properties of the DNA-bound protein. The free energy of DNA looping is logarithmically related to a generalization of the Jacobson-Stockmayer factor for DNA cyclization, termed the J factor. In the present article, we review the thermodynamic origins of this quantity, discuss how it is measured experimentally and connect the macroscopic interpretation of the J factor with a statistical-mechanical description of DNA looping and cyclization.

PMID:
23514145
DOI:
10.1042/BST20120324
[Indexed for MEDLINE]

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