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.
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Conference Article| March 21 2013
The thermodynamics of DNA loop formation, from J to Z
Stephen D. Levene;
Stephen D. Levene 1
*Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75083, U.S.A.
†Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083, U.S.A.
‡Department of Physics, University of Texas at Dallas, Richardson, TX 75083, U.S.A.
1To whom correspondence should be addressed (firstname.lastname@example.org).
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Stefan M. Giovan;
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Stephen D. Levene, Stefan M. Giovan, Andreas Hanke, Massa J. Shoura; The thermodynamics of DNA loop formation, from J to Z. Biochem Soc Trans 1 April 2013; 41 (2): 513–518. doi: https://doi.org/10.1042/BST20120324
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