title: The thermodynamics of DNA loop formation, from J to Z.
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.
authors.affiliation: Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083, U.S.A. sdlevene@utdallas.edu
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Levene
authors.forename: Stefan M
authors.initials: SM
authors.lastname: Giovan
authors.forename: Andreas
authors.initials: A
authors.lastname: Hanke
authors.forename: Massa J
authors.initials: MJ
authors.lastname: Shoura
mesh_terms: D001704:Biopolymers / Q000737:chemistry; D003500:Cyclization; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D001704:Biopolymers; D004247:DNA