The thermodynamics of DNA loop formation, from J to Z

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Biopolymers / chemistry
  • Cyclization
  • DNA / chemistry*
  • Nucleic Acid Conformation*
  • Thermodynamics


  • Biopolymers
  • DNA