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Biophysical Journal 85:167-173 (2003)
© 2003 The Biophysical Society

Entropy Loss in Long-Distance DNA Looping

Andreas Hanke * {dagger} and Ralf Metzler {ddagger} §

* Institute for Theoretical Physics, University of Stuttgart, Stuttgart, Germany; {dagger} Department of Physics–Theoretical Physics, University of Oxford, Oxford, United Kingdom; {ddagger} NORDITA–Nordic Institute for Theoretical Physics, Copenhagen, Denmark; and § Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts USA

Correspondence: Address reprint requests to Ralf Metzler, E-mail: metz{at}nordita.dk.

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow us to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor in comparison to both kBT and typical bond energies in biopolymers, which has to be overcome by the released bond energy between the looping contact sites.




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