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Biophys. J. BioFAST: First Published February 24, 2006. doi:10.1529/biophysj.105.077685
© 2006 by the Biophysical Society.

A more recent version of this article appeared on May 15, 2006.
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Davide Marenduzzo
Cristian Micheletti
Peter R Cook
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SUPRAMOLECULAR ASSEMBLIES

Entropy-driven genome organization

Davide Marenduzzo 1, Cristian Micheletti 2 and Peter R Cook 3*

1 University of Warwick
2 International School for Advanced Studies (SISSA)
3 University of Oxford

* To whom correspondence should be addressed. E-mail: peter.cook{at}path.ox.ac.uk.

Submitted on November 12, 2005
Revised on January 9, 2006
Accepted on 27 January 2006


  Abstract
DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription "factories" in both pro- and eu-karyotes. We conclude the second law of thermodynamics acts through non-specific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of base-pairs.

Key Words: Monte-Carlo simulation, chromatin loop, entropy, genome organization, replication, transcription




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Copyright © 2006 by the Biophysical Society.