D. Marenduzzo, C. Micheletti and P.R. Cook
Entropy-driven genome organization
Biophys. J. 90 3712-3721 (2006)
Link to online article.
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.