• 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.