Entropy-driven genome organization.

Journal 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 eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.

Authors: Marenduzzo, D; Micheletti, C; Cook, P

• Publication status: Published
• Journal: Biophysical journal
• Volume: 90
• Issue: 10
• Pages: 3712-3721
• Publication date: 2006-05-01
• DOI: 10.1529/biophysj.105.077685
• EISSN: 1542-0086
• ISSN: 0006-3495
• Language: English
• Keywords: Nucleic Acid Conformation; Genome; Computer Simulation; Models, Chemical; DNA-Directed RNA Polymerases; Entropy; DNA-Directed DNA Polymerase; DNA; Models, Molecular