Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes

Nucleic Acids Res. 2013 Aug;41(14):6808-15. doi: 10.1093/nar/gkt480. Epub 2013 Jun 5.


Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Bacterial / chemistry*
  • DNA Breaks, Double-Stranded*
  • Models, Molecular*
  • Monte Carlo Method