Theoretical models of DNA topology simplification by type IIA DNA topoisomerases

Nucleic Acids Res. 2009 Jun;37(10):3125-33. doi: 10.1093/nar/gkp250. Epub 2009 Apr 21.


It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology--the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA-protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Computer Simulation
  • DNA / chemistry*
  • DNA Topoisomerases, Type II / chemistry*
  • Models, Chemical
  • Models, Molecular*
  • Nucleic Acid Conformation


  • DNA
  • DNA Topoisomerases, Type II