Local site preference rationalizes disentangling by DNA topoisomerases

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Mar;81(3 Pt 1):031902. doi: 10.1103/PhysRevE.81.031902. Epub 2010 Mar 4.


To rationalize the disentangling action of type II topoisomerases, an improved wormlike DNA model was used to delineate the degree of unknotting and decatenating achievable by selective segment passage at specific juxtaposition geometries and to determine how these activities were affected by DNA circle size and solution ionic strength. We found that segment passage at hooked geometries can reduce knot populations as dramatically as seen in experiments. Selective segment passage also provided theoretical underpinning for an intriguing empirical scaling relation between unknotting and decatenating potentials.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • DNA Topoisomerases, Type I / chemistry*
  • DNA Topoisomerases, Type I / ultrastructure*
  • Enzyme Activation
  • Models, Chemical*
  • Models, Molecular*
  • Protein Binding


  • DNA
  • DNA Topoisomerases, Type I