Skip to main content

In the clutches of Maxwell’s demon: below-equilibrium DNA topology simplification by type II topoisomerases

Thursday, November 07, 2013 — Poster Session II

12:00 p.m. – 2:00 p.m.

FAES Academic Center (Upper-Level Terrace)




  • T.R. Litwin
  • S.K. Sarkar
  • A.H. Hardin
  • I.J. Holt
  • K.C. Neuman


Topoisomerases are divided into two classes: type I topoisomerases, which are ATP-independent enzymes that cut a single strand of DNA to relax supercoils, and type II topoisomerases, which are ATP-dependent enzymes that transiently cut both strands of one segment of DNA and pass another segment of DNA through the cut. Type I topoisomerases simplify topology to create a distribution of supercoils defined by thermal equilibrium. Type II topoisomerases use part of the energy from ATP hydrolysis to simplify DNA topology beyond thermal equilibrium such that the distribution of conformations is narrower, but the mechanism for this process is unresolved. Specifically, it is not known how type II topoisomerases acting locally on the nanometer scale can simplify the global topology of DNA, an extended substrate much larger than the enzyme. We propose that type II topoisomerases have a higher binding affinity for more highly supercoiled DNA and that this preferential binding can help explain below-equilibrium topology simplification. We developed a nitrocellulose filter binding assay to determine the topology-dependent binding of Topoisomerase IV, a bacterial type II topoisomerase. Computer simulations were also run to determine how empirical levels of differential binding can lead to non-equilibrium topology simplification.

back to top