DNA topology: Topoisomerases keep it simple

Abstract

The ability of type II DNA topoisomerases to perturb the equilibrium distributions of DNA topoisomers is a consequence of their ability to hydrolyse ATP. A sliding mechanism of topoisomerase action has been proposed to account for this phenomenon.

On Solutions to Euler-Lagrange Equations Governing Isotropic, Homogeneous, Naturally Curved Kirchhoff’s Elastic Rods

“…As s 0 = 0 is assumed for sake of convenience, it suggests that the solution with the initial data (k 1 k 2 (0)) and the solution with the initial data…”

“…Fig. 1 The initial data for the solution whose twisting density and its first and second derivatives are plotted by solid lines are k 1 …”

“…One way to resolve the ambiguity is to mark a normal cross section such that two sides of the cross section are considered ends of a closed rod. This resolution originates from [2] in which the authors studied terminal twist induced writhe of elastic rings through a cut-rotate-seal procedure performed on a normal cross section of the rings (type I topoisomerases change topology of closed circular DNA by using a mechanism equivalent to this procedure [1]). For any rod, we always assume that the arc length parameter s of the rod axis attains the value L at the point on the axis that belongs to the normal cross section on which the twist exerts.…”

A 4-string tangle analysis of DNA-protein complexes based on difference topology

“…For both cases, DNA is usually negatively supercoiled [1]. In this chapter, we would like to extend 3-string tangle analysis (section 3.4) to 4-string tangle analysis based on difference topology.…”

The regulation of RNA Polymerase I-mediated transcription in forebrain neurons.

“…The topoisomerases (I and II) catalyze DNA topology rearrangement to maintain its energetically stable forms from the relaxed or super-coiled DNA forms (Sharma and Mondragon, 1995;Bates and Maxwell, 1997). Topoisomerase I regulates DNA topology by cleaving one strand of DNA and creating a covalent 3' -phosphotyrosine bond at its catalytic center (Pommier, 2009 (Nur et aI., 2007).…”