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. 2001 Dec;64(6 Pt 1):061909.
doi: 10.1103/PhysRevE.64.061909. Epub 2001 Nov 26.

Removal of DNA-bound proteins by DNA twisting

A Sarkar  1 , J F Marko
Affiliations

Removal of DNA-bound proteins by DNA twisting

A Sarkar et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Dec.

Abstract

We present a simple model of how local torsional stress in DNA can eject a DNA-bound protein. An estimate of the torque tau(*) required to eject a typical DNA-bound protein is made through a two-state model of the equilibrium between the bound and unbound states of the protein. For the familiar case of a nucleosome octamer bound to double-stranded DNA, we find this critical torque to be approximately equal to 9k(B)T. More weakly bound proteins and large (approximately equal to kilobase) loops of DNA are shown to be destabilized by smaller torques of only a few k(B)T. We then use our model to estimate the maximum range R(max) at which a protein can be removed by a transient source of twisting. We model twist strain propagation along DNA by simple dissipative dynamics in order to estimate R(max). Given twist pulses of the type expected to be generated by RNA polymerase and DNA gyrase, we find R(max) approximately equal to 70 and 450 bp, respectively, for critical torques of approximately equal to 2k(B)T.

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