title: Removal of DNA-bound proteins by DNA twisting.
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.
authors.affiliation: Department of Physics, The University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607-7059, USA.
authors.forename: A
authors.initials: A
authors.lastname: Sarkar
authors.forename: J F
authors.initials: JF
authors.lastname: Marko
mesh_terms: D004247:DNA / Q000737:chemistry*; D027081:DNA Gyrase / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA; D027081:DNA Gyrase