title: Disruption of protein-mediated DNA looping by tension in the substrate DNA.
abstract: Protein-mediated DNA looping is important in a variety of biological processes, including gene regulation and genetic transformation. Although the biochemistry of loop formation is well established, the mechanics of loop closure in a constrained cellular environment has received less attention. Recent single molecule measurements show that mechanical constraints have a significant impact on DNA looping and motivate the need for a more comprehensive characterization of the effects of tension. By modeling DNA as a wormlike chain, we calculate how continuous stretching of the substrate DNA affects the loop formation probability. We find that when the loop size is >100 bp, a tension of 500 fN can increase the time required for loop closure by two orders of magnitude. This force is small compared to the piconewton forces that are associated with RNA polymerases and other molecular motors, indicating that intracellular mechanical forces might affect transcriptional regulation. In contrast to existing theory, we find that for loops <200 bp, the effect of tension is partly dependent on the relative orientation of the DNA-binding domains in the linker protein. Our results provide perspective on recent DNA looping experiments and suggestions for future micromechanical studies.
authors.affiliation: Department of Physics, Randall Laboratory, University of Michigan, Ann Arbor, Michigan 48109-1120, USA.
authors.forename: Seth
authors.initials: S
authors.lastname: Blumberg
authors.forename: Alexei V
authors.initials: AV
authors.lastname: Tkachenko
authors.forename: Jens-Christian
authors.initials: JC
authors.lastname: Meiners
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D004268:DNA-Binding Proteins / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D018625:Microscopy, Atomic Force / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010812:Physical Stimulation / Q000379:methods; D013314:Stress, Mechanical
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA