title: Cooperative kinking at distant sites in mechanically stressed DNA.
abstract: In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are capable of relieving mechanical stress within the template. DNA minicircles offer a robust model system to study stress-induced DNA structures. Using DNA minicircles on the order of 100 bp in size, we have been able to control the bending and torsional stresses within a looped DNA construct. Through a combination of cryo-EM image reconstructions, Bal31 sensitivity assays and Brownian dynamics simulations, we have been able to analyze the effects of biologically relevant underwinding-induced kinks in DNA on the overall shape of DNA minicircles. Our results indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small regulatory DNA loops, minimize their free energy by undergoing sequential, cooperative kinking at two sites that are located about 180° apart along the periphery of the minicircle. This novel form of structural cooperativity in DNA demonstrates that bending strain can localize hyperflexible kinks within the DNA template, which in turn reduces the energetic cost to tightly loop DNA.
authors.affiliation: Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA. talionberger@gmail.com
authors.forename: Troy A
authors.initials: TA
authors.lastname: Lionberger
authors.forename: Davide
authors.initials: D
authors.lastname: Demurtas
authors.forename: Guillaume
authors.initials: G
authors.lastname: Witz
authors.forename: Julien
authors.initials: J
authors.lastname: Dorier
authors.forename: Todd
authors.initials: T
authors.lastname: Lillian
authors.forename: Edgar
authors.initials: E
authors.lastname: Meyhöfer
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D020285:Cryoelectron Microscopy; D004270:DNA, Circular / Q000737:chemistry* / Q000648:ultrastructure; D004706:Endodeoxyribonucleases; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical
chemical_list: D004270:DNA, Circular; D004706:Endodeoxyribonucleases; C038407:exonuclease Bal 31