title: Working the kinks out of nucleosomal DNA.
abstract: Condensation of DNA in the nucleosome takes advantage of its double-helical architecture. The DNA deforms at sites where the base pairs face the histone octamer. The largest so-called kink-and-slide deformations occur in the vicinity of arginines that penetrate the minor groove. Nucleosome structures formed from the 601 positioning sequence differ subtly from those incorporating an AT-rich human α-satellite DNA. Restraints imposed by the histone arginines on the displacement of base pairs can modulate the sequence-dependent deformability of DNA and potentially contribute to the unique features of the different nucleosomes. Steric barriers mimicking constraints found in the nucleosome induce the simulated large-scale rearrangement of canonical B DNA to kink-and-slide states. The pathway to these states shows nonharmonic behavior consistent with bending profiles inferred from AFM measurements.
authors.affiliation: Rutgers- The State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854-8087, USA. wilma.olson@rutgers.edu
authors.forename: Wilma K
authors.initials: WK
authors.lastname: Olson
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D009707:Nucleosomes; D004247:DNA