title: Effect of sequence-dependent rigidity on plectoneme localization in dsDNA.
abstract: We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled double-stranded DNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test our results in vitro, and discuss the possible role played by plectoneme localization in the search process of transcription factors for their targets (promoter regions) on the bacterial genome.
authors.affiliation: Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Shlomi
authors.initials: S
authors.lastname: Medalion
authors.affiliation: Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Rabin
mesh_terms: D001483:Base Sequence; D004278:DNA, Superhelical / Q000737:chemistry*; D008956:Models, Chemical; D015394:Molecular Structure; D009010:Monte Carlo Method
chemical_list: D004278:DNA, Superhelical