title: Supercoiling induces denaturation bubbles in circular DNA.
abstract: We present a theoretical framework for the thermodynamic properties of supercoiling-induced denaturation bubbles in circular double-stranded DNA molecules. We explore how DNA supercoiling, ambient salt concentration, and sequence heterogeneity impact on the bubble occurrence. An analytical derivation of the probability distribution to find multiple bubbles is derived and the relevance for supercoiled DNA discussed. We show that in vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs. Single DNA plasmid imaging experiments clearly demonstrate the existence of bubbles in free solution.
authors.affiliation: Department of Physics, Technical University of Munich, 85747 Garching, Germany.
authors.forename: Jae-Hyung
authors.initials: JH
authors.lastname: Jeon
authors.forename: Jozef
authors.initials: J
authors.lastname: Adamcik
authors.forename: Giovanni
authors.initials: G
authors.lastname: Dietler
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D020029:Base Pairing; D004278:DNA, Superhelical / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000378:metabolism; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D010957:Plasmids / Q000737:chemistry*
chemical_list: D004278:DNA, Superhelical; D004268:DNA-Binding Proteins