title: Spontaneous sharp bending of DNA: role of melting bubbles.
abstract: The role of centrally located and distributed base pair mismatches ('melting bubbles') on localized bending and stiffness of short dsDNA fragments is evaluated using time-dependent fluorescence lifetime measurements. Distributed melting bubbles are found to induce larger bending angles and decreased levels of stiffness in DNA than centrally located ones of comparable overall size. Our results indicate that spontaneous local opening-up of the DNA duplex could facilitate sharp bending of short DNA strands even in the absence of DNA binding proteins. We also find that the occurrence of two closely spaced melting bubbles will generally be favored when a large energetic barrier must be overcome in forming the desired bent DNA structure.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Chongli
authors.initials: C
authors.lastname: Yuan
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Rhoades
authors.forename: Xiong Wen
authors.initials: XW
authors.lastname: Lou
authors.forename: Lynden A
authors.initials: LA
authors.lastname: Archer
mesh_terms: D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA