title: Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.
abstract: The classical view of DNA posits that DNA must be stiff below the persistence length [<150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the annealed species sampled in the traditional ligase-based assay. The looping rate has a weak length dependence between 67 and 106 bp that cannot be described by the worm-like chain model. Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Reza
authors.initials: R
authors.lastname: Vafabakhsh
authors.forename: Taekjip
authors.initials: T
authors.lastname: Ha
mesh_terms: D001360:Avidin / Q000737:chemistry; D001483:Base Sequence; D001710:Biotin / Q000737:chemistry; D003500:Cyclization; D004270:DNA, Circular / Q000737:chemistry*; D005453:Fluorescence; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D009690:Nucleic Acid Conformation; D011092:Polyethylene Glycols / Q000737:chemistry
chemical_list: D004270:DNA, Circular; C093483:neutravidin; D001360:Avidin; D011092:Polyethylene Glycols; D001710:Biotin