title: Bubble dynamics in double-stranded DNA.
abstract: We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Altan-Bonnet
authors.forename: Albert
authors.initials: A
authors.lastname: Libchaber
authors.forename: Oleg
authors.initials: O
authors.lastname: Krichevsky
mesh_terms: D004247:DNA / Q000737:chemistry*; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence; D013696:Temperature; D013816:Thermodynamics
chemical_list: D005456:Fluorescent Dyes; D004247:DNA