title: Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics.
abstract: We report stopped-flow kinetics experiments to study the folding and unfolding of 5 base-pair stem and 21 nucleotide polythymidine loop DNA hairpins over various concentrations of NaCl. The reactions occurred on a time scale of milliseconds, considerably longer than the microsecond time scale suggested by previous kinetics studies of similar-sized hairpins. In comparison to a recent fluorescence correlation spectroscopy study (J. Am. Chem. Soc. 2006, 128, 1240-1249), we suggest the microsecond time-scale reactions are due to intermediate states and the millisecond time-scale reactions reported here are due to the formation of the fully folded DNA hairpin. These results support our view that DNA hairpin folding occurs via a minimum three-state mechanism.
authors.affiliation: Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
authors.forename: Rajesh K
authors.initials: RK
authors.lastname: Nayak
authors.forename: Olve B
authors.initials: OB
authors.lastname: Peersen
authors.forename: Kathleen B
authors.initials: KB
authors.lastname: Hall
authors.forename: Alan
authors.initials: A
authors.lastname: Van Orden
mesh_terms: D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D017510:Protein Folding; D012965:Sodium Chloride / Q000737:chemistry; D013997:Time Factors
chemical_list: D012965:Sodium Chloride; D004247:DNA