Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics

Rajesh K. Nayak, Olve B. Peersen, Kathleen B. Hall, Alan Van Orden

Research output: Contribution to journalArticlepeer-review

34 Scopus citations

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.

Original languageEnglish
Pages (from-to)2453-2456
Number of pages4
JournalJournal of the American Chemical Society
Volume134
Issue number5
DOIs
StatePublished - Feb 8 2012

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