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Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics
Rajesh K Nayak1, Olve B Peersen, Kathleen B Hall
1Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA.
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.
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