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

doi:10.1021/ja208490w

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

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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 language	English
Pages (from-to)	2453-2456
Number of pages	4
Journal	Journal of the American Chemical Society
Volume	134
Issue number	5
DOIs	https://doi.org/10.1021/ja208490w
State	Published - Feb 8 2012

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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.",

author = "Nayak, {Rajesh K.} and Peersen, {Olve B.} and Hall, {Kathleen B.} and {Van Orden}, Alan",

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AU - Nayak, Rajesh K.

AU - Peersen, Olve B.

AU - Hall, Kathleen B.

AU - Van Orden, Alan

PY - 2012/2/8

Y1 - 2012/2/8

N2 - 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.

AB - 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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EP - 2456

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

IS - 5

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

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