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Published August 7, 2008 | Published + Cover Image
Journal Article Open

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes


A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 s predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

Additional Information

This journal is © the Owner Societies 2008. Received 18th March 2008, Accepted 6th May 2008. First published on the web 3rd June 2008. We are grateful to the National Science Foundation and National Institutes of Health (NIH grant # RO1-GM081520-01) for funding of this research. MML acknowledges financial support from the Krell Institute and the US Department of Energy (DoE grant # DE-FG02-97ER25308) for a graduate fellowship at Caltech.

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