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

Lin, Milo M. and Meinhold, Lars and Shorokhov, Dmitry and Zewail, Ahmed H. (2008) Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes. Physical Chemistry Chemical Physics, 10 (29). pp. 4227-4239. ISSN 1463-9076. PMCID PMC2548322. http://resolver.caltech.edu/CaltechAUTHORS:LINpccp08

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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1039/b804675cDOIArticle
http://pubs.rsc.org/en/Content/ArticleLanding/2008/CP/b804675cPublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2548322/PubMed CentralArticle
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.
Funders:
Funding AgencyGrant Number
NSFUNSPECIFIED
NIHRO1-GM081520-01
Krell InstituteUNSPECIFIED
Department of Energy (DOE)DE-FG02-97ER25308
Issue or Number:29
PubMed Central ID:PMC2548322
Record Number:CaltechAUTHORS:LINpccp08
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:LINpccp08
Official Citation:Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes Milo M. Lin, Lars Meinhold, Dmitry Shorokhov and Ahmed H. Zewail Phys. Chem. Chem. Phys., 2008,10, 4227-4239 DOI: 10.1039/B804675C
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11370
Collection:CaltechAUTHORS
Deposited By: Archive Administrator
Deposited On:08 Aug 2008 18:47
Last Modified:05 Aug 2016 19:17

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