Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 10, Issue 29, Pages 4227-4239Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/b804675c
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Funding
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM081520] Funding Source: NIH RePORTER
- NIGMS NIH HHS [R01 GM081520-01, R01-GM081520-01, R01 GM081520] Funding Source: Medline
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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. ndings. 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 mu 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.
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