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Issue 29, 2008
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Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

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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 μs 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.

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

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Publication details

The article was received on 18 Mar 2008, accepted on 06 May 2008, published on 03 Jun 2008 and first published online on 03 Jun 2008


Article type: Paper
DOI: 10.1039/B804675C
Citation: Phys. Chem. Chem. Phys., 2008,10, 4227-4239
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    Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes

    M. M. Lin, L. Meinhold, D. Shorokhov and A. H. Zewail, Phys. Chem. Chem. Phys., 2008, 10, 4227
    DOI: 10.1039/B804675C

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