Issue 29, 2008

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

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

Article information

Article type
Paper
Submitted
18 Mar 2008
Accepted
06 May 2008
First published
03 Jun 2008

Phys. Chem. Chem. Phys., 2008,10, 4227-4239

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

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements