A Landscape Model of DNA Hairpin Kinetics

Milo Lin, California Institute of Technology

A 2D free-energy landscape model is presented to describe the unfolding transition of hairpins together with molecular dynamics simulations and experimental findings. The dependence of the unfolding 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 simulations 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 unzipping is, in general, not a two-state process.

Abstract Author(s): Milo M. Lin<br />Lars Meinhold<br />Dmitry Shorokhov<br />Ahmed H. Zewail