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 Type
poster
Primary Author
Milo Lin
University
California Institute of Technology
Abstract Title
A Landscape Model of DNA Hairpin Kinetics
Abstract Author(s)
Milo M. Lin<br />Lars Meinhold<br />Dmitry Shorokhov<br />Ahmed H. Zewail
Username
lin
Fellowship Year
2007
First Name
Milo
Last Name
Lin
Program
CSGF
Area of Study
Physics
Poster Group
Group 2
Poster Number
46