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BP: Fachverband Biologische Physik
BP 7: Poster I
BP 7.59: Poster
Montag, 23. März 2009, 17:45–20:00, P3
Force-induced unfolding of G-quadruplex — •Hui Li1, En-hua Cao2, and Thomas Gisler1 — 1Universität Konstanz, Fachbereich Physik, 78457 Konstanz, Germany — 2Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
Telomeric DNA sequences can form four-stranded (quadruplex) structures both in vivo and in vitro in presence of cations. However, the folding process of quadruplex is still a mystery and has so far not been accessible with conventional molecular dynamics (MD) simulation. In this publication we study the unfolding of a parallel G-quadruplex from human telomeric DNA by mechanical stretching using steered molecular dynamics (MD) simulation. We find that the force curves and unfolding processes are strongly dependent on the pulling sites. If the stretching springs are connected to the sugar backbone, the force curve shows a single peak and the unfolding can be regarded as a two-state transition. When the stretching springs are connected to the terminal nucleobases, the force curve shows two peaks indicating that unfolding proceeds through an intermediate state. The free energy profile for the base-pulling scenario computed from the force-extension curves using the Jarzinsky equation shows a shoulder which corresponds to the intermediate state. After releasing the force constraint, equilibrium simulations for 8 ns show that the molecule does not refold back to its original structure once it was stretched to the intermediate state. Folding pathways of parallel G-quadruplex are proposed according to the simulated structures.