Dresden 2011 – scientific programme

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BP: Fachverband Biologische Physik

BP 4: DNA \& DNA Enzymes

BP 4.5: Talk

Monday, March 14, 2011, 15:15–15:30, ZEU 260

Unfolding mechanisms and the free energy landscape of the DNA i-motif — •Jens Smiatek and Andreas Heuer — Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, D-48149 Münster, Germany

Since the discovery of the DNA i-motif, the formation and function of this specific structure has attracted broad interest. Actually the pH-dependent reversible folding/unfolding mechanism has been nowadays used in technological applications like in the construction of nanocontainers. We investigate the unfolding mechanism in high temperature unfolding simulations and characterized it in terms of its eigenvectors. Furthermore we present the results of Molecular Dynamics simulations for the free energy landscape for different reaction coordinates which has been computed by a generalized version of the metadynamics approach. Our results indicate that at room temperature the planar hairpin structure is more stable than the totally stretched chain.