Regensburg 2013 – scientific programme
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BP: Fachverband Biologische Physik
BP 15: DNA/RNA and related enzymes
BP 15.4: Talk
Tuesday, March 12, 2013, 13:00–13:15, H43
Deprotonation mechanism and the unfolding free energy landscape of a DNA i-motif — •Jens Smiatek1 and Andreas Heuer2 — 1Institut für Computerphysik, Universität Stuttgart, Germany — 2Institut für Physikalische Chemie, WWU Münster, Germany
We present the results of atomistic Molecular Dynamics simulations of a single-stranded protonated DNA i-motif. We are able to determine the full unfolding and deprotonation mechanism by using a Metadynamics approach. The release of protons which form the stabilizing hemiprotonated cytidine pairs can be identified as a two-step process which is obligatory for a partial unfolding of the i-motif into a hairpin structure. The shape of the free energy landscape indicates the native configuration as the global energetic minimum with a free energy barrier of roughly 9 kcal/mol which validates the significant stability of the i-motif in acidic solution. We further present a kinetic model for the unfolding process in good agreement to experimental results.