Dresden 2014 – scientific programme

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BP: Fachverband Biologische Physik

BP 2: DNA/RNA and related enzymes

BP 2.3: Talk

Monday, March 31, 2014, 10:00–10:15, ZEU 250

Insights into the thermodynamic profile of "mutated" Cytosine rich DNA strands: A theoretical study — •Vasileios Tatsis and Andreas Heuer — Institut für Physikalische Chemie, Münster, Germany

Cytosine rich DNA sequences form four stranded structures (i-motif) under acidic conditions. The i-motif is an intercalated structure formed by association in a head to tail orientation of two parallel duplexes whose strands are held together by hemiprotonated Cytosine·Cytosine(+) pairs. Our theoretical work examines how point defects in the central strands and variations of the Cytosine sequences’ length affect the thermodynamical stability of the i-motif structure. We employ the fully atomistic Molecular Dynamics method with an explicit solvent model. We use as an initial structure for the "mutations" a single stranded deprotonated DNA i-motif. Furthermore, in order to enhance the conformational sampling and to compute the thermodynamic stability of the new "mutated" i-motif structures, we use the Metadynamics and the Steered Molecular Dynamics techniques. The output from this theoretical study is compared with experimental results derived from CD-experiments.