Berlin 2015 – scientific programme

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BP: Fachverband Biologische Physik

BP 25: Posters: DNA/RNA and related enzymes

BP 25.5: Poster

Tuesday, March 17, 2015, 14:00–16:00, Poster A

Uncovering the structural stability and unfolding pathway of a 7-bp DNA hairpin through high-temperature molecular dynamics simulation — •Ewa Anna Oprzeska-Zingrebe and Jens Smiatek — Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany

The formation of specific DNA secondary and tertiary structures have been reported to play a key role in various range of biological processes, such as transcription termination or intermolecular binding. Among them, a pivotal role has been ascribed to DNA i-Motif and G-Quadruplex structures, which due to their biological appearance in telomeric and centromeric DNA are considered as potential targets for various diseases. Recent studies on high-temperature unfolding simulations of the DNA i-Motifs have revealed the existence of the stable hairpin configurations as an intermediate step in the unfolding pathway of DNA higher-order structures. In our study, we investigate simple 7-nucleotide DNA hairpin structures with the sequence d(GCGAAGC) and its variations. Through high-temperature molecular dynamics simulation we intend to get insight into the stability of the DNA hairpins and the possible unfolding pathways. In addition, the unfolding free energy landscape of DNA hairpins will be analyzed such that sequential differences can be energetically evaluated. This serves as the first approach to unravel the complex nature of G-Quadruplex folding pathway and behavior.