Dresden 2017 – scientific programme

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BP: Fachverband Biologische Physik

BP 58: DNA & RNA

BP 58.1: Talk

Friday, March 24, 2017, 09:30–09:45, ZEU 250

Interactions between a short DNA oligonucleotide and urea in the light of Kirkwood-Buff theory: a Molecular Dynamics simulation study — •Ewa Anna Oprzeska-Zingrebe and Jens Smiatek — Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany

In nature, a wide range of biological processes, such as transcription termination or intermolecular binding, is dependent on the formation of specific DNA secondary and tertiary structures. These structures can be both stabilized or destabilized by the osmolytes, coexisting with the nucleic acids in the cellular environment. In our study, we investigate a simple 7-nucleotide DNA hairpin with the sequence d(GCGAAGC) in the presence of varying concentrations of urea.

The interaction between DNA and urea in unbiased molecular dynamics simulations has been analysed according to Kirkwood-Buff theory. We implemented the local/bulk partitioning model, complemented by the analysis of preferential hydration and preferential interaction coefficients, to get insight into the distribution of the cosolute in the vicinity of the DNA oligonucleotide. The free energy landscape of unfolding has been approached via Metadynamics upon the addition of a bias potential. This study allows us to get a more comprehensive understanding of the stability of the DNA structures in the presence of urea.