Berlin 2018 – scientific programme

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BP: Fachverband Biologische Physik

BP 9: Postersession I

BP 9.12: Poster

Monday, March 12, 2018, 17:30–19:30, Poster A

Preferential binding of urea to single-stranded DNA structures: 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, depend on the formation of specific DNA secondary and tertiary structures. These structures can be both stabilized or destabilized by different co-solutes, coexisting with nucleic acids in the cellular environment. In our molecular dynamics simulation study, we investigate the binding of urea at different concentrations to short 7-nucleotide single-stranded DNA structures in aqueous solution. The local concentration of urea around native DNA hairpin in comparison to an unfolded DNA conformation is analyzed by preferential binding model in the light of Kirkwood-Buff theory. All our findings indicate a pronounced accumulation of urea around DNA, which is driven by a combination of electrostatic and dispersion interactions and accomplished by a significant replacement of water molecules in terms of a dehydration effect. The outcomes of our study can be regarded as a first step into a deeper mechanistic understanding towards co-solute-induced effects on nucleotide structures in general.