Berlin 2018 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 15: Postersession III

BP 15.53: Poster

Dienstag, 13. März 2018, 14:00–16:00, Poster B

Developing a coarse-grained potential for double-stranded RNA from quantum-mechanical calculations — •Sergio Cruz-León^{1, 2}, Álvaro Vázquez-Mayagoitia³, Nadine Schwierz², and Maria Fyta¹ — ¹Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany — ²Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany — ³Argonne National Laboratory, 9700 S. Cass Avenue, Building 240, Argonne, Illinois, USA

A coarse-grained model for double-stranded (ds) RNA is derived based on quantum mechanical calculations. Our model extends a previous work developed for dsDNA by accounting for chemical and structural differences between dsDNA and dsRNA. Our coarse-grained model is a four bead representation where the total energy is derived from a bottom up approach using density functional theory calculations. The interactions within dsRNA are divided into four physical meaningful terms: hydrogen bonding, stacking, backbone, and electrostatic interactions. Our coarse-grained model is able to successfully reproduce the dsRNA structure. The model predicts a persistence length in good agreement with reported experimental data in a broad range of salt concentrations. Overall, our coarse-grained model has the potential to extent the relevant time and length scales in dynamic simulations of dsRNA.