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Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations

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Cruz-León,  Sergio
Emmy Noether Research Group, Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;
Institute for Computational Physics, Universität Stuttgart;

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Schwierz,  Nadine
Emmy Noether Research Group, Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Cruz-León, S., Vázquez-Mayagoitia, A., Melchionna, S., Schwierz, N., & Fyta, M. (2018). Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations. The Journal of Physical Chemistry B, 122(32), 7915-7928. doi:10.1021/acs.jpcb.8b03566.


Cite as: http://hdl.handle.net/21.11116/0000-0002-6890-6
Abstract
A coarse-grained model for simulating structural properties of double-stranded RNA is developed with parameters obtained from quantum-mechanical calculations. This model follows previous parametrization for double-stranded DNA, which is based on mapping the all-atom picture to a coarse-grained four-bead scheme. Chemical and structural differences between RNA and DNA have been taken into account for the model development. The parametrization is based on simulations using density functional theory (DFT) on separate units of the RNA molecule without implementing experimental data. The total energy is decomposed into four terms of physical significance: hydrogen bonding interaction, stacking interactions, backbone interactions, and electrostatic interactions. The first three interactions are treated within DFT, whereas the last one is included within a mean field approximation. Our double-stranded RNA coarse-grained model predicts stable helical structures for RNA. Other characteristics, such as structural or mechanical properties are reproduced with a very good accuracy. The development of the coarse-grained model for RNA allows extending the spatial and temporal length scales accessed by computer simulations and being able to model RNA-related biophysical processes, as well as novel RNA nanostructures.