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

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.

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Cruz-León, Sergio1, 2, Author              
Vázquez-Mayagoitia, Alvarao3, Author
Melchionna, Simone4, Author
Schwierz, Nadine1, Author              
Fyta, Maria2, Author
Affiliations:
1Emmy Noether Research Group, Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2364691              
2Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany, ou_persistent22              
3Argonne National Laboratory, 9700 S. Cass Avenue, Building 240, Argonne, Illinois, United States, ou_persistent22              
4Dipartimento di Fisica, ISC-CNR, Istituto Sistemi Complessi, Università Sapienza, P.le A. Moro 2, 00185 Rome, Italy, ou_persistent22              

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 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.

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Language(s): eng - English
 Dates: 2018-04-152018-07-252018-07-252018-08-16
 Publication Status: Published in print
 Pages: 14
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1021/acs.jpcb.8b03566
 Degree: -

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Title: The Journal of Physical Chemistry B
  Other : J. Phys. Chem. B
Source Genre: Journal
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Publ. Info: Washington, D.C. : American Chemical Society
Pages: - Volume / Issue: 122 (32) Sequence Number: - Start / End Page: 7915 - 7928 Identifier: ISSN: 1520-6106
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000293370_1