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Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

preprint
submitted on 22.11.2020, 22:21 and posted on 23.11.2020, 13:21 by Izabela Ferreira, Tauanne Dias Amarante, Gerald Weber
Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.

Funding

Fundação de Amparo à Pesquisa do Estado de Minas Gerais

Conselho Nacional de Desenvolvimento Científico de Tecnológico

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior

History

Email Address of Submitting Author

gweberbh@gmail.com

Institution

Universidade Federal de Minas Gerais

Country

Brazil

ORCID For Submitting Author

0000-0002-2935-1571

Declaration of Conflict of Interest

no conflict of interest

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