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• W3128783928 endingPage "106551" @default.
• W3128783928 startingPage "106551" @default.
• W3128783928 abstract "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." @default.
• W3128783928 created "2021-02-15" @default.
• W3128783928 creator A5015559679 @default.
• W3128783928 creator A5021741207 @default.
• W3128783928 creator A5085726797 @default.
• W3128783928 date "2021-04-01" @default.
• W3128783928 modified "2023-10-18" @default.
• W3128783928 title "Salt dependent mesoscopic model for RNA at multiple strand concentrations" @default.
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• W3128783928 doi "https://doi.org/10.1016/j.bpc.2021.106551" @default.
• W3128783928 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33662903" @default.
• W3128783928 hasPublicationYear "2021" @default.
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