Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
Biophys Chem. 2021 Apr;271:106551. doi: 10.1016/j.bpc.2021.106551. Epub 2021 Jan 29.
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.
介观模型可用于描述 RNA 双链体的热力学性质。通过使用实验熔解温度对其进行参数化，可以深入了解氢键和堆积相互作用，这已经在高钠浓度下完成。然而，由于发表的熔解温度数据有限，对于较低盐浓度的 RNA 参数化仍然缺失。虽然 Peyrard-Bishop (PB) 参数化被发现基本上与链浓度无关，但它要求所有温度都在相同的链浓度下提供。在这里，我们对 PB 模型进行了修改以处理多个链浓度，并且我们能够使用一组实验温度来模拟低浓度和中等浓度的钠离子的氢键和堆积相互作用。对于参数化，我们区分了末端和内部碱基对，并且得到的势能与我们之前为 DNA 获得的势能定性相似。与 DNA 参数的主要区别在于，低钠浓度下末端 r(AU)的 Morse 势更强于 d(AT)，这表明氢键强度更高。
