Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.
J Phys Chem A. 2022 Mar 10;126(9):1518-1529. doi: 10.1021/acs.jpca.1c10905. Epub 2022 Feb 24.
Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its p value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the p values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the p values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the p values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.
修饰碱基存在于 RNA 的功能重要区域，并且常常负责重要的结构作用。这些修饰碱基中的许多在自然界中是动态调节的，每种修饰都在 RNA 中具有不同的生物学作用。尽管修饰碱基的丰度很高，但它们的许多特性仍然知之甚少。碱基的一个重要性质是其 p 值，它已被广泛研究用于未修饰的碱基，但不适用于修饰版本。在这项研究中，通过使用 B3LYP 密度泛函和 6-31+G(d,p)基组以及隐式-显式溶剂化系统的组合进行从头量子力学计算来确定修饰碱基的 p 值。该方法之前被用于确定未修饰碱基的 p 值，可适用于各种修饰碱基。修饰碱基的 p 值比较可以深入了解它们在核酸中的结构和能量影响。
