Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India.
Surface Chemistry and Catalysis: Characterisation and Application Team (COK-KAT), Leuven (Arenberg) Celestijnenlaan 200f─Box 2461, 3001 Leuven, Belgium.
J Phys Chem B. 2023 Jul 13;127(27):6049-6060. doi: 10.1021/acs.jpcb.3c02268. Epub 2023 Jun 27.
Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.
转录后修饰碱基在涉及 RNA 的许多生化过程中发挥着重要作用。分析这些碱基在 RNA 中的非共价相互作用对于提供更完整的 RNA 结构和功能理解至关重要；然而，这些相互作用的特征仍然研究不足。为了解决这一限制，我们对涉及大量高分辨率 RNA 晶体结构中最具生物学相关性的修饰碱基的所有晶体学出现的碱基堆积进行了全面分析。同时，我们使用已建立的工具对堆积接触进行了几何分类。结合量子化学计算和这些堆积的特定结构背景分析，这为 RNA 中修饰碱基的堆积构象提供了一个图谱。总的来说，我们的分析有望促进对改变的 RNA 碱基的结构研究。
