Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
Architecture et Réactivité de l'ARN, UPR 9002, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 67084 Strasbourg, France.
Molecules. 2022 Jul 7;27(14):4365. doi: 10.3390/molecules27144365.
Z-DNA and Z-RNA have long appeared as oddities to nucleic acid scientists. However, their Z-step constituents are recurrently observed in all types of nucleic acid systems including ribosomes. Z-steps are NpN steps that are isostructural to Z-DNA CpG steps. Among their structural features, Z-steps are characterized by the presence of a lone pair…π contact that involves the stacking of the ribose O4' atom of the first nucleotide with the 3'-face of the second nucleotide. Recently, it has been documented that the CpG step of the ubiquitous r(UNCG) tetraloops is a Z-step. Accordingly, such r(UNCG) conformations were called Z-turns. It has also been recognized that an r(GAAA) tetraloop in appropriate conditions can shapeshift to an unusual Z-turn conformation embedding an ApA Z-step. In this report, we explore the multiplicity of RNA motifs based on Z-steps by using the WebFR3D tool to which we added functionalities to be able to retrieve motifs containing lone pair…π contacts. Many examples that underscore the diversity and universality of these motifs are provided as well as tutorial guidance on using WebFR3D. In addition, this study provides an extensive survey of crystallographic, cryo-EM, NMR, and molecular dynamics studies on r(UNCG) tetraloops with a critical view on how to conduct database searches and exploit their results.
Z-DNA 和 Z-RNA 长期以来一直被核酸科学家视为异类。然而，它们的 Z 步成分在包括核糖体在内的所有类型的核酸系统中都经常被观察到。Z 步是 NpN 步，与 Z-DNA CpG 步具有同构性。在它们的结构特征中，Z 步的特点是存在孤对……π接触，涉及第一个核苷酸的核糖 O4'原子与第二个核苷酸的 3'-面的堆叠。最近，已经有文献记录表明，普遍存在的 r(UNCG)四链体的 CpG 步是 Z 步。因此，这种 r(UNCG)构象被称为 Z 转弯。人们还认识到，在适当的条件下，r(GAAA)四链体可以构象转变为一种不寻常的 Z 转弯构象，其中嵌入一个 ApA Z 步。在本报告中，我们使用 WebFR3D 工具探索基于 Z 步的 RNA 基序的多样性，我们为其添加了能够检索包含孤对……π接触的基序的功能。提供了许多强调这些基序多样性和普遍性的示例，以及关于如何进行数据库搜索和利用其结果的教程指导。此外，本研究对 r(UNCG)四链体的晶体学、低温电镜、NMR 和分子动力学研究进行了广泛调查，并对如何进行数据库搜索和利用其结果提出了批判性看法。
