Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs
Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs
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DOI：
10.1016/j.jmb.2004.09.072
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发表时间：
2004-12-10
影响因子：
5.6
通讯作者：
Gutell, RR
中科院分区：
文献类型：
--
作者：
Lee, JC;Gutell, RR
除了包括标准沃森-克里克（C：G和U：A）和摆动U：G构象的典型碱基对，在高分辨率的晶体结构的嗜热栖热菌30 S和Haloarcula marismortui 50 S核糖体亚基的rRNA中的碱基对类型和构象的分析已经确定了各种各样的非典型碱基对类型和构象。然而，现有的命名法并没有描述所有观察到的非典型构象或描述它们有一些歧义。因此，需要一个标准化的系统来对所有这些非典型构象进行适当的分类。在这里，我们提出了一个新的，简单的和系统的命名法，明确地分类碱基对构象发生在碱基对，碱基三联体和碱基四联体，与二级和三级相互作用。该系统基于给定碱基对中两个碱基和糖苷键的拓扑排列。规则二级结构螺旋内部位置的碱基对通常与规范碱基对组（C：G、U：A和U：G）和规范构象（C：G WC、U：A WC和U：G Wb）形成。相反，规则结构螺旋之外的非螺旋碱基对通常具有非规范碱基对组和构象。此外，许多非螺旋碱基对参与RNA基序，形成一组定义的非规范构象。因此，每一种罕见的非典型构象可能在功能和结构上都很重要。最后，基于拓扑的碱基对构象的等排性可以使RNA分子进化中的碱基对交换合理化。(C)2004爱思唯尔有限公司保留所有权利。
In addition to the canonical base-pairs comprising the standard Watson-Crick (C:G and U:A) and wobble U:G conformations, an analysis of the base-pair types and conformations in the rRNAs in the high-resolution crystal structures of the Thermus thermophilus 30 S and Haloarcula marismortui 50 S ribosomal subunits has identified a wide variety of noncanonical base-pair types and conformations. However, the existing nomenclatures do not describe all of the observed non-canonical conformations or describe them with some ambiguity. Thus, a standardized system is required to classify all of these non-canonical conformations appropriately. Here, we propose a new, simple and systematic nomenclature that unambiguously classifies base-pair conformations occurring in base-pairs, base-triples and base-quadruples that are associated with secondary and tertiary interactions. This system is based on the topological arrangement of the two bases and glycosidic bonds in a given base-pair. Base-pairs in the internal positions of regular secondary structure helices usually form with canonical base-pair groups (C:G, U:A, and U:G) and canonical conformations (C:G WC, U:A WC, and U:G Wb). In contrast, non-helical base-pairs outside of regular structure helices usually have non-canonical base-pair groups and conformations. In addition, many non-helical base-pairs are involved in RNA motifs that form a defined set of non-canonical conformations. Thus, each rare non-canonical conformation may be functionally and structurally important. Finally, the topology-based isostericity of base-pair conformations can rationalize base-pair exchanges in the evolution of RNA molecules. (C) 2004 Elsevier Ltd. All rights reserved.