The non-Watson-Crick base pairs and their associated isostericity matrices
The non-Watson-Crick base pairs and their associated isostericity matrices
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DOI：
10.1093/nar/gkf481
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发表时间：
2002-08-15
影响因子：
14.9
通讯作者：
Westhof, E
中科院分区：
文献类型：
--
作者：
Leontis, NB;Stombaugh, J;Westhof, E
RNA 分子表现出复杂的结构，其中大部分碱基参与非沃森-克里克碱基配对，形成介导长程 RNA-RNA 相互作用并为蛋白质和小分子配体创建结合位点的基序。原子分辨率的三维 RNA 结构数量迅速增长，要求数据库包含此类碱基对的注释。最近提出了一种明确且描述性的命名法，其中根据参与相互作用的碱基边缘（Watson-Crick、Hoogsteen/CH 或糖边缘）和糖苷键相对于氢键的方向（顺式或反式）对 RNA 碱基对进行分类。确定了 12 个基本几何族，并且所有 12 个几何族都已在晶体结构中观察到。对于每个碱基配对家族，我们在此提出 4 x 4“等排矩阵”，总结了四个标准碱基 A、C、G 和 U 的 16 个成对组合之间的几何关系。只要有可能，就会提供从 X 射线晶体结构（3.0 埃分辨率或更高）观察到的每个碱基对的代表性示例，或者提供理论上合理的模型。这种格式使观察到的重复几何图案变得明显，并有助于识别同源分子序列中共变或互换的等排对，同时保持保守的三维图案。
RNA molecules exhibit complex structures in which a large fraction of the bases engage in non-Watson-Crick base pairing, forming motifs that mediate long-range RNA-RNA interactions and create binding sites for proteins and small molecule ligands. The rapidly growing number of three-dimensional RNA structures at atomic resolution requires that databases contain the annotation of such base pairs. An unambiguous and descriptive nomenclature was proposed recently in which RNA base pairs were classified by the base edges participating in the interaction (Watson-Crick, Hoogsteen/CH or sugar edge) and the orientation of the glycosidic bonds relative to the hydrogen bonds (cis or trans). Twelve basic geometric families were identified and all 12 have been observed in crystal structures. For each base pairing family, we present here the 4 x 4 'isostericity matrices' summarizing the geometric relationships between the 16 pairwise combinations of the four standard bases, A, C, G and U. Whenever available, a representative example of each observed base pair from X-ray crystal structures (3.0 Angstrom resolution or better) is provided or, otherwise, theoretically plausible models. This format makes apparent the recurrent geometric patterns that are observed and helps identify isosteric pairs that co-vary or interchange in sequences of homologous molecules while maintaining conserved three-dimensional motifs.