NCIR: a database of non-canonical interactions in known RNA structures

The secondary and tertiary structure of an RNA molecule typically includes a number of non-canonical base–base interactions. The known occurrences of these interactions are tabulated in the NCIR database, which can be accessed from http://prion.bchs.uh.edu/bp_type/. The number of examples is now over 1400, which is an increase of >700% since the database was first published. This dramatic increase reflects the addition of data from the recently published crystal structures of the 50S (2.4 Å) and 30S (3.0 Å) ribosomal subunits. In addition, non-canonical interactions observed in published crystal and NMR structures of tRNAs, group I introns, ribozymes, RNA aptamers and synthetic oligonucleotides are included. Properties associated with these interactions, such as sequence context, sugar pucker conformation, glycosidic angle conformation, melting temperature, chemical shift and free energy, are also reported when available. Out of the 29 anticipated pairs with at least two hydrogen bonds, 28 have been observed to date. In addition, several novel examples, not generally predicted, have also been encountered, bringing the total of such pairs to 36. Added to this list are a variety of single, bifurcated, triple and quadruple interactions. The most common non-canonical pairs are the sheared GA, GA imino, AU reverse Hoogsteen, and the GU and AC wobble pairs. The most frequent triple interaction connects N3 of an A with the amino of a G that is also involved in a standard Watson–Crick pair.

RNA分子的二级与三级结构通常包含多种非经典碱基-碱基相互作用（non-canonical base–base interactions）。此类相互作用的已知实例已被整理收录于NCIR数据库（NCIR database），可通过访问地址http://prion.bchs.uh.edu/bp_type/ 获取。目前该数据库收录的实例数量已突破1400条，自首次发布以来增幅超过700%。这一显著增长主要得益于新增了近期解析的50S（分辨率2.4 Å）与30S（分辨率3.0 Å）核糖体亚基的晶体结构数据。此外，数据库还收录了已发表的tRNA、I型内含子、核酶、RNA适配体以及合成寡核苷酸的晶体结构与核磁共振（NMR）结构中观测到的非经典相互作用。当相关属性数据可获取时，还会一并报告此类相互作用的相关参数，包括序列上下文、糖环折叠构象（sugar pucker conformation）、糖苷键角构象（glycosidic angle conformation）、解链温度、化学位移以及自由能等。在预期的29种至少包含两个氢键的碱基对中，截至目前已有28种被观测证实。此外，研究人员还发现了若干通常难以预测的新型实例，使得这类碱基对的总数增至36种。该列表还补充了多种单碱基相互作用、分叉相互作用、三重相互作用与四重相互作用。最常见的非经典碱基对包括剪切型GA对、GA亚氨基对、AU反向Hoogsteen对，以及GU与AC摆动（wobble）对。最为常见的三重相互作用为：一个腺嘌呤（A）的N3位点与同时参与标准Watson-Crick配对的鸟嘌呤（G）的氨基位点形成的相互作用。