NCIR: a database of non-canonical interactions in known RNA structures
NCIR: a database of non-canonical interactions in known RNA structures
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DOI：
10.1093/nar/30.1.395
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发表时间：
2002-01-01
影响因子：
14.9
通讯作者：
Fox, GE
中科院分区：
文献类型：
--
作者：
Nagaswamy, U;Larios-Sanz, M;Fox, GE
RNA分子的二级和三级结构通常包括许多非典型的碱基-碱基相互作用。这些相互作用的已知发生率在NCIR数据库中列表，可从http://prion.bchs.uh.edu/bp_type/访问。样本数量现已超过1400个，自数据库首次发布以来增加了700%以上。这种急剧增加反映了最近发表的50 S（2.4埃）和30 S（3.0埃）核糖体亚基晶体结构数据的增加。此外，非典型的相互作用中观察到的发表晶体和核磁共振结构的tRNA，第一组内含子，核酶，RNA适体和合成的寡核苷酸也包括在内。与这些相互作用相关的性质，如序列背景，糖折叠构象，糖苷角构象，解链温度，化学位移和自由能，也报告时可用。在29个预期的至少有两个氢键的对中，迄今为止已经观察到28个。此外，还遇到了几个通常没有预测到的新例子，使此类对的总数达到36个。在这个列表中增加了各种单，分叉，三重和四重相互作用。最常见的非正则对是剪切GA、GA亚氨基、Au反向Hoogsteen以及GU和AC摆动对。最常见的三重相互作用将A的N3与G的氨基连接起来，G也参与标准的沃森-克里克对。
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 Angstrom) and 30S (3.0 Angstrom) 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.