Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA.
J Mol Biol. 2012 Nov 23;424(1-2):54-67. doi: 10.1016/j.jmb.2012.09.012. Epub 2012 Sep 18.
The right angle (RA) motif, previously identified in the ribosome and used as a structural module for nano-construction, is a recurrent structural motif of 13 nucleotides that establishes a 90° bend between two adjacent helices. Comparative sequence analysis was used to explore the sequence space of the RA motif within ribosomal RNAs in order to define its canonical sequence space signature. We investigated the sequence constraints associated with the RA signature using several artificial self-assembly systems. Thermodynamic and topological investigations of sequence variants associated with the RA motif in both minimal and expanded structural contexts reveal that the presence of a helix at the 3' end of the RA motif increases the thermodynamic stability and rigidity of the resulting three-helix junction domain. A search for the RA in naturally occurring RNAs as well as its experimental characterization led to the identification of the RA in groups IC1 and ID intron ribozymes, where it is suggested to play an integral role in stabilizing peripheral structural domains. The present study exemplifies the need of empirical analysis of RNA structural motifs for facilitating the rational design and structure prediction of RNAs.
直角（RA）基序先前在核糖体中被发现，并被用作纳米构建的结构模块，它是一个由 13 个核苷酸组成的重复结构基序，在两个相邻的螺旋之间建立 90°的弯曲。比较序列分析被用于探索核糖体 RNA 中 RA 基序的序列空间，以定义其规范的序列空间特征。我们使用几种人工自组装系统研究了与 RA 特征相关的序列约束。与 RA 基序相关的序列变体在最小和扩展结构环境中的热力学和拓扑研究表明，RA 基序 3'端处的螺旋的存在增加了所得的三螺旋连接域的热力学稳定性和刚性。对自然发生的 RNA 中的 RA 的搜索及其实验表征导致了在 IC1 和 ID 内含子核酶中 RA 的鉴定，据推测它在稳定外围结构域中起着不可或缺的作用。本研究说明了对 RNA 结构基序进行经验分析以促进 RNA 的合理设计和结构预测的必要性。
