Jaeger Luc, Verzemnieks Erik J, Geary Cody
Chemistry and Biochemistry Department, University of California, Santa Barbara, CA 93106-9510, USA.
Nucleic Acids Res. 2009 Jan;37(1):215-30. doi: 10.1093/nar/gkn911. Epub 2008 Nov 26.
Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5'XU/AN(n)X3'). It consists of a U:A Watson-Crick: Hoogsteen trans base pair stacked over a classic Watson-Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.
稳定RNA是模块化且具有层次结构的三维架构，利用反复出现的结构基序形成广泛的非共价三级相互作用。序列和原子结构分析揭示了一种新型亚基序，它由一组最少的五个核苷酸组成，称为UA_handle基序（5'XU/AN(n)X3'）。它由一个U:A沃森-克里克:霍格steen反式碱基对堆叠在一个经典的沃森-克里克碱基对上，以及一个由一个或多个核苷酸组成的凸起，该凸起可作为进行不同类型远程相互作用的柄。这个基序是在稳定RNA中发现的最通用的构建模块之一。它参与了许多结构更复杂的反复出现的基序的组成，如T环、11个核苷酸的受体、UAA/GAN和G-核糖基序。我们的分析得出了一些与RNA基序相关的结构原理。一组有限的基本亚基序可以解释核糖体RNA和稳定RNA中发现的大多数结构基序的形成。尽管序列和结构存在差异，但结构基序可以作为结构支架，在功能和拓扑上是等效的。由这些RNA基序共享的结构关系产生的序列网络可作为一种原始语言，用于辅助RNA三级结构的预测和合理设计。
