Analysis of Four-Way Junctions in RNA Structures
Analysis of Four-Way Junctions in RNA Structures
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DOI：
10.1016/j.jmb.2009.04.084
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发表时间：
2009-07-17
影响因子：
5.6
通讯作者：
Schlick, Tamar
中科院分区：
文献类型：
--
作者：
Laing, Christian;Schlick, Tamar
RNA二级结构可以分为由典型的沃森-克里克和相关碱基对组成的螺旋区域，以及单链区域，如发夹环，内环和接头。这些元件在细胞中具有各种基本功能的各种RNA分子的设计中起构建块的作用。为了更好地理解三维（3D）RNA的复杂结构，我们分析了现有的RNA四向连接的碱基对相互作用和3D配置。具体来说，我们确定了九个广泛的交界家庭根据同轴堆叠模式和螺旋配置。我们发现，在路口内的螺旋往往安排在大致平行和垂直的模式，并稳定其构象使用常见的三级图案，如同轴堆叠，环螺旋相互作用，螺旋包装的相互作用。我们的分析还揭示了一些高度保守的碱基对相互作用模式和新的三级图案，如A-小调同轴堆叠组合和八叠菌素/蓖麻毒素基序变体。这种对RNA构建模块的分析最终可以帮助完成RNA 3D结构预测的艰巨任务。(C)2009爱思唯尔有限公司保留所有权利。
RNA secondary structures can be divided into helical regions composed of canonical Watson-Crick and related base pairs, as well as single-stranded regions such as hairpin loops, internal loops, and junctions. These elements function as building blocks in the design of diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze existing RNA four-way junctions in terms of base-pair interactions and 3D configurations. Specifically, we identify nine broad junction families according to coaxial stacking patterns and helical configurations. We find that helices within junctions tend to arrange in roughly parallel and perpendicular patterns and stabilize their conformations using common tertiary motifs such as coaxial stacking, loop-helix interaction, and helix packing interaction. Our analysis also reveals a number of highly conserved base-pair interaction patterns and novel tertiary motifs such as A-minor-coaxial stacking combinations and sarcin/ricin motif variants. Such analyses of RNA building blocks can ultimately help in the difficult task of RNA 3D structure prediction. (C) 2009 Elsevier Ltd. All rights reserved.