Structural characterization of naturally occurring RNA single mismatches
Structural characterization of naturally occurring RNA single mismatches
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DOI：
10.1093/nar/gkq793
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发表时间：
2011-02-01
影响因子：
14.9
通讯作者：
Znosko, Brent M.
中科院分区：
文献类型：
--
作者：
Davis, Amber R.;Kirkpatrick, Charles C.;Znosko, Brent M.
众所周知，RNA参与了几个细胞过程；然而，它只有在折叠成正确的三维构象时才有活性。RNA分子的折叠、弯曲和扭曲依赖于大量的规范和非规范二级结构基序。这些基序有助于RNA的结构复杂性，但也具有重要的整体生物学功能，例如作为其他生物分子或小配体的识别和结合位点。最常见的RNA二级结构基序类型之一是单错配，当两个规范对被单个非规范对分开时发生。为了确定序列-结构关系并确定结构模式，我们系统地定位、注释和比较了30个最常见的单不匹配最近邻序列组合，这些序列组合是在实验确定的储存在蛋白质数据库中的含rna分子的3D结构中发现的。描述和比较了不匹配和最近邻碱基对的核苷酸边缘的氢键，堆叠和相互作用，从而确定了几种结构模式。这样的数据库和比较将使研究人员能够深入了解未研究序列的结构特征，并快速查找已研究的序列。
RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence-structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.