Non-canonical base pairs and higher order structures in nucleic acids: Crystal structure database analysis
Non-canonical base pairs and higher order structures in nucleic acids: Crystal structure database analysis
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DOI：
10.1080/07391102.2006.10507108
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发表时间：
2006-10-01
影响因子：
4.4
通讯作者：
Bhattacharyya, Dhananjay
中科院分区：
文献类型：
--
作者：
Das, Jhuma;Mukherjee, Shayantani;Bhattacharyya, Dhananjay
非正则碱基对，主要存在于RNA中，通常在保持其结构多样性方面发挥着重要作用。像碱基三联体这样的高阶结构在定义和稳定RNA的三级折叠结构方面也很重要。我们开发了一个新的程序BPFIND来分析不同类型的正则和非正则碱基对和碱基三元组，这些碱基对和碱基三元组中至少有两个直接氢键形成在碱基或糖的O_2‘之间。我们考虑了104种可能的碱基对，其中87种碱基对类型的例子被发现出现在可用的RNA晶体结构中。分析表明，在功能RNA结构中，约有32.7%的碱基对是非规范的，其中包括不同类型的GA和GU摆动碱基对，以及广泛的碱基对可能性。我们进一步注意到，超过10.4%的碱基对参与了三联体的形成，其中大多数在RNA的三维折叠结构中起着维持远程三级接触的重要作用。除了检测之外，该程序还给出了与理想平面碱基对相比，所检测碱基对的构象变形的定量估计。这有助于我们深入了解它们结构变化的程度，从而有助于理解它们对结构和功能多样性的具体作用。
Non-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintaining their structural diversity. Higher order structures like base triples are also important in defining and stabilizing the tertiary folded structure of RNA. We have developed a new program BPFIND to analyze different types of canonical and non-canonical base pairs and base triples involving at least two direct hydrogen bonds formed between polar atoms of the bases or sugar O2' only. We considered 104 possible types of base pairs, out of which examples of 87 base pair types are found to occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% base pairs in the functional RNA structures are non-canonical, which include different types of GA and GU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed that more than 10.4% of these base pairs are involved in triplet formation, most of which play important role in maintaining long-range tertiary contacts in the three-dimensional folded structure of RNA. Apart from detection, the program also gives a quantitative estimate of the conformational deformation of detected base pairs in comparison to an ideal planar base pair. This helps us to gain insight into the extent of their structural variations and thus assists in understanding their specific role towards structural and functional diversity.