Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence.
Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence.
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DOI：
10.1093/nar/gkj463
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发表时间：
2006
影响因子：
14.9
通讯作者：
Perreault JP
中科院分区：
文献类型：
--
作者：
Nehdi A;Perreault JP
为了重温抗基因组丁型肝炎病毒(HDV)核酶催化中心的结构，我们开发了一种无偏见的体外选择程序，该程序可以从相对较小的序列集中有效地选择新的变异体。使用这一程序，我们检查了HDV核酶池中的所有可能的变种，这些核酶在25个位置被随机排列(425个)。分离的一组序列比自然变异体表现出更多的可变性。在所有随机位置都发现了核苷酸变异，甚至在一般认为特定碱基是催化活性绝对必需的位置上也是如此。协变分析支持几个碱基对的存在，尽管它没有提出任何新的三级接触。就能够支持催化切割的序列而言，HDV核酶似乎比其他催化RNA具有更多的限制条件。这支持这样一种观点，即这种催化RNA结构的出现概率很低(即，这是一种罕见的事件)，这可能解释了为什么迄今为止只在HDV中发现了这种催化RNA结构。这与锤头自分裂基序形成对比，锤头自裂基序被认为有多个来源，而且在不同的有机体中广泛存在。因此，仅仅因为自分裂的RNA基序很小并不意味着它很容易发生。
In order to revisit the architecture of the catalytic center of the antigenomic hepatitis delta virus (HDV) ribozyme we developed an unbiased in vitro selection procedure that efficiently selected novel variants from a relatively small set of sequences. Using this procedure we examined all possible variants from a pool of HDV ribozymes that had been randomized at 25 positions (425). The isolated set of sequences shows more variability than do the natural variants. Nucleotide variations were found at all randomized positions, even at positions when the general belief was that the specific base was absolutely required for catalytic activity. Covariation analysis supports the presence of several base pairs, although it failed to propose any new tertiary contacts. HDV ribozyme appears to possess a greater number of constraints, in terms of sequences capable of supporting the catalysed cleavage, than do other catalytic RNAs. This supports the idea that the appearance of this catalytic RNA structure has a low probability (i.e. is a rare event), which may explain why to date it has been found in nature only in the HDV. These contrasts with the hammerhead self-cleaving motif that is proposed to have multiple origins, and that is widespread among different organisms. Thus, just because a self-cleaving RNA motif is small does not imply that it occurs easily.