The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids
The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids
复制标题
结合使用计算机辅助结构预测和 SHAPE 探测来阐明五种类病毒的二级结构。
DOI：
10.1111/j.1364-3703.2011.00776.x
复制
发表时间：
2012-09-01
影响因子：
4.9
通讯作者：
Perreault, Jean-Pierre
中科院分区：
文献类型：
--
作者：
Xu, Wenxing;Bolduc, Francois;Perreault, Jean-Pierre
类病毒，非编码感染性RNA物种的结构的阐明，是至关重要的，以获得其生命周期的各个方面的理解（包括复制，运输和发病机制）。一般而言，已使用计算机软件程序预测类病毒的二级结构，这些程序已被证明具有几个重要的局限性。显然，类病毒的预测结构在用于任何机理研究的准确解释之前需要得到物理支持。在这里，SHAPE探测耦合到计算机辅助的结构预测使用RNAstructure软件程序被用来确定五个类病毒的结构。这些物种属于四个属的Pospiviroidae家庭，并没有他们的结构特点的解决方案。此外，通过研究各种序列变体或改变SHAPE条件来解决几个有趣的问题。更重要的是，这种方法在类病毒的研究中是新颖的，并且应该在确定其他RNA种类的结构方面具有重要的帮助。
The elucidation of the structures of viroids, noncoding infectious RNA species, is paramount to obtain an understanding of the various aspects of their life cycles (including replication, transport and pathogenesis). In general, the secondary structures of viroids have been predicted using computer software programs which have been shown to possess several important limitations. Clearly, the predicted structure of a viroid needs to receive physical support prior to its use in the accurate interpretation of any mechanistic studies. Here, SHAPE probing coupled to computer-assisted structure prediction using the RNAstructure software program was employed to determine the structures of five viroids. These species belong to four genera of the Pospiviroidae family, and none have had their structure characterized in solution. In addition, several interesting questions were addressed by either studying various sequence variants or varying the SHAPE conditions. More importantly, this approach is novel in the study of viroids, and should be of significant aid in the determination of the structures of other RNA species.