In vitro selection of L-DNA aptamers that bind a structured D-RNA molecule
In vitro selection of L-DNA aptamers that bind a structured D-RNA molecule
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DOI：
10.1093/nar/gkz1236
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发表时间：
2020-02-28
影响因子：
14.9
通讯作者：
Sczepanski, Jonathan T.
中科院分区：
文献类型：
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作者：
Dey, Sougata;Sczepanski, Jonathan T.
结构特异性RNA结合试剂的开发仍然是RNA生物化学和药物发现的核心挑战。以前，我们表明体外选择技术可用于进化与结构化D-RNA紧密结合的L-RNA适体。然而，使用由L-DNA组成的适体是否可以实现类似的RNA结合特性仍然是未知的，与L-RNA相比，L-DNA具有几个实际优势。在这里，我们报告了第一个L-DNA适体对结构化RNA分子（前体microRNA-155）的发现和表征，从而建立了DNA和RNA分子的反手性能力，以形成紧密和特定的“交叉手性”相互作用。尽管L-DNA不能通过沃森-克里克碱基配对与天然D-RNA相互作用，但L-DNA适体以低纳摩尔亲和力和高选择性结合pre-miR-155。此外，L-DNA适体抑制Dicer介导的pre-miRNA-155加工。L-DNA适体的序列和结构与先前报道的针对pre-miR-155的L-RNA适体不同，表明L-DNA和L-RNA通过独特的识别模式与相同的RNA序列相互作用。总体而言，这项工作表明，L-DNA可以作为L-RNA的替代品，用于产生RNA结合适体，为靶向结构化RNA提供了一种强大而实用的方法。
The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve L-RNA aptamers that bind tightly to structured D-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of L-DNA, which has several practical advantages compared to L-RNA, remains unknown. Here, we report the discovery and characterization of the first L-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific 'cross-chiral' interactions with each other. L-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of L-DNA to interact with native D-RNA via Watson- Crick base pairing. Furthermore, L-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of L-DNA aptamers are distinct from previously reported L-RNA aptamers against pre-miR-155, indicating that L-DNA and L-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that L-DNA may be pursued as an alternative to L-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.