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.

中文翻译：

---

结合结构化d-RNA分子的l-DNA适体的体外选择。

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中的主要挑战。以前，我们显示了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，与1-RNA相比具有多个实际优势的，由1-DNA组成的适体是否能够获得类似的RNA结合特性仍是未知的。在这里，我们报道了针对结构化的RNA分子前体microRNA-155的第一个l-DNA适体的发现和表征，从而建立了反手性的DNA和RNA分子形成紧密而特异性的“跨手性”相互作用的能力彼此。尽管l-DNA无法通过Watson-Crick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，1-DNA适体抑制Dicer介导的pre-miRNA-155的加工。1-DNA适体的序列和结构与先前报道的针对pre-miR-155的1-RNA适体不同，表明1-DNA和1-RNA通过独特的识别方式与相同的RNA序列相互作用。总体而言，这项工作表明，可以使用l-DNA替代l-RNA来生成RNA结合适体，从而为靶向结构化RNA提供了可靠而实用的方法。1-DNA适体的序列和结构与先前报道的针对pre-miR-155的1-RNA适体不同，表明1-DNA和1-RNA通过独特的识别方式与相同的RNA序列相互作用。总体而言，这项工作表明，可以使用l-DNA替代l-RNA来生成RNA结合适体，从而为靶向结构化RNA提供了可靠而实用的方法。1-DNA适体的序列和结构与先前报道的针对pre-miR-155的1-RNA适体不同，表明1-DNA和1-RNA通过独特的识别方式与相同的RNA序列相互作用。总体而言，这项工作表明，可以使用l-DNA替代l-RNA来生成RNA结合适体，从而为靶向结构化RNA提供了可靠而实用的方法。