Self-powered RNA nanomachine driven by metastable structure
Self-powered RNA nanomachine driven by metastable structure
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DOI：
10.1093/nar/gkz364
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发表时间：
2019-05
影响因子：
14.9
通讯作者：
Shungo Kobori;Yoko Nomura;Y. Yokobayashi
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文献类型：
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作者：
Shungo Kobori;Yoko Nomura;Y. Yokobayashi
摘要许多非编码和调控RNA元件已经进化到利用转录过程中出现的瞬时或亚稳态结构来控制复杂的折叠途径或编码动态功能。然而，工程化合成RNA装置的努力主要集中在化学稳定的结构上。因此，在明确利用共转录产生的瞬时或亚稳态结构的工程化功能RNA中存在重大挑战和机遇。在这项工作中，我们设计了一个短的RNA序列，采用了强大的亚稳态结构时，由RNA聚合酶转录。虽然亚稳结构在低温下持续数小时，但在热变性后冷却时，它几乎完全重新折叠成热稳定结构。合成的RNA还配备有花椰菜适体，使得其可以结合其配体并且仅在化学稳定的结构中变得荧光。我们进一步证明，弛豫的药物稳定和荧光结构可以催化由短触发RNA在一个序列特异性的方式。最后，重新设计RNA架构以感知和响应微小RNA序列。总之，我们设计了RNA纳米机器，可以检测RNA序列，放大信号并产生光学输出，所有这些都编码在单个RNA转录物中，由亚稳态结构自供电。
Abstract Many non-coding and regulatory RNA elements have evolved to exploit transient or metastable structures that emerge during transcription to control complex folding pathways or to encode dynamic functions. However, efforts to engineer synthetic RNA devices have mostly focused on the thermodynamically stable structures. Consequently, significant challenges and opportunities exist in engineering functional RNAs that explicitly take advantage of cotranscriptionally generated transient or metastable structures. In this work, we designed a short RNA sequence that adopts a robust metastable structure when transcribed by an RNA polymerase. Although the metastable structure persists for hours at low temperature, it refolds almost completely into the thermodynamically stable structure upon heat denaturation followed by cooling. The synthetic RNA was also equipped with the Broccoli aptamer so that it can bind its ligand and become fluorescent only in the thermodynamically stable structure. We further demonstrated that the relaxation to the thermodynamically stable and fluorescent structure can be catalyzed by a short trigger RNA in a sequence-specific manner. Finally, the RNA architecture was redesigned to sense and respond to microRNA sequences. In summary, we designed RNA nanomachines that can detect an RNA sequence, amplify signal and produce an optical output, all encoded in a single RNA transcript, self-powered by a metastable structure.