Functionalization of RNA conformational switch focusing on co-transcriptional transition of nascent RNA structure

在这项研究中，我们将RNA构象开关功能化，以构建生物传感器和基因调控系统，重点关注亚稳态RNA结构，它是在转录过程中通过共转录折叠形成的。我们从由新霉素适配子和TAR-RNA组成的随机核苷酸序列连接的文库中筛选出对新霉素有反应的构象变化的RNA。然后，基于所选择的RNA的二级结构，我们合理地设计了对硫胺素焦磷酸(TPP)反应的RNA构象开关。该RNA通过新生RNA结构的共转录转变，在转录过程中检测到TPP。我们还设计了RNA，将其结构从共转录折叠形成的亚稳定二级结构转变为最稳定的四链结构。细胞内基因的表达依赖于构象转换的速率。

In this study, we functionalized RNA conformational switch for constructing biosensors and gene regulation systems by focusing on metastable RNA structure, which is formed by co-transcriptional folding during transcription. We selected RNAs, which show conformational transition in response to neomycin, from a library consists of neomycin aptamer and TAR-RNA connected by random nucleotides sequence. Then, based on a secondary structure of the selected RNA, we rationally designed RNA conformational switch that responds to thiamine pyrophosphate (TPP). The RNA enabled detection of TPP during transcription through co-transcriptional transition of nascent RNA structure. We also designed RNAs, which transition its structure from metastable secondary structure formed by co-transcriptional folding to most stable quadruplex structure. Intracellular gene expression depended on the rate of the conformation transition.