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Near-infrared fluorogenic RNA for in vivo imaging and sensing

Chen Zhenyin,Chen Wei,Xu Cun,Song Haozhi,Ji Xin,Jiang Haodong,Duan Hongtao,Li Zehao,Gao Wankai,Yao Tuoxin,Zhang Zhongxuan,He Liuqin,Yin Yulong,Yang Nanyang,Tian Wenjing,Wu Jiahui,Li Xing

Fluorogenic RNA aptamers have various applications, including use as fluorescent tags for imaging RNA trafficking and as indicators of RNA-based sensors that exhibit fluorescence upon binding small-molecule fluorophores in living cells. Current fluorogenic RNA:fluorophore complexes typically emit visible fluorescence. However, it is challenging to develop fluorogenic RNA with near-infrared (NIR) fluorescence for in vivo imaging and sensing studies. To address this issue, we identify and modulate red fluorescent protein-like fluorophores to bind Squash, a highly folded fluorogenic RNA. One of these fluorophores, DFQL-1T, exhibits photostable NIR fluorescence when bound to Squash, enabling RNA visualization in living mammalian cells and mice. With Squash:DFQL-1T complexes, we generate RNA-based sensors for detecting non-coding RNAs and small molecule targets in living mammalian cells and in mice. These studies reveal a fluorogenic RNA:fluorophore complex that can be readily developed into NIR fluorescent RNA tags for in vivo imaging and sensing.