Near-Infrared Fluorogenic RNA for In vivo Imaging and Sensing. 

Chen,Z.#; Chen,W.#; Xu,C.#; Song,H.; Ji，X.; Jiang,H.; Duan,H.; Li,Z.; Gao,W.; Yao,T.; Zhang,Z.; He,L.; Yin,Y.; Yang,N.; Tian,W.; Wu,J.; Li,X.* 

Nature Communications, 2025

https://www.nature.com/articles/s41467-024-55093-1 

Abstract

Fluorogenic RNA aptamers have various applications, including use as a fluorescent tag 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.