Journal Article

Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells

Chen, Xianjun, Fang, Mengyue, Zhu, Linyong, Yu, Jingwei, Lin, Qiuning, Yang, Lipeng, Zhang, Bibi, Huang, Xinyi, Li, Huiwen, Zeng, Qingmei, Huang, Kaiyi, Ren, Aiming, Xu, Xiaochen, Liu, Renmei, Su, Ni, Zuo, Fangting, Jiang, Li, Chen, Zhengda, Zhao, Yuzheng, Bao, Bingkun, Zhang, Rui, Zhang, Dasheng, Xie, Xin, Yang, Yi

2023

Overview

Fluorescent RNAs, aptamers that bind and activate small fluorogenic dyes, have provided a particularly attractive approach to visualizing RNAs in live cells. However, the simultaneous imaging of multiple RNAs remains challenging due to a lack of bright and stable fluorescent RNAs with bio-orthogonality and suitable spectral properties. Here, we develop the Clivias, a series of small, monomeric and stable orange-to-red fluorescent RNAs with large Stokes shifts of up to 108 nm, enabling the simple and robust imaging of RNA with minimal perturbation of the target RNA’s localization and functionality. In combination with Pepper fluorescent RNAs, the Clivias enable the single-excitation two-emission dual-color imaging of cellular RNAs and genomic loci. Clivias can also be used to detect RNA–protein interactions by bioluminescent imaging both in live cells and in vivo. We believe that these large Stokes shift fluorescent RNAs will be useful tools for the tracking and quantification of multiple RNAs in diverse biological processes. The Clivias are a series of small, monomeric fluorescent RNAs that emit with a large Stokes shift in the orange–red. They enable multiplexed RNA imaging in live cells and BRET-based detection of protein–RNA interactions in mice.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/1647/1888/1493 / 631/1647/1888/1891 / 631/1647/245/2225 / 631/337/384 / 631/92/500 / Aptamers / Bioinformatics / Biological activity / Biological Microscopy / Biological Techniques / Bioluminescence / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Emission / Emissions / Fluorescence / Fluorine / Gene loci / Hydrocarbons / Imaging / Life Sciences / Ligands / Localization / Microscopy / Orthogonality / Perturbation / Protein interaction / Proteins / Proteomics / Ribonucleic acid / RNA / Transfer RNA