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  3. Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA

Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA

  • Nat Chem Biol. 2024 May 23. doi: 10.1038/s41589-024-01629-x.
Fangting Zuo # 1 2,  Li Jiang # 3,  Ni Su # 1 2,  Yaqiang Zhang 1 2,  Bingkun Bao 3,  Limei Wang 1 2,  Yajie Shi 1,  Huimin Yang 1 2,  Xinyi Huang 3,  Ruilong Li 1,  Qingmei Zeng 3,  Zhengda Chen 1 2,  Qiuning Lin 3,  Yingping Zhuang 4,  Yuzheng Zhao 1 2 5,  Xianjun Chen 6 7 8,  Linyong Zhu 9 10,  Yi Yang 11 12
Affiliations

Affiliations

  • 1 Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
  • 2 Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
  • 3 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
  • 4 School of Bioengineering, East China University of Science and Technology, Shanghai, China.
  • 5 Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China.
  • 6 Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. xianjunchen@ecust.edu.cn.
  • 7 Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China. xianjunchen@ecust.edu.cn.
  • 8 Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China. xianjunchen@ecust.edu.cn.
  • 9 Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. linyongzhu@sjtu.edu.cn.
  • 10 School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. linyongzhu@sjtu.edu.cn.
  • 11 Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. yiyang@ecust.edu.cn.
  • 12 Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China. yiyang@ecust.edu.cn.
  • # Contributed equally.
PMID: 38783134 DOI: 10.1038/s41589-024-01629-x
Abstract

Fluorescent RNAs (FRs) provide an attractive approach to visualizing RNAs in live cells. Although the color palette of FRs has been greatly expanded recently, a green FR with high cellular brightness and photostability is still highly desired. Here we develop a fluorogenic RNA aptamer, termed Okra, that can bind and activate the fluorophore ligand ACE to emit bright green fluorescence. Okra has an order of magnitude enhanced cellular brightness than currently available green FRs, allowing the robust imaging of messenger RNA in both live Bacterial and mammalian cells. We further demonstrate the usefulness of Okra for time-resolved measurements of ACTB mRNA trafficking to stress granules, as well as live-cell dual-color superresolution imaging of RNA in combination with Pepper620, revealing nonuniform and distinct distributions of different RNAs throughout the granules. The favorable properties of Okra make it a versatile tool for the study of RNA dynamics and subcellular localization.

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