Near-infrared fluorogenic RNA for in vivo imaging and sensing
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.
Authors
- Hongtao Duan (ORCID: https://orcid.org/0000-0002-1985-2292)
- Zhenyin Chen (ORCID: https://orcid.org/0000-0002-1118-1690)
- Caihong Xu
- Zhongxuan Zhang (ORCID: https://orcid.org/0000-0003-2367-9805)
- Xin Ji (ORCID: https://orcid.org/0000-0002-7903-5497)
- Wenjing Tian (ORCID: https://orcid.org/0000-0001-5766-8050)
- Jiahui Wu (ORCID: https://orcid.org/0000-0003-2406-6728)
- Haodong Jiang (ORCID: https://orcid.org/0000-0001-6760-5336)
- Liuqin He (ORCID: https://orcid.org/0000-0003-1184-6944)
- Wei Chen (ORCID: https://orcid.org/0000-0003-3233-8877)
- Xing Li (ORCID: https://orcid.org/0000-0003-3149-9783)
- Yulong Yin (ORCID: https://orcid.org/0000-0001-6112-6975)
- Tao Yao (ORCID: https://orcid.org/0000-0001-8699-8294)
- Zehao Li (ORCID: https://orcid.org/0000-0003-0008-194X)
- Wankai Gao
- Nanyang Yang (ORCID: https://orcid.org/0000-0001-9883-8386)
- Haozhi Song
Institutions
- Central South University (CN)
- Hunan Normal University (CN)
- Jilin University (CN)
- Chinese Academy of Sciences (CN)
- University of Massachusetts Amherst (US)
- Affiliated Hospital of Southwest Medical University (CN)
- Institute of Subtropical Agriculture (CN)
- Institute of Zoology (KZ)
- Hengyang Academy of Agricultural Sciences (CN)
- Institute of Chemistry (CN)
- Yueyang Changling Equipment Research Institute (China) (CN)
- University of Chinese Academy of Sciences (CN)
- Institute of Zoology (CN)
- Hebei University (CN)
- State Key Laboratory of Supramolecular Structure and Materials
- University of South China (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-01-09
- DOI
- https://doi.org/10.1038/s41467-024-55093-1
- Citations
- 22
- Primary Topic
- RNA and protein synthesis mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 17.73
Funders
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- Natural Science Foundation of Hunan Province
- University of Massachusetts Amherst
- Institute of Zoology, Chinese Academy of Sciences