ArticleNature methods2023
Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- A miniature bioluminescent platform for imaging structured RNAs.bioRxiv : the preprint server for biology · 2026Article
- Application of Pepper aptamer-based reporter system for bacterial transcription studies.Archives of microbiology · 2026Article
- A G-Quadruplex-Activated Near-Infrared Chemiluminescent Probe for In Situ Hepatic Imaging of the Hepatitis C Virus Genome.Angewandte Chemie (International ed. in English) · 2026Article
- Lighting Up Biology: GFP-Inspired Fluorescent Probes for Sensing and Imaging.Journal of the American Chemical Society · 2026Article
- Live-cell imaging of RNA dynamics using bright and stable fluorescent RNAs.Nature protocols · 2026Review
- Honeydew: A Fluorescent Aptamer for Low-Cost Azo Food Dyes.Chembiochem : a European journal of chemical biology · 2026Article
- Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform.Nature communications · 2026Article
- Molecular rotor-based probes for protein monitoring in biomedical research.Nature reviews. Chemistry · 2026Review
- NirFAP680: a highly bright and stable large Stokes shift near-infrared fluorogen-activating protein.Nature methods · 2026Article
- An orthogonal RNA aptamer for targeted RNA regulation in phase-separated subcellular compartments.Nature communications · 2026Article
- Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.Chemical & biomedical imaging · 2026Review
- RNA-stabilized coat proteins for sensitive and simultaneous imaging of distinct single mRNAs in live cells.Nature methods · 2026Article
- Visualizing intracellular glycine with two-dye and single-dye ratiometric RNA-based sensors.Nucleic acids research · 2025Article
- A twisted chromophore powers a turn-on fluorescent protein chloride sensor.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- In Situ Assembly of Fluorogenic RNA for Screening Natural Anti-Liver Fibrosis Products via Dynamic Visualization of COL1A1 mRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Continuous in situ synthesis of a complete set of tRNAs sustains steady-state translation in a recombinant cell-free system.Nature communications · 2025Article
- Peri-centrosomal localization of small interfering RNAs in C. elegans.Science China. Life sciences · 2025Article
- 1000 fold Ultra-Photosensitized Fluorescent Protein Mimics Toward Photocatalytic Proximity Labeling and Proteomic Profiling Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Phase separation of hnRNPA1 and TERRA regulates telomeric stability.Journal of molecular cell biology · 2025Article
- Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes.Nucleic acids research · 2025Article
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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