ArticleNature chemical biology2024
Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Article in Nature chemical biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- 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
- Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform.Nature communications · 2026Article
- NirFAP680: a highly bright and stable large Stokes shift near-infrared fluorogen-activating protein.Nature methods · 2026Article
- Advanced CRISPR Technologies for RNA Imaging in Live Cells.Chemical & biomedical imaging · 2026Review
- Advancing Single-Molecule Biophysics: Next-Generation Organic Fluorophores with Tailored Labeling Strategies.Chemical & biomedical imaging · 2025Review
- Near-infrared II cyanine fluorophores with large stokes shift engineered by regulating respective absorption and emission.Nature communications · 2025Article
- Structure-based insights into fluorogenic RNA aptamers.Acta biochimica et biophysica Sinica · 2024Review
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
RNA-based fluorogenic modules have revolutionized the spatiotemporal localization of RNA molecules. Recently, a fluorophore named 5-((Z)-4-((2-hydroxyethyl)(methyl)amino)benzylidene)-3-methyl-2-((E)-styryl)-3,5-dihydro-4H-imidazol-4-one (NBSI), emitting in red spectrum, and its cognate aptamer named Clivia were identified, exhibiting a large Stokes shift. To explore the underlying molecular basis of this unique RNA-fluorophore complex, we determined the tertiary structure of Clivia-NBSI. The overall structure uses a monomeric, non-G-quadruplex compact coaxial architecture, with NBSI sandwiched at the core junction. Structure-based fluorophore recognition pattern analysis, combined with fluorescence assays, enables the orthogonal use of Clivia-NBSI and other fluorogenic aptamers, paving the way for both dual-emission fluorescence and bioluminescence imaging of RNA molecules within living cells. Furthermore, on the basis of the structure-based substitution assay, we developed a multivalent Clivia fluorogenic aptamer containing multiple minimal NBSI-binding modules. This innovative design notably enhances the recognition sensitivity of fluorophores both in vitro and in vivo, shedding light on future efficient applications in various biomedical and research contexts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.