ArticleNucleic acids research2015
Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 84 citations in OpenAlex.
- Application of Pepper aptamer-based reporter system for bacterial transcription studies.Archives of microbiology · 2026Article
- Nucleotide flipping correlates with fluorescence activation in the RhoBAST imaging platform.Nature communications · 2026Article
- Imaging of endogenous RNA in live cells using sequence-activated fluorescent RNA probes.Nucleic acids research · 2025Article
- Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA.Nature chemical biology · 2024Article
- Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs.Nucleic acids research · 2024Article
- Structure-based insights into fluorogenic RNA aptamers.Acta biochimica et biophysica Sinica · 2024Review
- Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives.Biosensors · 2024Review
- Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.Nature communications · 2024Article
- Establishing Riboglow-FLIM to visualize noncoding RNAs inside live zebrafish embryos.Biophysical reports · 2023Article
- Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging in live cells.Nature methods · 2023Article
- Biogenic Imaging Contrast Agents.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Review
- Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging.Nature communications · 2023Article
- Avidity-based bright and photostable light-up aptamers for single-molecule mRNA imaging.Nature chemical biology · 2023Article
- Structure-based investigation of fluorogenic Pepper aptamer.Nature chemical biology · 2021Article
- A Color-Shifting Near-Infrared Fluorescent Aptamer-Fluorophore Module for Live-Cell RNA Imaging.Angewandte Chemie (International ed. in English) · 2021Article
- Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics.Nature biotechnology · 2021Article
- Review
- Rational Design of Allosteric Fluorogenic RNA Sensors for Cellular Imaging.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Following the messenger: Recent innovations in live cell single molecule fluorescence imaging.Wiley interdisciplinary reviews. RNA · 2020Review
- RNA-based fluorescent biosensors for live cell imaging of small molecules and RNAs.Current opinion in biotechnology · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In order to gain deeper insight into the functions and dynamics of RNA in cells, the development of methods for imaging multiple RNAs simultaneously is of paramount importance. Here, we describe a modular approach to image RNA in living cells using an RNA aptamer that binds to dinitroaniline, an efficient general contact quencher. Dinitroaniline quenches the fluorescence of different fluorophores when directly conjugated to them via ethylene glycol linkers by forming a non-fluorescent intramolecular complex. Since the binding of the RNA aptamer to the quencher destroys the fluorophore-quencher complex, fluorescence increases dramatically upon binding. Using this principle, a series of fluorophores were turned into fluorescent turn-on probes by conjugating them to dinitroaniline. These probes ranged from fluorescein-dinitroaniline (green) to TexasRed-dinitroaniline (red) spanning across the visible spectrum. The dinitroaniline-binding aptamer (DNB) was generated by in vitro selection, and was found to bind all probes, leading to fluorescence increase in vitro and in living cells. When expressed in E. coli, the DNB aptamer could be labelled and visualized with different-coloured fluorophores and therefore it can be used as a genetically encoded tag to image target RNAs. Furthermore, combining contact-quenched fluorogenic probes with orthogonal DNB (the quencher-binding RNA aptamer) and SRB-2 aptamers (a fluorophore-binding RNA aptamer) allowed dual-colour imaging of two different fluorescence-enhancing RNA tags in living cells, opening new avenues for studying RNA co-localization and trafficking.
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