ArticleNucleic acids research2017
Use of Baby Spinach and Broccoli for imaging of structured cellular RNAs.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 59 citations in OpenAlex.
- Lighting Up Biology: GFP-Inspired Fluorescent Probes for Sensing and Imaging.Journal of the American Chemical Society · 2026Article
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.Chemical & biomedical imaging · 2026Review
- Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing.Nature biotechnology · 2026Article
- Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement.ACS biomaterials science & engineering · 2025Article
- Bright and pH-sensitive Baby Spinach aptamer with RNA triplex fusion.Nucleic acids research · 2025Article
- 1000 fold Ultra-Photosensitized Fluorescent Protein Mimics Toward Photocatalytic Proximity Labeling and Proteomic Profiling Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Challenges in observing transcription-translation for bottom-up synthetic biology.QRB discovery · 2025Review
- Aptamer-based assay for high-throughput substrate profiling of RNA decapping enzymes.Nucleic acids research · 2024Article
- Structure-based insights into fluorogenic RNA aptamers.Acta biochimica et biophysica Sinica · 2024Review
- A Prebiotic Genetic Nucleotide as an Early Darwinian Ancestor for Pre-RNA Evolution.ACS omega · 2024Article
- Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA.Frontiers in molecular biosciences · 2022Article
- Review
- Photophysics of DFHBI bound to RNA aptamer Baby Spinach.Scientific reports · 2021Article
- In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects.Molecules (Basel, Switzerland) · 2021Review
- Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques.Analytical chemistry · 2021Review
- Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription.Nature biomedical engineering · 2020Article
- Nucleic-Acid Structures as Intracellular Probes for Live Cells.Advanced materials (Deerfield Beach, Fla.) · 2020Review
- Development of encoded Broccoli RNA aptamers for live cell imaging of alphavirus genomic and subgenomic RNAs.Scientific reports · 2020Article
- Nanomechanics and co-transcriptional folding of Spinach and Mango.Nature communications · 2019Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorogenic RNA aptamers provide a powerful tool for study of RNA analogous to green fluorescent protein for the study of proteins. Spinach and Broccoli are RNAs selected in vitro or in vivo respectively to bind to an exogenous chromophore. They can be genetically inserted into an RNA of interest for live-cell imaging. Spinach aptamer has been altered to increase thermal stability and stabilize the desired folding. How well these fluorogenic RNA aptamers behave when inserted into structured cellular RNAs and how aptamer properties might be affected remains poorly characterized. Here, we report a study of the performance of distinct RNA Spinach and Broccoli aptamer sequences in isolation or inserted into the small subunit of the bacterial ribosome. We found that the ribosomal context helped maintaining the yield of the folded Baby Spinach aptamer; other versions of Spinach did not perform well in the context of ribosomes. In vivo, two aptamers clearly stood out. Baby Spinach and Broccoli aptamers yielded fluorescence levels markedly superior to all previous Spinach sequences including the super-folder tRNA scaffolded tSpinach2. Overall, the results suggest the use of Broccoli and Baby Spinach aptamers for live cell imaging of structured RNAs.
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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.