ArticleChemistry & biology2015
In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies.
Article in Chemistry & biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
What it found
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Who cites it
103 citing papers in PubMed, 194 citations in OpenAlex.
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- Phosphoarginine modulates oligomerization and repressor activity of mycobacterial ClpC2.bioRxiv : the preprint server for biology · 2026Article
- Lifetime-based multiplexed detection of viral RNA using fluorogenic aptamers.bioRxiv : the preprint server for biology · 2026Article
- Programmable, target-induced fluorogenic CRISPR-tDeg platform for live-cell RNA visualization.Nucleic acids research · 2026Article
- Programmable and Switchable RNA Scaffolds for Synthetic Condensate Engineering in Mammalian Cells.bioRxiv : the preprint server for biology · 2026Article
- Expression of nano-engineered RNA organelles in bacteria.Nature communications · 2026Article
- A Nonviral Neo-Nucleocapsid for Cell-Specific RNA Delivery Developed by Pseudo-Cyclic Peptide Grafting and Directed Evolution.Angewandte Chemie (International ed. in English) · 2026Article
- Mechanism and reconstitution of circadian transcription in cyanobacteria.Nature structural & molecular biology · 2026Article
- Orthogonal RNA-regulated destabilization domains for three-color RNA imaging with minimal RNA perturbation.Nature methods · 2026Article
- Scaffolding Light-Up Aptamers on DNA Nanostructures for Fluorescence Enhancement.ACS biomaterials science & engineering · 2025Article
- Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.RNA (New York, N.Y.) · 2025Article
- Loading of Extracellular Vesicles with Nucleic Acids via Hybridization with Non-Lamellar Liquid Crystalline Lipid Nanoparticles.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells.Journal of the American Chemical Society · 2025Article
- Near-infrared fluorogenic RNA for in vivo imaging and sensing.Nature communications · 2025Article
- Live-Cell Imaging of mRNA Using a Pepper RNA Tag.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Artificial dynamic structure ensemble-guided rational design of a universal RNA aptamer-based sensing tag.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Super-Resolved Protein Imaging Using Bifunctional Light-Up Aptamers.Angewandte Chemie (International ed. in English) · 2024Article
- Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
RNA aptamers can be expressed in cells to influence and image cellular processes. Aptamer folding is maintained by inserting the aptamers into highly structured RNA scaffolds. Here, we show that commonly used RNA scaffolds exhibit unexpected instability and cleavage in bacterial and mammalian cells. Using an in-gel staining approach for rapid and simple detection of Spinach- or Broccoli-tagged RNAs in cells, we monitored the processing of RNAs tagged with scaffolded aptamers, revealing endonucleolytic cleavage, RNA instability, and poor expression. We reengineered a natural three-way junction structure to generate an alternative scaffold that enables stable aptamer expression in cells. This scaffold was used to create cassettes containing up to four Broccoli units, markedly enhancing the brightness of mammalian cells expressing cassette-tagged RNAs. These experiments describe methods for screening RNA cleavage events in cells and identify cell-compatible scaffolds that enable efficient tagging of RNAs with aptamers for cellular expression.
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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.