ArticleNucleic acids research2023
RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Nucleic acid aptamers: new methods for selection, target validation, molecular diagnostics and therapeutics.Signal transduction and targeted therapy · 2026Review
- Scaffolds with optimized quaternary symmetry for de novo cryoEM structure determination of small RNAs.Nature methods · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- Article
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- RNA sample optimization for cryo-EM analysis.Nature protocols · 2025Review
- Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA.bioRxiv : the preprint server for biology · 2025Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.Biophysical reviews · 2024Review
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- Investigating the Effect of RNA Scaffolds on the Multicolor Fluorogenic Aptamer Pepper in Different Bacterial Species.ACS synthetic biology · 2024Article
- CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.Proteins · 2023Article
- RNA target highlights in CASP15: Evaluation of predicted models by structure providers.Proteins · 2023Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- Tumor targeting and therapeutic assessments of RNA nanoparticles carrying α9-nAChR aptamer and anti-miR-21 in triple-negative breast cancers.Molecular therapy. Nucleic acids · 2023Article
- Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing.International journal of molecular sciences · 2023Article
- RNA origami: design, simulation and application.RNA biology · 2023Review
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Cryogenic electron microscopy (cryo-EM) is a promising method for characterizing the structure of larger RNA structures and complexes. However, the structure of individual aptamers is difficult to solve by cryo-EM due to their low molecular weight and a high signal-to-noise ratio. By placing RNA aptamers on larger RNA scaffolds, the contrast for cryo-EM can be increased to allow the determination of the tertiary structure of the aptamer. Here we use the RNA origami method to scaffold two fluorescent aptamers (Broccoli and Pepper) in close proximity and show that their cognate fluorophores serve as donor and acceptor for FRET. Next, we use cryo-EM to characterize the structure of the RNA origami with the two aptamers to a resolution of 4.4 Å. By characterizing the aptamers with and without ligand, we identify two distinct modes of ligand binding, which are further supported by selective chemical probing. 3D variability analysis of the cryo-EM data show that the relative position between the two bound fluorophores on the origami fluctuate by only 3.5 Å. Our results demonstrate a general approach for using RNA origami scaffolds for characterizing small RNA motifs by cryo-EM and for positioning functional RNA motifs with high spatial precision.
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