ArticleRNA (New York, N.Y.)2021
Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Article in RNA (New York, N.Y.), 2021. 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.
- Article
- DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure.Briefings in bioinformatics · 2026Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling.Nature communications · 2025Article
- Deep generative design of RNA aptamers using structural predictions.Nature computational science · 2024Article
- Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.Nature communications · 2024Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.Proteins · 2023Article
- RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair.Nucleic acids research · 2023Article
- Red light-emitting short Mango-based system enables tracking a mycobacterial small noncoding RNA in infected macrophages.Nucleic acids research · 2023Article
- FRET Based Biosensor: Principle Applications Recent Advances and Challenges.Diagnostics (Basel, Switzerland) · 2023Review
- Characterizing Fluorescence Properties of Turn-on RNA Aptamers.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Reconsidering theACS bio & med chem Au · 2022Article
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
- The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.Nature chemical biology · 2022Article
- An uncommon [KRNA (New York, N.Y.) · 2021Article
- RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds.Nature chemistry · 2021Article
- The emerging structural complexity of G-quadruplex RNAs.RNA (New York, N.Y.) · 2021Review
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10 authors.
Funding
Abstract
To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.
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