ArticleNature communications2023
Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 17 citations in OpenAlex.
- Fluorogenic RNA aptamers in cancer: emerging platforms for molecular imaging, biosensing, and precision oncology.Molecular biology reports · 2026Review
- Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.International journal of molecular sciences · 2026Article
- Article
- Topological rules and anomalies in intramolecular G-quadruplex folding: a comprehensive study.Nucleic acids research · 2026Article
- Development of an RNA aptamer-assisted CRISPR/Cas9 system for efficiently generating and isolating Cas9-free mutants in plant.PLoS genetics · 2025Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.Biophysical reviews · 2024Review
- 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
- Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization.Proceedings of the National Academy of Sciences of the United States of America · 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
- Evaluating Riboglow-FLIM probes for RNA sensing.RSC chemical biology · 2024Article
- G-quadruplex formation in RNA aptamers selected for binding to HIV-1 capsid.Frontiers in chemistry · 2024Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.
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