ArticleNature chemical biology2022
The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.
Article in Nature chemical biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 39 citations in OpenAlex.
- Honeydew: A Fluorescent Aptamer for Low-Cost Azo Food Dyes.Chembiochem : a European journal of chemical biology · 2026Article
- Lighting Up Endogenous RNA: Fluorescent Aptamer Sensors for Live-Cell Imaging.Chemical & biomedical imaging · 2026Review
- Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.Nucleic acids research · 2025Article
- Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.Nucleic acids research · 2025Article
- Biochemical Characterization of a Non-G4-Type RNA Aptamer That Lights Up a GFP-like Fluorogenic Ligand.Molecules (Basel, Switzerland) · 2025Article
- A Small-Molecule Approach Enables RNA Aptamers to Function as Sensors for Reactive Inorganic Targets.Angewandte Chemie (International ed. in English) · 2025Article
- Near-infrared fluorogenic RNA for in vivo imaging and sensing.Nature communications · 2025Article
- Structure-based insights into fluorogenic RNA aptamers.Acta biochimica et biophysica Sinica · 2024Review
- Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD.Nucleic acids research · 2024Article
- Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives.Biosensors · 2024Review
- Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.Nature communications · 2024Article
- Fluorogenic CRISPR for genomic DNA imaging.Nature communications · 2024Article
- RNA structure determination: From 2D to 3D.Fundamental research · 2023Review
- Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.Nature communications · 2023Article
- Structure-based investigations of the NAD+-II riboswitch.Nucleic acids research · 2023Article
- Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells.RNA biology · 2023Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.
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