ArticleNucleic acids research2023
Exploiting natural riboswitches for aptamer engineering and validation.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- Protein Nanocages as Versatile Vectors for Nucleic Acid Delivery: Main Systems and Their Loading Mechanisms.Molecular biotechnology · 2026Review
- Exploiting conformational changes in a caffeine aptamer to engineer synthetic RNA devices.Nucleic acids research · 2026Article
- Scaffolds with optimized quaternary symmetry for de novo cryoEM structure determination of small RNAs.Nature methods · 2026Article
- Programming Next-Generation Synthetic Biosensors by Genetic Circuit Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- Design of orthogonal and portable RNA devices for post-transcriptional regulation by reverse engineering type I toxin-antitoxin systems.Nucleic acids research · 2025Article
- Integration of the hammerhead ribozyme into structured RNAs to measure ligand-binding events for riboswitch candidates and aptamers.Acta biochimica et biophysica Sinica · 2025Article
- Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer.Nucleic acids research · 2025Article
- Rapid discovery of functional RNA domains.Nucleic acids research · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- gRNAde: Geometric Deep Learning for 3D RNA inverse design.bioRxiv : the preprint server for biology · 2025Article
- An Ultrahigh Affinity DNA Aptamer for Quinine and Its Intrinsic Fluorescence Based Label-Free Detection.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Examining the Relationship between Aptamer Complexity and Molecular Discrimination of a Low-Epitope Target.ACS central science · 2024Article
- Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives.Biosensors · 2024Review
- Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches.ACS chemical biology · 2024Article
- Programmable melanoma-targeted radio-immunotherapy via fusogenic liposomes functionalized with multivariate-gated aptamer assemblies.Nature communications · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- Single-Round Circular Aptamer Discovery Using Bioinspired Magnetosome-Like Magnetic Chain Cross-Linked Graphene Oxide.Research (Washington, D.C.) · 2024Article
- Genetically Encoded Biosensor Engineering for Application in Directed Evolution.Journal of microbiology and biotechnology · 2023Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Over the past three decades, researchers have found that some engineered aptamers can be made to work well in test tubes but that these same aptamers might fail to function in cells. To help address this problem, we developed the 'Graftamer' approach, an experimental platform that exploits the architecture of a natural riboswitch to enhance in vitro aptamer selection and accelerate in vivo testing. Starting with combinatorial RNA pools that contain structural features of a guanine riboswitch aptamer interspersed with regions of random sequence, we performed multiplexed in vitro selection with a collection of small molecules. This effort yielded aptamers for quinine, guanine, and caffeine that appear to maintain structural features of the natural guanine riboswitch aptamer. Quinine and caffeine aptamers were each grafted onto a natural guanine riboswitch expression platform and reporter gene expression was monitored to determine that these aptamers function in cells. Additionally, we determined the secondary structure features and survival mechanism of a class of RNA sequences that evade the intended selection strategy, providing insight into improving this approach for future efforts. These results demonstrate that the Graftamer strategy described herein represents a convenient and straightforward approach to develop aptamers and validate their in vivo function.
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Registered trials
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