ArticleNucleic acids research2018
Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 75 citations in OpenAlex.
- Structure-guided engineering of an aptamer-PROTAC for targeted degradation of vaccinia-related kinase 1.Chemical science · 2026Article
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- Reagentless Real-Time ATP Monitoring with New DNA Aptamers.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Structural basis and affinity improvement for an ATP-binding DNA aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Engineering functionally-optimized aptamers against SARS-Cov-2 for blocking spike-ACE2 interaction and aptasensor detection.Materials today. Bio · 2025Article
- Dissociation Constant (KSmall methods · 2025Review
- Rapid nanomolar detection of cocaine in biofluids by electrochemical aptamer-based sensor with low-temperature effect for drugged driving screening.Mikrochimica acta · 2024Article
- Developing Aptamer-Based Colorimetric Opioid Tests.JACS Au · 2024Article
- Exploring the Landscape of Aptamers: From Cross-Reactive to Selective to Specific, High-Affinity Receptors for Cocaine.JACS Au · 2024Article
- High-Affinity Aptamers forJournal of the American Chemical Society · 2024Article
- Efforts toward the continuous monitoring of molecular markers of performance.Journal of science and medicine in sport · 2023Review
- High-throughput quantitative binding analysis of DNA aptamers using exonucleases.Nucleic acids research · 2023Article
- Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets.Biosensors · 2022Review
- Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules.Langmuir : the ACS journal of surfaces and colloids · 2022Article
- Using dual exonucleases to finely distinguish structural adjustment of aptamers for small-molecule detection.RSC advances · 2021Article
- A kinetically controlled platform for ligand-oligonucleotide transduction.Nature communications · 2021Article
- Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development.Angewandte Chemie (International ed. in English) · 2021Review
- Aptamer-Integrated Multianalyte-Detecting Paper Electrochemical Device.ACS applied materials & interfaces · 2021Article
- Immobilization Strategies for Enhancing Sensitivity of Electrochemical Aptamer-Based Sensors.ACS applied materials & interfaces · 2021Article
- Accelerating Post-SELEX Aptamer Engineering Using Exonuclease Digestion.Journal of the American Chemical Society · 2021Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
We report a broadly applicable enzyme digestion strategy for introducing structure-switching functionality into small-molecule-binding aptamers. This procedure is based on our discovery that exonuclease III (Exo III) digestion of aptamers is greatly inhibited by target binding. As a demonstration, we perform Exo III digestion of a pre-folded three-way-junction (TWJ)-structured cocaine-binding aptamer and a stem-loop-structured ATP-binding aptamer. In the absence of target, Exo III catalyzes 3'-to-5' digestion of both aptamers to form short, single-stranded products. Upon addition of target, Exo III digestion is halted four bases prior to the target-binding domain, forming a major target-bound aptamer digestion product. We demonstrated that target-binding is crucial for Exo III inhibition. We then determine that the resulting digestion products of both aptamers exhibit a target-induced structure-switching functionality that is absent in the parent aptamer, while still retaining high target-binding affinity. We confirm that these truncated aptamers have this functionality by using an exonuclease I-based digestion assay and further evaluate this characteristic in an electrochemical aptamer-based cocaine sensor and a fluorophore-quencher ATP assay. We believe our Exo III-digestion method should be applicable for the generation of structure-switching aptamers from other TWJ- or stem-loop-containing small-molecule-binding aptamers, greatly simplifying the generation of functionalized sensor elements for folding-based aptasensors.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.