ArticleProceedings of the National Academy of Sciences of the United States of America2023
Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- Threading Precision: Progress and Emerging Trends in Aptamer-Based Nanopore Sensing.Biosensors · 2026Review
- Improving All-Atom Molecular Dynamics Models for Quantitative Prediction of Nanopore Blockade Current.bioRxiv : the preprint server for biology · 2026Article
- Scalable Production of DNA-Probe-Functionalized Heteromeric MspA Nanopores for Biosensing.ACS applied materials & interfaces · 2026Article
- Nanopipette-DNA-Nanopore Hybrid System for Small Molecule Detection.ChemPlusChem · 2026Article
- Nanopore Label-Free Monitoring of B-DNA and Z-DNA Conformational Transition in Real Time.ACS nano · 2026Article
- Construction and characterization of a nanopore derived from the transmembrane domain of a trimeric autotransporter adhesin.Frontiers in bioengineering and biotechnology · 2026Article
- Selective Identification of Allosteric Inhibitors and Co-Drug Combinations Targeting Kinases by Using a Nanopore Tweezer Approach.ACS nano · 2025Article
- Decoding information stored in DNAs through single-molecule electrical detection platforms.Innovation (Cambridge (Mass.)) · 2025Review
- Single-Molecule Protein Profiling Using Nanopores and Dimeric Aptamer-Modified DNA Carriers.Angewandte Chemie (International ed. in English) · 2025Article
- DNA Hydrogel-Interfaced Organic Electrochemical Transistor for the Investigation of Binding-Induced Conformational Change of Small Molecule Aptamers.ACS applied materials & interfaces · 2025Article
- Advancing synthesis-free and enzyme-free rewritable DNA memory through frameshift encoding and nanopore duplex interruption decoding.PNAS nexus · 2025Article
- Engineering functionally-optimized aptamers against SARS-Cov-2 for blocking spike-ACE2 interaction and aptasensor detection.Materials today. Bio · 2025Article
- Nanopore discrimination of rare earth elements.Nature nanotechnology · 2025Article
- Redesign of Translocon EXP2 Nanopore for Detecting Peptide Fragments.Small methods · 2025Article
- Nanopore Detection of Small Molecules Based on Replacement and Complexation Chemical Interactions.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells.Journal of the American Chemical Society · 2025Article
- Tracking flaviviral protease conformational dynamics by tuning single-molecule nanopore tweezers.Biophysical journal · 2025Article
- Nucleic acid-based wearable and implantable electrochemical sensors.Chemical Society reviews · 2024Review
- Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision.ACS nano · 2024Article
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.
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