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Chingarande RG, Tian K, Kuang Y, Sarangee A, Hou C, Ma E, Ren J, Hawkins S, Kim J, Adelstein R, Chen S, Gillis KD, Gu LQ. Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor. Proc Natl Acad Sci U S A 2023; 120:e2108118120. [PMID: 37276386 PMCID: PMC10268594 DOI: 10.1073/pnas.2108118120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
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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Affiliation(s)
- Rugare G. Chingarande
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Kai Tian
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Yu Kuang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Aby Sarangee
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Chengrui Hou
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Emily Ma
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Jarett Ren
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sam Hawkins
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Joshua Kim
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Ray Adelstein
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sally Chen
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Kevin D. Gillis
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Li-Qun Gu
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
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