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Roelen Z, Tabard-Cossa V. Synthesis of length-tunable DNA carriers for nanopore sensing. PLoS One 2023; 18:e0290559. [PMID: 37611030 PMCID: PMC10446168 DOI: 10.1371/journal.pone.0290559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise hard-to-detect molecules such as small, weakly-charged proteins. However, existing carrier designs can often introduce drawbacks to nanopore experiments including higher levels of cost/complexity and carrier-pore interactions that lead to ambiguous signals and elevated clogging rates. In this work, we present a simple method of carrier production based on sticky-ended DNA molecules that emphasizes ease-of-synthesis and compatibility with nanopore sensing and analysis. In particular, our method incorporates the ability to flexibly control the length of the DNA carriers produced, enhancing the multiplexing potential of this carrier system through the separable nanopore signals they could generate for distinct targets. A proof-of-concept nanopore experiment is also presented, involving carriers produced by our method with multiple lengths and attached to DNA nanostructure targets, in order to validate the capabilities of the system. As the breadth of applications for nanopore sensors continues to expand, the availability of tools such as those presented here to help translate the outcomes of these applications into robust nanopore signals will be of major importance.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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2
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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3
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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4
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Dong J, Qiu X, Huang M, Chen X, Li Y. G-quadruplex-hemin DNAzyme functionalized nanopipettes: Fabrication and sensing application. Talanta 2023; 257:124384. [PMID: 36812658 DOI: 10.1016/j.talanta.2023.124384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
Solid-nanopores/nanopipettes have the exquisite ability to reveal the changes in molecular volume due to the advantages of adjustable size, good rigidity and low noise. Herein, a new platform for sensing application was established based on G-quadruplex-hemin DNAzyme (GQH) functionalized gold-coated nanopipettes. In this method, GQH was immobilized on gold-coated nanopipette, which could be used as a catalyst for the reaction of H2O2 with 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) to promote the conversion of ABTS to ABTS+ ions inside gold-coated nanopipette, and the change of transmembrane ion current could be monitored in real time. At the optimal conditions, there was a correlation between the ion current and the concentration of H2O2 in a certain range, which could be used for the hydrogen peroxide sensing. The GQH immobilized nanopipette provides a useful platform to investigate enzymatic catalysis in confined environment, which can be used in electrocatalysis, sensing and fundamental electrochemistry.
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Affiliation(s)
- Jingyi Dong
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Mimi Huang
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Xiaohu Chen
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids (Ministry of Education), Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China.
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5
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Li H, Li Y, Gui C, Chen D, Chen L, Luo L, Huang G, Yuan Y, He R, Xia F, Wang J. Bare glassy nanopore for length-resolution reading of PCR amplicons from various pathogenic bacteria and viruses. Talanta 2023; 256:124275. [PMID: 36701856 DOI: 10.1016/j.talanta.2023.124275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/16/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
In this study, it is confirmed that without addition of organic solvent and embedding polymer hydrogel into glass nanopore, bare glass nanopore can faithfully measure various lengths of DNA duplexes from 200 to 3000 base pairs with 200 base pairs resolution, showing well-separated peak amplitudes of blockage currents. Furthermore, motivated by this readout capability of duplex DNA, amplicons from Polymerase Chain Reaction (PCR) amplification are straightforwardly discriminated by bare glassy nanopore without fluorescent labeling. Except simultaneous discrimination of up to 7 different segments of the same lambda genome, various pathogenic bacteria and viruses including SARS-CoV-2 and its mutants in clinical samples can be discriminated at high resolution. Moreover, quantitative measurement of PCR amplicons is obtained with detection range spanning from 0.75 aM to 7.5 pM and detection limit of 7.5 aM, which reveals that bare glass nanopore can faithfully disclose PCR results without any extra labeling.
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Affiliation(s)
- Huizhen Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yunhui Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Lanfang Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Le Luo
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Guobao Huang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, Yulin, Guangxi, 537000, China
| | - Yang Yuan
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Rong He
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510440, China.
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, 430074, China.
| | - Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
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6
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Wang J, Chen L, Gui C, Zhu J, Zhu B, Zhu Z, Li Y, Chen D. A nanopore counter for highly sensitive evaluation of DNA methylation and its application in in vitro diagnostics. Analyst 2023; 148:1492-1499. [PMID: 36880569 DOI: 10.1039/d3an00035d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
DNA methylation has been considered an essential epigenetic biomarker for diagnosing various diseases, such as cancer. A simple and sensitive way for DNA methylation level detection is necessary. Inspired by the label-free and ultra-high sensitivity of solid-state nanopores to double-stranded DNA (dsDNA), we proposed a nanopore counter for evaluating DNA methylation by integrating a dual-restriction endonuclease digestion strategy coupled with polymerase chain reaction (PCR) amplification. Simultaneous application of BstUI/HhaI endonucleases can ensure the full digestion of the unmethylated target DNA but shows no effect on the methylated ones. Therefore, only the methylated DNA remains intact and can trigger the subsequent PCR reaction, producing a large quantity of fixed-length PCR amplicons, which can be directly detected through glassy nanopores. By simply counting the event rate of the translocation signals, the concentration of methylated DNA can be determined to range from 1 aM to 0.1 nM, with the detection limit as low as 0.61 aM. Moreover, a 0.01% DNA methylation level was successfully distinguished. The strategy of using the nanopore counter for highly sensitive DNA methylation evaluation would be a low-cost but reliable alternative in the analysis of DNA methylation.
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Affiliation(s)
- Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Lanfang Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Jianji Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Baian Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Zhuobin Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Yunhui Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, 510006, China.
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7
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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8
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Zhu J, Kong J, Keyser UF, Wang E. Parallel DNA circuits by autocatalytic strand displacement and nanopore readout. NANOSCALE 2022; 14:15507-15515. [PMID: 36227155 DOI: 10.1039/d2nr04048d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA nanotechnology provides a unique opportunity for molecular computation, with strand displacement reactions enabling controllable reorganization of nanostructures. Additional DNA strand exchange strategies with high selectivity for input will enable novel complex systems including biosensing applications. Herein, we propose an autocatalytic strand displacement (ACSD) circuit: initiated by DNA breathing and accelerated by a seesaw catalytic reaction, ACSD ensures that only the correct base sequence starts the catalytic cycle. Analogous to an electronic circuit with a variable resistor, two ACSD reactions with different rates are connected in parallel to mimic a parallel circuit containing branches with different resistances. Finally, we introduce a multiplexed nanopore sensing platform to report the output results of a parallel path selection system at the single-molecule level. By combining the ACSD strategy with fast and sensitive single-molecule nanopore readout, a new generation of DNA-based computing tools is established.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, UK.
| | - Jinglin Kong
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, UK.
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, UK.
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.
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9
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Zhang K, Chen YJ, Wilde D, Doroschak K, Strauss K, Ceze L, Seelig G, Nivala J. A nanopore interface for higher bandwidth DNA computing. Nat Commun 2022; 13:4904. [PMID: 35987925 PMCID: PMC9392746 DOI: 10.1038/s41467-022-32526-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractDNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.
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10
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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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Zhu J, Bošković F, Keyser UF. Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids. NANO LETTERS 2022; 22:4993-4998. [PMID: 35730196 PMCID: PMC9228402 DOI: 10.1021/acs.nanolett.2c01764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/28/2022] [Indexed: 05/22/2023]
Abstract
Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.
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Wang L, Wang H, Chen X, Zhou S, Wang Y, Guan X. Chemistry solutions to facilitate nanopore detection and analysis. Biosens Bioelectron 2022; 213:114448. [PMID: 35716643 DOI: 10.1016/j.bios.2022.114448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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Alawami MF, Bošković F, Zhu J, Chen K, Sandler SE, Keyser UF. Lifetime of glass nanopores in a PDMS chip for single-molecule sensing. iScience 2022; 25:104191. [PMID: 35479403 PMCID: PMC9036133 DOI: 10.1016/j.isci.2022.104191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/16/2022] [Accepted: 03/30/2022] [Indexed: 11/09/2022] Open
Abstract
Nanopore sensing is an emerging technology that has many biosensing applications ranging from DNA sequencing using biological pores to biomolecular analysis using solid-state pores. Solid-state nanopores that are more stable are an attractive choice for biosensing applications. Still, biomolecule interactions with the nanopore surface reduce nanopore stability and increase usage costs. In this study, we investigated the biosensing capability for 102 quartz glass nanopores with a diameter of 11–18 nm that were fabricated using laser-assisted capillary pulling. Nanopores were assembled into multiple microfluidic chips that were repeatedly used for up to 19 weeks. We find that using vacuum storage combined with minimal washing steps improved the number of use cycles for nanopores. The single-molecule biosensing capability over repeated use cycles was demonstrated by quantitative analysis of a DNA carrier designed for detection of short single-stranded DNA oligonucleotides. Maintaining low noise and linear current-voltage relation is crucial for biosensing Multiple nanopores embedded in a chip can make more than 90 different measurements Nanopores can be reused weekly over 19 weeks Nanopore failure can be attributed to contaminant accumulation and dissolution
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14
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Zhang L, Chen J, He M, Su X. Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection. EXPLORATION (BEIJING, CHINA) 2022; 2:20210265. [PMID: 37324584 PMCID: PMC10190925 DOI: 10.1002/exp.20210265] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 06/16/2023]
Abstract
Single nucleotide variant (SNV) has become an emerging biomarker for various diseases such as cancers and infectious diseases. Toehold-mediated strand displacement (TMSD), the core reaction of DNA nanotechnology, has been widely leveraged to identify SNVs. However, inappropriate choice of mismatch location results in poor discrimination ability. Here, we comprehensively investigate the effect of mismatch location on TMSD kinetics by molecular dynamic simulation tool oxDNA through umbrella sampling and forward flux sampling disclosing that mismatches at the border of the toehold and branch migration domain yield the lowest TMSD reaction rate. Nine disease-related SNVs (SARS-CoV-2-D614G, EGFR-L858R, EGFR-T790M, KRAS-G12R, etc.) were tested experimentally showing a good agreement with simulation. The best choice of mismatch location enables high discrimination factor with a median of 124 for SNV and wild type. Coupling with a probe-sink system, a low variant allele frequency of 0.1% was detected with 3 S/N. We successfully used the probes to detect SNVs with high confidence in the PCR clones of constructed plasmids. This work provides mechanistic insights into TMSD process at the single-nucleotide level and can be a guidance for the design of TMSD system with fine-tuning kinetics for various applications in biosensors and nanotechnology.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Jing Chen
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Mengya He
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Xin Su
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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15
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Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
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Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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16
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Liu X, Bu S, Wei H, Wang Z, Yu S, Li Z, Hao Z, He X, Wan J. Visual assay of Escherichia coli O157:H7 based on an isothermal strand displacement and hybrid chain reaction amplification strategy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3379-3385. [PMID: 34235517 DOI: 10.1039/d1ay00644d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Here, we describe a simple, sensitive, and enzyme-free method for visual point-of-care detection of 16S rRNA of Escherichia coli O157:H7 based on an isothermal strand displacement-hybrid chain reaction (ISD-HCR) and lateral flow strip (LFS). In this study, the secondary structure of 16S rRNA of E. coli O157:H7 was unwound by two helper oligonucleotides to expose the single-strand-specific nucleic acid sequence. The free specific sequence promoted the toehold-mediated strand displacement reaction to output a large number of FITC-labeled single-stranded DNA probes (capture probe [CP]). The 3'-end sequence of the reporter probe propagated a chain reaction of hybridization events between the two hairpin probes modified with biotin to form long nicked DNA polymers with multiple biotins (RP-HCR complexes); the free CP and RP-HCR complexes then form CP/RP-HCR complexes. The biotin-labeled double-stranded DNA CP/RP-HCR polymers then introduced numerous streptavidin (SA)-labeled gold nanoparticles (AuNPs) on the LFS. The accumulation of AuNPs produced a characteristic red band, which enabled visual detection of changes in the signal of 16S rRNA of E. coli O157:H7. The current approach could detect E. coli O157:H7 at concentrations as low as 102 CFU mL-1 without instrumentation. This approach thus provides a simple, sensitive, and low-cost tool for point-of-care detection of pathogenic bacteria, especially in resource-limited countries.
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Affiliation(s)
- Xiu Liu
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun 130022, China.
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17
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Luchian T, Mereuta L, Park Y, Asandei A, Schiopu I. Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores. Proteomics 2021; 22:e2100046. [PMID: 34275186 DOI: 10.1002/pmic.202100046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.
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Affiliation(s)
- Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
| | - Irina Schiopu
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
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18
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Zhu J, Ermann N, Chen K, Keyser UF. Image Encoding Using Multi-Level DNA Barcodes with Nanopore Readout. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100711. [PMID: 34133074 DOI: 10.1002/smll.202100711] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2021] [Indexed: 05/25/2023]
Abstract
Deoxyribonucleic acid (DNA) nanostructure-based data encoding is an emerging information storage mode, offering rewritable, editable, and secure data storage. Herein, a DNA nanostructure-based storage method established on a solid-state nanopore sensing platform to save and encrypt a 2D grayscale image is proposed. DNA multi-way junctions of different sizes are attached to a double strand of DNA carriers, resulting in distinct levels of current blockades when passing through a glass nanopore with diameters around 14 nm. The resulting quaternary encoding doubles the capacity relative to a classical binary system. Through toehold-mediated strand displacement reactions, the DNA nanostructures can be precisely added to and removed from the DNA carrier. By encoding the image into 16 DNA carriers using the quaternary barcodes and reading them in one simultaneous measurement, the image is successfully saved, encrypted, and recovered. Avoiding any proteins or enzymatic reactions, the authors thus realize a pure DNA storage system on a nanopore platform with increased capacity and programmability.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge, CB3 0HE, UK
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19
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Nanodiagnostics: A review of the medical capabilities of nanopores. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102425. [PMID: 34174420 DOI: 10.1016/j.nano.2021.102425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 04/22/2021] [Accepted: 05/09/2021] [Indexed: 11/20/2022]
Abstract
Modern diagnostics strive to be accurate, fast, and inexpensive in addition to properly identifying the presence of a disease, infection, or illness. Early diagnosis is key; catching a disease in its early stages can be the difference between fatality and treatment. The challenge with many diseases is that detectability of the disease scales with disease progression. Since single molecule sensors, e.g., nanopores, can sense biomolecules at low concentrations, they have the potential to become clinically relevant in many of today's medical settings. With nanopore-based sensing, lower volumes and concentrations are required for detection, enabling it to be clinically beneficial. Other advantages to using nanopores include that they are tunable to an enormous variety of molecules and boast low costs, and fabrication is scalable for manufacturing. We discuss previous reports and the potential for incorporating nanopores into the medical field for early diagnostics, therapeutic monitoring, and identifying relapse/recurrence.
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20
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Mukhtar M, Sargazi S, Barani M, Madry H, Rahdar A, Cucchiarini M. Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1384. [PMID: 34073904 PMCID: PMC8225127 DOI: 10.3390/nano11061384] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 01/02/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) are the simplest and most common type of DNA variations in the human genome. This class of attractive genetic markers, along with point mutations, have been associated with the risk of developing a wide range of diseases, including cancer, cardiovascular diseases, autoimmune diseases, and neurodegenerative diseases. Several existing methods to detect SNPs and mutations in body fluids have faced limitations. Therefore, there is a need to focus on developing noninvasive future polymerase chain reaction (PCR)-free tools to detect low-abundant SNPs in such specimens. The detection of small concentrations of SNPs in the presence of a large background of wild-type genes is the biggest hurdle. Hence, the screening and detection of SNPs need efficient and straightforward strategies. Suitable amplification methods are being explored to avoid high-throughput settings and laborious efforts. Therefore, currently, DNA sensing methods are being explored for the ultrasensitive detection of SNPs based on the concept of nanotechnology. Owing to their small size and improved surface area, nanomaterials hold the extensive capacity to be used as biosensors in the genotyping and highly sensitive recognition of single-base mismatch in the presence of incomparable wild-type DNA fragments. Different nanomaterials have been combined with imaging and sensing techniques and amplification methods to facilitate the less time-consuming and easy detection of SNPs in different diseases. This review aims to highlight some of the most recent findings on the aspects of nanotechnology-based SNP sensing methods used for the specific and ultrasensitive detection of low-concentration SNPs and rare mutations.
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Affiliation(s)
- Mahwash Mukhtar
- Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, University of Szeged, 6720 Szeged, Hungary;
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan 98167-43463, Iran;
| | - Mahmood Barani
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran;
| | - Henning Madry
- Center of Experimental Orthopaedics, Saarland University Medical Center, D-66421 Homburg/Saar, Germany;
| | - Abbas Rahdar
- Department of Physics, Faculty of Science, University of Zabol, Zabol 538-98615, Iran
| | - Magali Cucchiarini
- Center of Experimental Orthopaedics, Saarland University Medical Center, D-66421 Homburg/Saar, Germany;
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21
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Nouri R, Jiang Y, Lian XL, Guan W. Sequence-Specific Recognition of HIV-1 DNA with Solid-State CRISPR-Cas12a-Assisted Nanopores (SCAN). ACS Sens 2020; 5:1273-1280. [PMID: 32370494 DOI: 10.1021/acssensors.0c00497] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleic acid detection methods are crucial for many fields such as pathogen detection and genotyping. Solid-state nanopore sensors represent a promising platform for nucleic acid detection due to its unique single molecule sensitivity and label-free electronic sensing. Here, we demonstrated the use of the glass nanopore for highly sensitive quantification of single-stranded circular DNAs (reporters), which could be degraded under the trans-cleavage activity of the target-specific CRISPR-Cas12a. We developed and optimized the Cas12a assay for HIV-1 analysis. We validated the concept of the solid-state CRISPR-Cas12a-assisted nanopores (SCAN) to specifically detect the HIV-1 DNAs. We showed that the glass nanopore sensor is effective in monitoring the cleavage activity of the target DNA-activated Cas12a. We developed a model to predict the total experimental time needed for making a statistically confident positive/negative call in a qualitative test. The SCAN concept combines the much-needed specificity and sensitivity into a single platform, and we anticipate that the SCAN would provide a compact, rapid, and low-cost method for nucleic acid detection at the point of care.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Yuqian Jiang
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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22
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Chang W, Liu W, Shen H, Chen S, Liao P, Liu Y. Molecular AND logic gate for multiple single-nucleotide mutations detection based on CRISPR/Cas9n system-trigged signal amplification. Anal Chim Acta 2020; 1112:46-53. [DOI: 10.1016/j.aca.2020.03.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/26/2022]
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23
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Zhang D, Yan Y, Que H, Yang T, Cheng X, Ding S, Zhang X, Cheng W. CRISPR/Cas12a-Mediated Interfacial Cleaving of Hairpin DNA Reporter for Electrochemical Nucleic Acid Sensing. ACS Sens 2020; 5:557-562. [PMID: 32013399 DOI: 10.1021/acssensors.9b02461] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A rapid and sensitive isothermal method is crucial for point-of-care (POC) nucleic acid testing. Recently, RNA-guided CRISPR/Cas12a proteins were discovered to exhibit target-triggered nonspecific single-stranded deoxyribonuclease (ssDNase) activity. Herein, the ssDNase cleavage capacity of the CRISPR/Cas12a system for interfacial hairpin DNA (hpDNA) and linear DNA was investigated in detailed. A novel electrochemical DNA biosensor was then developed via target-induced Cas12a cleaving interfacial hpDNA. In this strategy, the RNA-guided target DNA binding activates the robust Cas12a ssDNase activity. The immobilized hpDNA electrochemical reporters with a low surface coverage and incompact morphological structure present accessible substrates for highly efficient Cas12a cleavage, leading to a highly sensitive electrochemical DNA biosensor. Under the optimal conditions, as low as 30 pM target DNA was detected in about 60 min with 3.5 orders of magnitude dynamic range from 50 pM to 100 nM. Furthermore, the practical application ability of the established sensing method for detecting the target in complex matrices was also demonstrated. The proposed strategy enables rapid and sensitive DNA determination, providing a potential tool for POC molecular diagnostics.
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Affiliation(s)
- Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Haiying Que
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiuming Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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24
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Tang H, Wang H, Yang C, Zhao D, Qian Y, Li Y. Nanopore-based Strategy for Selective Detection of Single Carcinoembryonic Antigen (CEA) Molecules. Anal Chem 2020; 92:3042-3049. [DOI: 10.1021/acs.analchem.9b04185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Yuanyuan Qian
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P.R. China
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25
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Fang Z, Liu L, Wang Y, Xi D, Zhang S. Unambiguous Discrimination of Multiple Protein Biomarkers by Nanopore Sensing with Double-Stranded DNA-Based Probes. Anal Chem 2019; 92:1730-1737. [DOI: 10.1021/acs.analchem.9b02965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhen Fang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Liping Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
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26
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Akkilic N, Geschwindner S, Höök F. Single-molecule biosensors: Recent advances and applications. Biosens Bioelectron 2019; 151:111944. [PMID: 31999573 DOI: 10.1016/j.bios.2019.111944] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.
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Affiliation(s)
- Namik Akkilic
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Division of Biological Physics, Chalmers University of Technology, Gothenburg, Sweden.
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27
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Tang Z, Choi G, Nouri R, Guan W. Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing. NANO LETTERS 2019; 19:7927-7934. [PMID: 31657939 DOI: 10.1021/acs.nanolett.9b03040] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Gihoon Choi
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Reza Nouri
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Weihua Guan
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biomedical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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28
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Tian K, Chen X, Luan B, Lin M, Mustapha A, Gu LQ. Single Locked Nucleic Acid-enhanced nanopore genetic discrimination of pathogenic serotypes and cancer driver mutations. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:4492-4495. [PMID: 30441349 DOI: 10.1109/embc.2018.8513177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rapid and accurate detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for broad fields from food safety monitoring to disease diagnostics and prognosis. Here, we developed a nanopore single-molecule sensor, coupled with the locked nucleic acid (LNA) technique, to accurately discriminate SNPs for detection of Shiga toxin producing Escherichia coli (STEC) O157:H7 pathogen serotype, and cancer-derived driver mutations EGFR L858R and KRAS G12D. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, can be applied in food science and medical detection that need rapid and accurate determination of genetic variations.
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29
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Beamish E, Tabard-Cossa V, Godin M. Programmable DNA Nanoswitch Sensing with Solid-State Nanopores. ACS Sens 2019; 4:2458-2464. [PMID: 31449750 DOI: 10.1021/acssensors.9b01053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sensing performance of solid-state nanopores is limited by the fast kinetics of small molecular targets. To address this challenge, we translate the presence of a small target to a large conformational change of a long polymer. In this work, we explore the performance of solid-state nanopores for sensing the conformational states of molecular nanoswitches assembled using the principles of DNA origami. These programmable single-molecule switches show great potential in molecular diagnostics and long-term information storage. We investigate the translocation properties of linear and looped nanoswitch topologies using nanopores fabricated in thin membranes, ultimately comparing the performance of our nanopore platform for detecting the presence of a DNA analogue to a sequence found in a Zika virus biomarker gene with that of conventional gel electrophoresis. We found that our system provides a high-throughput method for quantifying several target concentrations within an order of magnitude by sensing only several hundred molecules using electronics of moderate bandwidth that are conventionally used in nanopore sensing systems.
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He L, Karau P, Tabard-Cossa V. Fast capture and multiplexed detection of short multi-arm DNA stars in solid-state nanopores. NANOSCALE 2019; 11:16342-16350. [PMID: 31386731 DOI: 10.1039/c9nr04566j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fast and multiplexed detection of low-abundance disease biomarkers at the point-of-need would transform medicine. Nanopores have gained attention as single-molecule counters to electrically detect a range of biological molecules in a handheld format, but challenges remain before diagnostic applications can emerge. For solid-state nanopore sensors, the specificity of the ionic current signatures and the rate of target capture required to simultaneously recognize and rapidly count a mixture of molecular targets in a complex sample are active areas of research. Herein, we study the capture and translocation characteristics of short N-arm star shaped DNA nanostructures to evaluate their potential as a family of surrogate label molecules for biomarkers of interest, designed for fast and reliable multiplexed detection based on conductance blockages. Simple hybridization of a varying number of short, easily synthesized 50 bp ssDNA strands allows the number of arms in the star shape DNA to be controlled from N = 3 to 12. By introducing more arms to the nanostructures, we show that we can controllably increase the nanopore signal-to-noise ratio for a range of pore sizes, producing conductance blockages which increase linearly with the number of arms, and we demonstrate conductance-based multiplexing through simultaneous detection of three such nanostructures. Moreover, the increased molecular signal strength facilitates detection under salt concentration asymmetries, allowing for a capture rate enhancement of two orders of magnitude without compromising the nanopore temporal and ionic signals. Together, these attributes (strong signal, multiplexing potential and increased counting rate) make the N-arm star DNA-based nanostructures promising candidates as proxy labels for the detection of multiple biomarkers of interest in future high sensitivity single-molecule solid-state nanopore-based assays.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, ON, Canada.
| | - Philipp Karau
- Department of Physics, University of Ottawa, Ottawa, ON, Canada.
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31
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Shao N, Han X, Song Y, Zhang P, Qin L. CRISPR-Cas12a Coupled with Platinum Nanoreporter for Visual Quantification of SNVs on a Volumetric Bar-Chart Chip. Anal Chem 2019; 91:12384-12391. [DOI: 10.1021/acs.analchem.9b02925] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ning Shao
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- Deartment of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Xin Han
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- Deartment of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, United States
- School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yanni Song
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Pengchao Zhang
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- Deartment of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, United States
- Deartment of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York 10065, United States
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32
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Lam MH, Briggs K, Kastritis K, Magill M, Madejski GR, McGrath JL, de Haan HW, Tabard-Cossa V. Entropic Trapping of DNA with a Nanofiltered Nanopore. ACS APPLIED NANO MATERIALS 2019; 2:4773-4781. [PMID: 32577609 PMCID: PMC7310961 DOI: 10.1021/acsanm.9b00606] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elucidating the kinetics of DNA passage through a solid-state nanopore is a fertile field of research, and mechanisms for controlling capture, passage, and trapping of biopolymers are likely to find numerous technological applications. Here we present a nanofiltered nanopore device, which forms an entropic cage for DNA following first passage through the nanopore, trapping the translocated DNA and permitting recapture for subsequent reanalysis and investigation of kinetics of passage under confinement. We characterize the trapping properties of this nanodevice by driving individual DNA polymers into the nanoscale gap separating the nanofilter and the pore, forming an entropic cage similar to a "two pores in series" device, leaving polymers to diffuse in the cage for various time lengths, and attempting to recapture the same molecule. We show that the cage results in effectively permanent trapping when the radius of gyration of the target polymer is significantly larger than the radii of the pores in the nanofilter. We also compare translocation dynamics as a function of translocation direction in order to study the effects of confinement on DNA just prior to translocation, providing further insight into the nanopore translocation process. This nanofiltered nanopore device realizes simple fabrication of a femtoliter nanoreactor in which to study fundamental biophysics and biomolecular reactions on the single-molecule level. The device provides an electrically-permeable single-molecule trap with a higher entropic barrier to escape than previous attempts to fabricate similar structures.
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Affiliation(s)
- Michelle H. Lam
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | | | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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Wu F, Lin Q, Wang L, Zou Y, Chen M, Xia Y, Lan J, Chen J. A DNA electrochemical biosensor based on triplex DNA-templated Ag/Pt nanoclusters for the detection of single-nucleotide variant. Talanta 2019; 207:120257. [PMID: 31594620 DOI: 10.1016/j.talanta.2019.120257] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 01/24/2023]
Abstract
A label-free electrochemical biosensor based on the triplex DNA-templated Ag/Pt bimetallic nanoclusters (triplex-Ag/PtNCs) and locked nucleic acid (LNA) modified X-shaped DNA probe was developed for the detection of single-nucleotide variant (SNV) related to β-thalassemia. Firstly, using triplex DNA as template, a site-specific and homogeneous Ag/PtNCs was prepared, which can effectively catalyze the 3,3,5,5-tetramethylbenzidine-H2O2 system and thus be employed as a signal reporter in the field of electrochemical biosensor. Secondly, the LNA modified X-shaped probes were assembled on gold electrode surface, which can only be dissociated in the presence of target, leading to the hybridization with triplex-Ag/PtNCs and significant increase of current signal. In this way, the detection limit for SNV of β-thalassemia was 0.8 fM with variant allele frequency (VAF) as low as 0.0001%.
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Affiliation(s)
- Fang Wu
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Qian Lin
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Liangliang Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yulian Zou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Mei Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Yaokun Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jianming Lan
- Department of Basic Chemistry, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China
| | - Jinghua Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, Fujian Province, 350108, China.
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Zhu J, Haynes CJE, Kieffer M, Greenfield JL, Greenhalgh RD, Nitschke JR, Keyser UF. Fe II4L 4 Tetrahedron Binds to Nonpaired DNA Bases. J Am Chem Soc 2019; 141:11358-11362. [PMID: 31283214 PMCID: PMC7007224 DOI: 10.1021/jacs.9b03566] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A water-soluble self-assembled supramolecular FeII4L4 tetrahedron binds to single stranded DNA, mismatched DNA base pairs, and three-way DNA junctions. Binding of the coordination cage quenches fluorescent labels on the DNA strand, which provides an optical means to detect the interaction and allows the position of the binding site to be gauged with respect to the fluorescent label. Utilizing the quenching and binding properties of the coordination cage, we developed a simple and rapid detection method based on fluorescence quenching to detect unpaired bases in double-stranded DNA.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Cally J E Haynes
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Marion Kieffer
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Jake L Greenfield
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ryan D Greenhalgh
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jonathan R Nitschke
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
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Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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Gu C, Kong X, Liu X, Gai P, Li F. Enzymatic Biofuel-Cell-Based Self-Powered Biosensor Integrated with DNA Amplification Strategy for Ultrasensitive Detection of Single-Nucleotide Polymorphism. Anal Chem 2019; 91:8697-8704. [DOI: 10.1021/acs.analchem.9b02510] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Chengcheng Gu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xinke Kong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
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Abstract
Advances in nucleic acid sequencing and genotyping technologies have facilitated the discovery of an increasing number of single-nucleotide variations (SNVs) associated with disease onset, progression, and response to therapy. The reliable detection of such disease-specific SNVs can ensure timely and effective therapeutic action, enabling precision medicine. This has driven extensive efforts in recent years to develop novel methods for the fast and cost-effective analysis of targeted SNVs. In this Review, we highlight the most recent and significant advances made toward the development of such methodologies.
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Affiliation(s)
- Alireza Abi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
| | - Afsaneh Safavi
- Department of Chemistry, Faculty of Sciences, Shiraz University, Shiraz 7194684795, Iran
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38
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Chen K, Kong J, Zhu J, Ermann N, Predki P, Keyser UF. Digital Data Storage Using DNA Nanostructures and Solid-State Nanopores. NANO LETTERS 2019; 19:1210-1215. [PMID: 30585490 DOI: 10.1021/acs.nanolett.8b04715] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopores are powerful tools for reading the three-dimensional shape of molecules, allowing for the translation of molecular structure information into electric signals. Here, we show a high-resolution integrated nanopore system for identifying DNA nanostructures that has the capability of distinguishing attached short DNA hairpins with only a stem length difference of 8 bp along a DNA double strand named the DNA carrier. Using our platform, we can read up to 112 DNA hairpins with a separating distance of 114 bp attached on a DNA carrier that carries digital information. Our encoding strategy allows for the creation of a library of molecules with a size of up to 5 × 1033 (2112) that is only built from a few hundred types of base molecules for data storage and has the potential to be extended by linking multiple DNA carriers. Our platform provides a nanopore- and DNA nanostructure-based data storage method with convenient access and the potential for miniature-scale integration.
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Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jinglin Kong
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Niklas Ermann
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - Paul Predki
- Iridia Incorporated , 3156 Lionshead Avenue , Suite 1, Carlsbad , California 92010 , United States
| | - Ulrich F Keyser
- Cavendish Laboratory , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , United Kingdom
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39
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Yu JS, Hong SC, Wu S, Kim HM, Lee C, Lee JS, Lee JE, Kim KB. Differentiation of selectively labeled peptides using solid-state nanopores. NANOSCALE 2019; 11:2510-2520. [PMID: 30672547 DOI: 10.1039/c8nr09315f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Determination of the amino acid sequence of a protein is critical for understanding various biological processes. Mass spectrometry has mainly been used for protein identification; however, there are limitations to its sensitivity when detecting low abundance proteins. In this study, we attempted to distinguish between three similar peptide sequences (∼40 amino acids, ∼5 kDa) that differed only by the location or number of cysteine residues with solid-state nanopores. The cysteine residues are located at one end, one at the center, and at both ends for each of the three peptides. We found that differentiation of the three types of peptides by nanopore signals was difficult. However, when the cysteine residue was labeled with a negatively charged molecule, Flamma® 496, the labeled peptides showed distinct signals for each peptide. Comparing the relative current blockades of labeled peptides with applied voltages, we found that the label was able to change peptide conformations and the resulting ionic current signals from the three labeled peptides were distinguished based on the relative current blockade, full width at half-maximum of the current blockade distribution, and single-molecule level peak shape analysis. Our results suggest that solid-state nanopores combined with a targeted labeling strategy could be used to obtain characteristic peptide signatures that could ultimately be used for protein identification.
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Affiliation(s)
- Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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40
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Loh AYY, Burgess CH, Tanase DA, Ferrari G, McLachlan MA, Cass AEG, Albrecht T. Electric Single-Molecule Hybridization Detector for Short DNA Fragments. Anal Chem 2018; 90:14063-14071. [PMID: 30398852 DOI: 10.1021/acs.analchem.8b04357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
By combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipets, we demonstrate an electric, label-free hybridization sensor for short DNA sequences (<100 nucleotides). Such short fragments are known to occur as circulating cell-free DNA in various bodily fluids, such as blood plasma and saliva, and have been identified as disease markers for cancer and infectious diseases. To this end, we use as a model system an 88-mer target from the RV1910c gene in Mycobacterium tuberculosis, which is associated with antibiotic (isoniazid) resistance in TB. Upon binding to short probes attached to long carrier DNA, we show that resistive-pulse sensing in nanopipets is capable of identifying rather subtle structural differences, such as the hybridization state of the probes, in a statistically robust manner. With significant potential toward multiplexing and high-throughput analysis, our study points toward a new, single-molecule DNA-assay technology that is fast, easy to use, and compatible with point-of-care environments.
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Affiliation(s)
- A Y Y Loh
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - C H Burgess
- Department of Materials and Centre for Plastic Electronics , Imperial College London , London SW7 2AZ , United Kingdom
| | - D A Tanase
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - G Ferrari
- Dipartimento di Elettronica, Informazione e Bioingegneria , Politecnico di Milano , Piazza Leonardo da Vinci 32 , Milano 20133 , Italy
| | - M A McLachlan
- Department of Materials and Centre for Plastic Electronics , Imperial College London , London SW7 2AZ , United Kingdom
| | - A E G Cass
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom
| | - T Albrecht
- Department of Chemistry , Imperial College London , Exhibition Road , London SW7 2AZ , United Kingdom.,School of Chemistry , University of Birmingham , Edgbaston Campus, Birmingham B15 2TT , United Kingdom
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41
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Ermann N, Hanikel N, Wang V, Chen K, Weckman NE, Keyser UF. Promoting single-file DNA translocations through nanopores using electro-osmotic flow. J Chem Phys 2018; 149:163311. [DOI: 10.1063/1.5031010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Niklas Ermann
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Nikita Hanikel
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Vivian Wang
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Nicole E. Weckman
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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42
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Yang W, Restrepo-Pérez L, Bengtson M, Heerema SJ, Birnie A, van der Torre J, Dekker C. Detection of CRISPR-dCas9 on DNA with Solid-State Nanopores. NANO LETTERS 2018; 18:6469-6474. [PMID: 30187755 PMCID: PMC6187524 DOI: 10.1021/acs.nanolett.8b02968] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/05/2018] [Indexed: 05/18/2023]
Abstract
Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the CRISPR-dCas9 variant employed here does not cut DNA but instead remains tightly bound at a user-defined binding site, thus providing an excellent target for biosensing. In our nanopore experiments, we observe the CRISPR-dCas9 proteins as local spikes that appear on top of the ionic current blockade signal of DNA molecules that translocate through the nanopore. The proteins exhibit a pronounced blockade signal that allows for facile identification of the targeted sequence. Even at the high salt conditions (1 M LiCl) required for nanopore experiments, dCas9 proteins are found to remain stably bound. The binding position of the target sequence can be read from the spike position along the DNA signal. We anticipate applications of this nanopore-based CRISPR-dCas9 biosensing approach in DNA-typing based diagnostics such as quick disease-strain identification, antibiotic-resistance detection, and genome typing.
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Affiliation(s)
- Wayne Yang
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Michel Bengtson
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Stephanie J. Heerema
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Anthony Birnie
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli
Institute of Nanoscience, Delft University
of Technology, 2629 HZ Delft, The Netherlands
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43
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Misiunas K, Ermann N, Keyser UF. QuipuNet: Convolutional Neural Network for Single-Molecule Nanopore Sensing. NANO LETTERS 2018; 18:4040-4045. [PMID: 29845855 PMCID: PMC6025884 DOI: 10.1021/acs.nanolett.8b01709] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopore sensing is a versatile technique for the analysis of molecules on the single-molecule level. However, extracting information from data with established algorithms usually requires time-consuming checks by an experienced researcher due to inherent variability of solid-state nanopores. Here, we develop a convolutional neural network (CNN) for the fully automated extraction of information from the time-series signals obtained by nanopore sensors. In our demonstration, we use a previously published data set on multiplexed single-molecule protein sensing. The neural network learns to classify translocation events with greater accuracy than previously possible, while also increasing the number of analyzable events by a factor of 5. Our results demonstrate that deep learning can achieve significant improvements in single molecule nanopore detection with potential applications in rapid diagnostics.
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44
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Tian K, Chen X, Luan B, Singh P, Yang Z, Gates KS, Lin M, Mustapha A, Gu LQ. Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations. ACS NANO 2018; 12:4194-4205. [PMID: 29664612 PMCID: PMC6157732 DOI: 10.1021/acsnano.8b01198] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.
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Affiliation(s)
- Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiaowei Chen
- Food Science Program, Division of Food Systems and Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Binquan Luan
- Computational Biology Center, IBM Thomas J. Watson Research, Yorktown Heights, New York 10598, United States
| | - Prashant Singh
- Food Science Program, Division of Food Systems and Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Mengshi Lin
- Food Science Program, Division of Food Systems and Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Azlin Mustapha
- Food Science Program, Division of Food Systems and Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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45
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Chang PL, Graf M, Hung CH, Radenovic A. Orthogonal Tip-to-Tip Nanocapillary Alignment Allows for Easy Detection of Fluorescent Emitters in Femtomolar Concentrations. NANO LETTERS 2018; 18:3165-3171. [PMID: 29616553 DOI: 10.1021/acs.nanolett.8b00831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we present the realization of a novel fluorescence detection method based on the electromigration of fluorescent molecules within a nanocapillary combined with the laser excitation through a platinum (Pt)-coated nanocapillary. By using the Pt nanocapillary assisted focusing of a laser beam, we completely remove the background scattering on the tip of the electrophoretic nanocapillary. In this excitation geometry, we demonstrate a 1000-fold sensitivity enhancement (1.0 nM to 1.0 pM) compared to the detection in microcapillaries with epifluorescence illumination and fluorescence spectrophotometry. Due to a significant electroosmotic flow, we observe a decelerating migration of DNA molecules close to the tip of the electrophoretic nanocapillary. The reduced DNA translocation velocity causes a two-step stacking process of molecules in the tip of the nanocapillary and can be used as a way to locally concentrate molecules. The sensitivity of our method is further improved by a continuous electrokinetic injection of DNA molecules followed by sample zone stacking on the tip of the nanocapillary. Concentrations ranging from 0.1 pM to 1.0 fM can be directly observed on the orifice of the electrophoretic nanocapillary. This is a 1000-fold improvement compared to traditional capillary electrophoresis with laser-induced fluorescence.
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Affiliation(s)
- Po-Ling Chang
- Department of Chemistry , Tunghai University , Taichung 40704 , Taiwan
| | - Michael Graf
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
| | - Chao-Hsuan Hung
- Department of Chemistry , Tunghai University , Taichung 40704 , Taiwan
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering , EPFL , 1015 Lausanne , Switzerland
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46
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Beamish E, Tabard-Cossa V, Godin M. Identifying Structure in Short DNA Scaffolds Using Solid-State Nanopores. ACS Sens 2017; 2:1814-1820. [PMID: 29182276 DOI: 10.1021/acssensors.7b00628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of molecular tags along nucleic acid sequences has many potential applications in bionanotechnology, disease biomarker detection, and DNA sequencing. An attractive approach to this end is the use of solid-state nanopores, which can electrically detect molecular substructure and can be integrated into portable lab-on-a-chip sensors. We present here a DNA origami-based approach of molecular assembly in which solid-state nanopores are capable of differentiating 165 bp scaffolds containing zero, one, and two dsDNA protrusions. This highly scalable technique requires minimal sample preparation and is customizable for a wide range of targets and applications. As a proof-of-concept, an aptamer-based DNA displacement reaction is performed in which a dsDNA protrusion is formed along a 255 bp scaffold in the presence of ATP. While ATP is too small to be directly sensed using conventional nanopore methods, our approach allows us to detect ATP by identifying molecular substructure along the DNA scaffold.
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Affiliation(s)
- Eric Beamish
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Vincent Tabard-Cossa
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michel Godin
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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47
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Long Z, Zhan S, Gao P, Wang Y, Lou X, Xia F. Recent Advances in Solid Nanopore/Channel Analysis. Anal Chem 2017; 90:577-588. [DOI: 10.1021/acs.analchem.7b04737] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zi Long
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Shenshan Zhan
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Pengcheng Gao
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Yongqian Wang
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Xiaoding Lou
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Fan Xia
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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48
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Gu LQ, Gates KS, Wang MX, Li G. What is the potential of nanolock- and nanocross-nanopore technology in cancer diagnosis? Expert Rev Mol Diagn 2017; 18:113-117. [PMID: 29171309 DOI: 10.1080/14737159.2018.1410060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Li-Qun Gu
- a Department of Bioengineering and Dalton Cardiovascular Research Center , University of Missouri , Columbia , MO , USA
| | - Kent S Gates
- b Department of Chemistry and Department of Biochemistry , University of Missouri , Columbia , MO , USA
| | - Michael X Wang
- c Department of Pathology and Immunology , Washington University School of Medicine , St. Louis , MO , USA
| | - Guangfu Li
- d Department of Surgery and Ellis Fischel Cancer Center , University of Missouri , Columbia , MO , USA
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49
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Wang Y, Tian K, Shi R, Gu A, Pennella M, Alberts L, Gates KS, Li G, Fan H, Wang MX, Gu LQ. Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue. ACS Sens 2017; 2:975-981. [PMID: 28750524 DOI: 10.1021/acssensors.7b00235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hongxin Fan
- Department
of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
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50
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Yu RJ, Ying YL, Hu YX, Gao R, Long YT. Label-Free Monitoring of Single Molecule Immunoreaction with a Nanopipette. Anal Chem 2017; 89:8203-8206. [DOI: 10.1021/acs.analchem.7b01921] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ru-Jia Yu
- Key Laboratory for Advanced
Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced
Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Yong-Xu Hu
- Key Laboratory for Advanced
Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Rui Gao
- Key Laboratory for Advanced
Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced
Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
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