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Xu Q, Xi Y, Wang L, Xu M, Ruan T, Du Z, Jiang C, Cao J, Zhu X, Wang X, Yang B, Liu J. In situ self-referenced intracellular two-electrode system for enhanced accuracy in single-cell analysis. Biosens Bioelectron 2024; 253:116173. [PMID: 38432075 DOI: 10.1016/j.bios.2024.116173] [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: 12/04/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Since the emergence of single-cell electroanalysis, the two-electrode system has become the predominant electrochemical system for real-time behavioral analysis of single-cell and multicellular populations. However, due to the transmembrane placement of the two electrodes, cellular activities can be interrupted by the transmembrane potentials, and the test results are susceptible to influences from factors such as intracellular solution, membrane, and bulk solution. These limitations impede the advancement of single-cell analysis. Here, we propose a highly miniaturized and integrated in situ self-referenced intracellular two-electrode system (IS-SRITES), wherein both the working and reference electrodes are positioned inside the cell. Additionally, we demonstrated the stability (0.28 mV/h) of the solid-contact in situ Ag/AgCl reference electrode and the ability of the system to conduct standard electrochemical testing in a wide pH range (pH 6.0-8.0). Cell experiments confirmed the non-destructive performance of the electrode system towards cells and its capacity for real-time monitoring of intra- and extracellular pH values. Moreover, through equivalent circuits, finite element simulations, and drug delivery experiments, we illustrated that the IS-SRITES can yield more accurate test results and exhibit enhanced resistance to interference from the extracellular environment. Our proposed system holds the potential to enable the precise detection of intracellular substances and optimize the existing model of the electrode system for intracellular signal detection, thereby spearheading advancements in single-cell analysis.
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Affiliation(s)
- Qingda Xu
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ye Xi
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Longchun Wang
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengfei Xu
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Ruan
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiyuan Du
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunpeng Jiang
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Cao
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiantao Zhu
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China; Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolin Wang
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Yang
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jingquan Liu
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Qiu X, Dong J, Dai Q, Huang M, Li Y. Functionalized nanopores based on hybridization chain reaction: Fabrication and microRNA sensing. Biosens Bioelectron 2023; 240:115594. [PMID: 37660458 DOI: 10.1016/j.bios.2023.115594] [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: 06/08/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023]
Abstract
Enzyme-free hybridization chain reaction (HCR) technology is often used as a signal amplification tool for the detection of different targets. In this study, an ultrasensitive and label-free method for detecting miRNA-21 was developed using the nanopore ionic current rectification (ICR) technology coupled with HCR technology. The probe oligonucleotide (DNA1) was combined with the gold-coated nanopore through the Au-S bond to form a DNA1-functionalized gold-coated nanopore (DNA1-Au-coated nanopore). Since miRNA-21 is partially complementary to DNA1, it can be selectively recognized by DNA1-functionalized gold-coated nanopores. The target (miRNA-21) can induce the opening of hairpin DNA and HCR reaction after the introduction of hairpin DNA H1 and H2. The concentration of miRNA-21 will affect the combination of H1 and H2 on the inner wall of the nanopore, and its surface charge will change with the internal modification, thereby changing the ion current rectification ratio. Under the condition that the concentration of H1, H2 and HCR reaction time are constant, the change of ICR ratio is linearly correlated with the logarithm of miRNA-21 concentration within a certain range, which shows that the sensing strategy we designed can achieve target miRNA-21 detection. This ultrasensitive miRNA holds great promise in the field of cancer diagnosis.
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Affiliation(s)
- Xia Qiu
- Key Laboratory of Functional Molecular Solid, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Jingyi Dong
- Key Laboratory of Functional Molecular Solid, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, PR China
| | - Qingshan Dai
- Key Laboratory of Functional Molecular Solid, 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 Solid, 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 Solid, 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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3
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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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4
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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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5
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Guan X, Li H, Chen L, Qi G, Jin Y. Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection. ACS Sens 2023; 8:427-442. [PMID: 36670058 DOI: 10.1021/acssensors.2c02102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.
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Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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6
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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7
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Zhang S, Liu M, Cui H, Ziaee MA, Sun R, Chen L, Chen D, Garoli D, Wang J. Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system. Analyst 2022; 147:905-914. [PMID: 35142306 DOI: 10.1039/d1an02313f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The fabrication of nanopores with a matched pore size, and the existence of multiple interferents make the reproducible detection of small-sized molecules by means of solid-state nanopores still challenging. A useful method to solve these problems is based on the detection of large DNA nanostructures related to the existence of small-sized targets. In particular, a DNA tetrahedron with a well-defined 3D nanostructure is the ideal candidate for use as a signal transducer. Here, we demonstrate the detection of an L1-encoding gene of HPV18 as a test DNA target sequence in a reaction buffer solution, where long single-stranded DNA linking DNA tetrahedra onto the surface of the magnetic beads is cleaved by a target DNA-activated CRISPR-cas12 system. The DNA tetrahedra are subsequently released and can be detected by the current pulse in a glassy nanopore. This approach has several advantages: (1) one signal transducer can be used to detect different targets; (2) a glassy nanopore with a pore size much larger than the target DNA fragment can boost the tolerance of the contaminants and interferents which often degrade the performance of a nanopore sensor.
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Affiliation(s)
- Shumin Zhang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Minyi Liu
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Haofa Cui
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Muhammad Asad Ziaee
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Rongwei Sun
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Liting Chen
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Daqi Chen
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego 30, 16136 Genova, Italy. .,Liberà Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy
| | - Jiahai Wang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
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8
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9
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Zhou Y, Sun L, Watanabe S, Ando T. Recent Advances in the Glass Pipet: from Fundament to Applications. Anal Chem 2021; 94:324-335. [PMID: 34841859 DOI: 10.1021/acs.analchem.1c04462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuanshu Zhou
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Linhao Sun
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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10
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Cao M, Wang H, Tang H, Zhao D, Li Y. Enzyme-Encapsulated Zeolitic Imidazolate Frameworks Formed Inside the Single Glass Nanopore: Catalytic Performance and Sensing Application. Anal Chem 2021; 93:12257-12264. [PMID: 34459201 DOI: 10.1021/acs.analchem.1c01790] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metal-organic frameworks (MOFs) can improve the stability and activity of enzymes under the MOF encapsulation. However, it remains a challenge to explore the effects of the MOF environment on enzymatic activity in a confined space. In this work, we immobilized the enzyme inside a glass nanopore to study the catalytic activity and stability of the enzyme in the MOF environment. Horseradish peroxidase (HRP) is encapsulated in zeolitic imidazolate framework-90 (ZIF-90) and zeolitic imidazolate framework-8 (ZIF-8), which are used as the catalytic platforms. The HRP can catalyze 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt (ABTS) molecules to generate ABTS+ ions, and the change of the transmembrane ion current will be monitored in real time. As the concentration of H2O2 increases, the amount of produced ABTS+ will increase; thus, the ionic current increases. The effects of the MOF structure on enzyme activity and stability are also investigated. The HRP encapsulated in the MOF and modified inside the nanopore provides a novel and unlabeled design for studying enzymatic catalysis in a confined environment, which should have extensive applications in chemical-/bio-sensing, electrocatalysis, and fundamental electrochemistry.
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Affiliation(s)
- Mengya Cao
- 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
| | - Haoran Tang
- 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
| | - 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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11
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Shen Q, Zhou PL, Huang BT, Zhou J, Liu HL, Ahmed SA, Ding XL, Li J, Zhai YM, Wang K. Mass transport through a sub-10 nm single gold nanopore: SERS and ionic current measurement. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Hong T, Qiu L, Zhou S, Cai Z, Cui P, Zheng R, Wang J, Tan S, Jiang P. How does DNA 'meet' capillary-based microsystems? Analyst 2021; 146:48-63. [PMID: 33211035 DOI: 10.1039/d0an01336f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
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13
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Chen K, Gularek F, Liu B, Weinhold E, Keyser UF. Electrical DNA Sequence Mapping Using Oligodeoxynucleotide Labels and Nanopores. ACS NANO 2021; 15:2679-2685. [PMID: 33478224 PMCID: PMC7905879 DOI: 10.1021/acsnano.0c07947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Identifying DNA species is crucial for diagnostics. For DNA identification, single-molecule DNA sequence mapping is an alternative to DNA sequencing toward fast point-of-care testing, which traditionally relies on targeting and labeling DNA sequences with fluorescent labels and readout using optical imaging methods. A nanopore is a promising sensor as a complement to optical mapping with advantages of electric measurement suitable for portable devices and potential for high resolution. Here, we demonstrate a high-resolution nanopore-based DNA sequence mapping by labeling specific short sequence motifs with oligodeoxynucleotides (ODNs) using DNA methyltransferase (MTase) and detecting them using nanopores. We successfully detected ODNs down to the size of 11 nucleotides without introducing extra reporters and resolved neighboring sites with a distance of 141 bp (∼48 nm) on a single DNA molecule. To accurately locate the sequence motif positions on DNA, a nanopore data analysis method is proposed by considering DNA velocity change through nanopores and using ensemble statistics to translate the time-dependent signals to the location information. Our platform enables high-resolution detection of small labels on DNA and high-accuracy localization of them for DNA species identification in an all-electrical format. The method presents an alternative to optical techniques relying on fluorescent labels and is promising for miniature-scale integration for diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Boyao Liu
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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14
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Huo W, Ling W, Wang Z, Li Y, Zhou M, Ren M, Li X, Li J, Xia Z, Liu X, Huang X. Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.628861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.
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15
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Zhao D, Tang H, Wang H, Yang C, Li Y. Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores. ACS Sens 2020; 5:2177-2183. [PMID: 32588619 DOI: 10.1021/acssensors.0c00798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag+), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.
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Affiliation(s)
- Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - 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
| | - 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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16
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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17
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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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18
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Zhou Y, Wu R, Wang D, Hu P, Jin Y. Single-Molecule Translocation Conformational Sensing of Multiarm DNA Concatemers Using Glass Capillary Nanopore. ACS Sens 2019; 4:3119-3123. [PMID: 31797666 DOI: 10.1021/acssensors.9b01880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glass capillary-based nanopore is exploited for single-molecule conformational sensing of multiarm DNA concatemers during translocation. Both translocation frequency and orientation preference were found related with the number of arms of the DNA concatemers.
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Affiliation(s)
- Ya Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Ruiping Wu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Ping Hu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, 130022, China
- University of Science and Technology of China, Hefei, 230026, China
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19
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Wang Z, Liu Y, Yu L, Li Y, Qian G, Chang S. Nanopipettes: a potential tool for DNA detection. Analyst 2019; 144:5037-5047. [PMID: 31290857 DOI: 10.1039/c9an00633h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.
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Affiliation(s)
- Zhe Wang
- The State Key Laboratory of Refractories and Metallurgy, and Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, China.
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20
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Watanabe S, Kitazawa S, Sun L, Kodera N, Ando T. Development of high-speed ion conductance microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:123704. [PMID: 31893861 DOI: 10.1063/1.5118360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Scanning ion conductance microscopy (SICM) can image the surface topography of specimens in ionic solutions without mechanical probe-sample contact. This unique capability is advantageous for imaging fragile biological samples but its highest possible imaging rate is far lower than the level desired in biological studies. Here, we present the development of high-speed SICM. The fast imaging capability is attained by a fast Z-scanner with active vibration control and pipette probes with enhanced ion conductance. By the former, the delay of probe Z-positioning is minimized to sub-10 µs, while its maximum stroke is secured at 6 μm. The enhanced ion conductance lowers a noise floor in ion current detection, increasing the detection bandwidth up to 100 kHz. Thus, temporal resolution 100-fold higher than that of conventional systems is achieved, together with spatial resolution around 20 nm.
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Affiliation(s)
- Shinji Watanabe
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Satoko Kitazawa
- Department of Physics, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Linhao Sun
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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21
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Wang H, Tang H, Yang C, Li Y. Selective Single Molecule Nanopore Sensing of microRNA Using PNA Functionalized Magnetic Core-Shell Fe 3O 4-Au Nanoparticles. Anal Chem 2019; 91:7965-7970. [PMID: 31132236 DOI: 10.1021/acs.analchem.9b02025] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid-state nanopores have been employed as useful tools for single molecule analysis due to their advantages of easy fabrication and controllable diameter, but selectivity is always a big concern for complicated samples. In this work, functionalized magnetic core-shell Fe3O4-Au nanoparticles, which acted as a molecular carrier, were introduced into nanopore electrochemical system for microRNA sensing in complicated samples with high sensitivity, selectivity and signal-to-noise ratio (SNR). This strategy is based on the specific affinity between neutral peptide nucleic acids (PNA)-modified Fe3O4-Au nanoparticles and negative miRNA, and the formation of negative Fe3O4-Au-PNA-miRNA complex, which can pass through the nanopore by application of a positive potential and eliminate neutral Fe3O4-Au-PNA complex. To detect miRNA in complicated samples, a magnet has been used to separate Fe3O4-Au-PNA-miRNA complex with good selectivity. We think this is a facile and effective method for the detection of different targets at single molecular level, including nucleic acids, proteins, and other small molecules, which will open up a new approach in the nanopore sensing field.
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Affiliation(s)
- Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science , Anhui Normal University , Wuhu 241000 , P. R. China
| | - Haoran Tang
- 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
| | - 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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22
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Zhou Y, Wang D, Li C, Hu P, Jin Y. Resistive-Pulse Sensing and Surface Charge Analysis of a Single Nanoparticle Collision at a Conical Glass Nanopore. Anal Chem 2019; 91:7648-7653. [DOI: 10.1021/acs.analchem.9b00553] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ya Zhou
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dandan Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chuanping Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Hu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yongdong Jin
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
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23
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Pan Z, Nie X, Yang J, Liu H, Li J, Wang K. Gas molecule modulated ionic migration through graphene oxide laminates. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Wang D, Xu X, Zhou Y, Li H, Qi G, Hu P, Jin Y. Short-chain oligonucleotide detection by glass nanopore using targeting-induced DNA tetrahedron deformation as signal amplifier. Anal Chim Acta 2019; 1063:57-63. [PMID: 30967186 DOI: 10.1016/j.aca.2019.02.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 01/22/2023]
Abstract
Glass capillary nanopore has been developed as a promising sensing platform for bioassay with single-molecule resolution. Although the diameter of glass capillary nanopore can be easily tuned, direct event-readouts of small biomacromolecules, like short-chain oligonucleotide fragments (within ∼20 nucleotides) remain great challenge, which limited by the configuration of the conical-shaped nanopore and the instrumental temporal resolution. Here, we exploit a smart strategy for glass nanopore detection of short-chain oligonucleotides by using relatively big-sized tetrahedral DNA nanostructures as a signal amplifier, which can amplify the signals and retard the translocation speed meanwhile. The tetrahedral DNA nanostructure with a hairpin loop sequence in one edge, undergoes a shape transformation upon the complementary combination of the target oligonucleotides, in which the presence of short-chain target oligonucleotide can be readout due to obvious variation in amplitude of ion current pulse that caused by volume change of the DNA tetrahedral. Therefore, this strategy is promising for extending glass nanopore sensing platform for sensitive detection of short-chain oligonucleotides.
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Affiliation(s)
- Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiaolong Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Ya Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Hu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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25
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Kaur H, Nandivada S, Acharjee MC, McNabb DS, Li J. Estimating RNA Polymerase Protein Binding Sites on λ DNA Using Solid-State Nanopores. ACS Sens 2019; 4:100-109. [PMID: 30561195 DOI: 10.1021/acssensors.8b00976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, using a silicon nitride nanopore based device, we measure the binding locations of RNA Polymerase (RNAP) on 48.5 kbp (16.5 μm) long λ DNA. To prevent the separation of bound RNAPs from a λ DNA molecule in the high electric field inside a nanopore, we cross-linked RNAP proteins to λ DNA by formaldehyde. We compare the current blockage event data measured with a mixture of λ DNA and RNAP under cross-link conditions with our control samples: RNAP, λ DNA, RNAP, and λ DNA incubated in formaldehyde separately and in a mixture. By analyzing the time durations and amplitudes of current blockage signals of events and their subevents, as well as subevent starting times, we can estimate the binding efficiency and locations of RNAPs on a λ DNA. Our data analysis shows that under the conditions of our experiment with the ratio of 6 to 1 for RNAP to λ DNA molecules, the probability of an RNAP molecule to bind a λ DNA is ∼42%, and that RNAP binding has a main peak at 3.51 μm ± 0.53 μm, most likely corresponding to the two strong promoter regions at 3.48 and 4.43 μm of λ DNA. However, individual RNAP binding sites were not distinguished with this nanopore setup. This work brings out new perspectives and complications to study transcription factor RNAP binding at various positions on very long DNA molecules.
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Abstract
Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.
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