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Shah A, Pathak S, Li K, Garaj S, Bazant MZ, Gupta A, Doyle PS. A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes. NANO LETTERS 2024. [PMID: 38437028 DOI: 10.1021/acs.nanolett.3c04997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.
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Affiliation(s)
- Arjav Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Shakul Pathak
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kun Li
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Slaven Garaj
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
- Department of Physics, National University of Singapore, Singapore 119077
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
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2
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Secme A, Kucukoglu B, Pisheh HS, Alatas YC, Tefek U, Uslu HD, Kaynak BE, Alhmoud H, Hanay MS. Dielectric Detection of Single Nanoparticles Using a Microwave Resonator Integrated with a Nanopore. ACS OMEGA 2024; 9:7827-7834. [PMID: 38405444 PMCID: PMC10882703 DOI: 10.1021/acsomega.3c07506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 02/27/2024]
Abstract
The characterization of individual nanoparticles in a liquid constitutes a critical challenge for the environmental, material, and biological sciences. To detect nanoparticles, electronic approaches are especially desirable owing to their compactness and lower costs. While electronic detection in the form of resistive-pulse sensing has enabled the acquisition of geometric properties of various analytes, impedimetric measurements to obtain dielectric signatures of nanoparticles have scarcely been reported. To explore this orthogonal sensing modality, we developed an impedimetric sensor based on a microwave resonator with a nanoscale sensing gap surrounding a nanopore built on a 220 nm silicon nitride membrane. The microwave resonator has a coplanar waveguide configuration with a resonance frequency of approximately 6.6 GHz. The approach of single nanoparticles near the sensing region and their translocation through the nanopores induced sudden changes in the impedance of the structure. The impedance changes, in turn, were picked up by the phase response of the microwave resonator. We worked with 100 and 50 nm polystyrene nanoparticles to observe single-particle events. Our current implementation was limited by the nonuniform electric field at the sensing region. This work provides a complementary sensing modality for nanoparticle characterization, where the dielectric response, rather than ionic current, determines the signal.
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Affiliation(s)
- Arda Secme
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Berk Kucukoglu
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Hadi S. Pisheh
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Yagmur Ceren Alatas
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Uzay Tefek
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Hatice Dilara Uslu
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Batuhan E. Kaynak
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Hashim Alhmoud
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - M. Selim Hanay
- Department
of Mechanical Engineering, Bilkent University, Ankara 06800, Turkey
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
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3
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Schiopu I, Dragomir I, Asandei A. Single molecule technique unveils the role of electrostatic interactions in ssDNA-gp32 molecular complex stability. RSC Adv 2024; 14:5449-5460. [PMID: 38352678 PMCID: PMC10862658 DOI: 10.1039/d3ra07746b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability.
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Affiliation(s)
- Irina Schiopu
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Isabela Dragomir
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
| | - Alina Asandei
- The Institute of Interdisciplinary Research, Department of Exact Sciences and Natural Sciences, "Alexandru Ioan Cuza" University of Iaşi 700506 Iasi Romania
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4
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Yasuura M, Tan ZL, Horiguchi Y, Ashiba H, Fukuda T. Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components. SENSORS (BASEL, SWITZERLAND) 2023; 23:6830. [PMID: 37571612 PMCID: PMC10422600 DOI: 10.3390/s23156830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.
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Affiliation(s)
- Masato Yasuura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Z.L.T.); (Y.H.); (H.A.); (T.F.)
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5
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Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis. BIOSENSORS 2022; 12:bios12080596. [PMID: 36004992 PMCID: PMC9405897 DOI: 10.3390/bios12080596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022]
Abstract
Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore’s vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen–antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.
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Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. ASTROBIOLOGY 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Vieira LF, Weinhofer AC, Oltjen WC, Yu C, de Souza Mendes PR, Hore MJA. Combining dynamic Monte Carlo with machine learning to study nanoparticle translocation. SOFT MATTER 2022; 18:5218-5229. [PMID: 35770621 DOI: 10.1039/d2sm00431c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Resistive pulse sensing (RPS) measurements of nanoparticle translocation have the ability to provide information on single-particle level characteristics, such as diameter or mobility, as well as ensemble averages. However, interpreting these measurements is complex and requires an understanding of nanoparticle dynamics in confined spaces as well as the ways in which nanoparticles disrupt ion transport while inside a nanopore. Here, we combine Dynamic Monte Carlo (DMC) simulations with Machine Learning (ML) and Poisson-Nernst-Planck calculations to simultaneously simulate nanoparticle dynamics and ion transport during hundreds of independent particle translocations as a function of nanoparticle size, electrophoretic mobility, and nanopore length. The use of DMC simulations allowed us to explicitly investigate the effects of Brownian motion and nanoparticle/nanopore characteristics on the amplitude and duration of translocation signals. Simulation results were verified with experimental RPS measurements and found to be in quantitative agreement.
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Affiliation(s)
- Luiz Fernando Vieira
- Department of Macromolecular Science & Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
- Department of Mechanical Engineering, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente 225, Rio de Janeiro, RJ 22451-900, Brazil
- Instituto Nacional de Tecnologia, Ministry of Science, Technology & Innovation, Av. Venezuela, 82 - Rio de Janeiro, RJ 20081-312, Brazil
| | - Alexandra C Weinhofer
- Department of Macromolecular Science & Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - William C Oltjen
- Department of Macromolecular Science & Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Cindy Yu
- Hathaway Brown School, 19600 North Park Blvd., Shaker Heights, OH 44122, USA
| | - Paulo Roberto de Souza Mendes
- Department of Mechanical Engineering, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente 225, Rio de Janeiro, RJ 22451-900, Brazil
| | - Michael J A Hore
- Department of Macromolecular Science & Engineering, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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Horiguchi Y, Naono N, Sakamoto O, Takeuchi H, Yamaoka S, Miyahara Y. Methodology to Detect Biological Particles Using a Biosensing Surface Integrated in Resistive Pulse Sensing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20168-20178. [PMID: 35446533 DOI: 10.1021/acsami.1c25006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Resistive pulse sensing (RPS) is an analytical method that can be used to individually count particles from a small sample. RPS simply monitors the physical characteristics of particles, such as size, shape, and charge density, and the integration of RPS with biosensing is an attractive theme to detect biological particles such as virus and bacteria. In this report, a methodology of biosensing on RPS was investigated. Polydopamine (PD), an adhesive component of mussels, was used as the base material to create a sensing surface. PD adheres to most materials, such as noble metals, metal oxides, semiconductors, and polymers; as a result, PD is a versatile intermediate layer for the fabrication of a biosensing surface. As an example of a biological particle, human influenza A virus (H1N1 subtype) was used to monitor translocation of particles through the pore membrane. When virus-specific ligands (6'-sialyllactose) were immobilized on the pore surface, the translocation time of the virus particles was considerably extended. The detailed translocation data suggest that the viral particles were trapped on the sensing surface by specific interactions. In addition, virus translocation processes on different pore surfaces were distinguished using machine learning. The result shows that the simple and versatile PD-based biosensor surface design was effective. This advanced RPS measurement system could be a promising analytical technique.
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Affiliation(s)
- Yukichi Horiguchi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Norihiko Naono
- Aipore Inc., Cerulean Tower 15F, 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Osamu Sakamoto
- Aipore Inc., Cerulean Tower 15F, 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
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9
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Xia Z, Lin CY, Drndić M. Protein-enabled detection of ibuprofen and sulfamethoxazole using solid-state nanopores. Proteomics 2022; 22:e2100071. [PMID: 34974637 DOI: 10.1002/pmic.202100071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023]
Abstract
Enabled by proteins, we present an all-electrical method for rapid detection of small pharmaceuticals (ibuprofen and sulfamethoxazole [SMZ]) in aqueous media using silicon nitride pores. Specifically, we use carrier proteins, bovine serum albumin (BSA), and take advantage of their interactions with two small drug molecules to form BSA-drug complexes which can be detected by nm-diameter pores, thereby confirming the presence of small pharmaceuticals. We demonstrate detection of ibuprofen and SMZ at concentrations down to 100 nM (∼21 μg/L) and 48.5 nM (12 μg/L), respectively. We observe changes in electrical signal characteristics (reflected in event durations, rates, current magnitudes, and estimated particle diameters) of BSA-drug complexes compared to BSA-only, and differences between these two small pharmaceuticals, possibly paving a path toward developing selective sensors by identifying "electrical fingerprints" of these molecules in the future. These distinct electrical signals are likely a combined result of diffusion, electrophoretic and electroosmotic effects, interactions between the pore and particles, which depend on pore diameters, pH, and the resulting surface charges. The use of single-molecule-counting nanopores allows sensing of small pharmaceuticals, studies of protein conformational changes, and may aid in efforts to evaluate the impact of small drug molecules on aquatic and human life.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Akhtarian S, Miri S, Doostmohammadi A, Brar SK, Rezai P. Nanopore sensors for viral particle quantification: current progress and future prospects. Bioengineered 2021; 12:9189-9215. [PMID: 34709987 PMCID: PMC8810133 DOI: 10.1080/21655979.2021.1995991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.
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Affiliation(s)
- Shiva Akhtarian
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Saba Miri
- Department of Civil Engineering, York University, Toronto, ON, Canada
| | - Ali Doostmohammadi
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
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Tang W, Wu Y, Mehdipour M, Chen HS, Tilley RD, Gooding JJ. Key Parameters That Determine the Magnitude of the Decrease in Current in Nanopore Blockade Sensors. NANO LETTERS 2021; 21:9374-9380. [PMID: 34726925 DOI: 10.1021/acs.nanolett.1c01855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore blockade sensors were developed to address the challenges of sensitivity and selectivity for conventional nanopore sensors. To date, the parameters affecting the current of the sensor have not been elucidated. Herein, the impacts of nanopore size and charge and the shape, size, surface charge, and aggregation state of magnetic nanoparticles were assessed. The sensor was tolerant to all parameters contrary to predictions from electronic or geometric arguments on the current change. Theoretical models showed the greater importance of the polymers around nanoparticles and the access resistance of nanopores to the current, when compared with translocation-based nanopore sensors. The signal magnitude was dominated by the change in access resistance of ∼4.25 MΩ for all parameters, resulting in a robust system. The findings provide understandings of changes in current when nanopores are blocked, like in RNA trapping or nanopore blockade sensors, and are important for designing sensors based on nanopore blockades.
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Affiliation(s)
- Wenxian Tang
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Milad Mehdipour
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Hsiang-Sheng Chen
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
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12
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Kim E, Lim EK, Park G, Park C, Lim JW, Lee H, Na W, Yeom M, Kim J, Song D, Haam S. Advanced Nanomaterials for Preparedness Against (Re-)Emerging Viral Diseases. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2005927. [PMID: 33586180 DOI: 10.1002/adma.202005927] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Indexed: 05/24/2023]
Abstract
While the coronavirus disease (COVID-19) accounts for the current global pandemic, the emergence of other unknown pathogens, named "Disease X," remains a serious concern in the future. Emerging or re-emerging pathogens continue to pose significant challenges to global public health. In response, the scientific community has been urged to create advanced platform technologies to meet the ever-increasing needs presented by these devastating diseases with pandemic potential. This review aims to bring new insights to allow for the application of advanced nanomaterials in future diagnostics, vaccines, and antiviral therapies, thereby addressing the challenges associated with the current preparedness strategies in clinical settings against viruses. The application of nanomaterials has advanced medicine and provided cutting-edge solutions for unmet needs. Herein, an overview of the currently available nanotechnologies is presented, highlighting the significant features that enable them to control infectious diseases, and identifying the challenges that remain to be addressed for the commercial production of nano-based products is presented. Finally, to conclude, the development of a nanomaterial-based system using a "One Health" approach is suggested. This strategy would require a transdisciplinary collaboration and communication between all stakeholders throughout the entire process spanning across research and development, as well as the preclinical, clinical, and manufacturing phases.
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Affiliation(s)
- Eunjung Kim
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon, 34113, Republic of Korea
| | - Geunseon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Chaewon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Jong-Woo Lim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Hyo Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Woonsung Na
- College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Minjoo Yeom
- College of Pharmacy, Korea University, Sejong-ro, Sejong, 30019, Republic of Korea
| | - Jinyoung Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Daesub Song
- College of Pharmacy, Korea University, Sejong-ro, Sejong, 30019, Republic of Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
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Park G, Kim HO, Lim JW, Park C, Yeom M, Song D, Haam S. Rapid detection of influenza A (H1N1) virus by conductive polymer-based nanoparticle via optical response to virus-specific binding. NANO RESEARCH 2021; 15:2254-2262. [PMID: 34567436 PMCID: PMC8453473 DOI: 10.1007/s12274-021-3772-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 05/28/2023]
Abstract
UNLABELLED A recurrent pandemic with unpredictable viral nature has implied the need for a rapid diagnostic technology to facilitate timely and appropriate countermeasures against viral infections. In this study, conductive polymer-based nanoparticles have been developed as a tool for rapid diagnosis of influenza A (H1N1) virus. The distinctive property of a conductive polymer that transduces stimulus to respond, enabled immediate optical signal processing for the specific recognition of H1N1 virus. Conductive poly(aniline-co-pyrrole)-encapsulated polymeric vesicles, functionalized with peptides, were fabricated for the specific recognition of H1N1 virus. The low solubility of conductive polymers was successfully improved by employing vesicles consisting of amphiphilic copolymers, facilitating the viral titer-dependent production of the optical response. The optical response of the detection system to the binding event with H1N1, a mechanical stimulation, was extensively analyzed and provided concordant information on viral titers of H1N1 virus in 15 min. The specificity toward the H1N1 virus was experimentally demonstrated via a negative optical response against the control group, H3N2. Therefore, the designed system that transduces the optical response to the target-specific binding can be a rapid tool for the diagnosis of H1N1. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (Table S1 and Figs. S1-S8) is available in the online version of this article at 10.1007/s12274-021-3772-6.
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Affiliation(s)
- Geunseon Park
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul, 03722 Republic of Korea
| | - Hyun-Ouk Kim
- Division of Chemical Engineering and Bioengineering College of Art, Culture and Engineering, Kangwon National University, Chuncheon-si, Gangwon-do, 24341 Republic of Korea
- Biohealth-machinery Convergence Engineering, Kangwon National University, Chuncheon, Gangwon-do, 24341 Republic of Korea
| | - Jong-Woo Lim
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul, 03722 Republic of Korea
| | - Chaewon Park
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul, 03722 Republic of Korea
| | - Minjoo Yeom
- College of Pharmacy, Korea University, Sejong, 30019 Republic of Korea
| | - Daesub Song
- College of Pharmacy, Korea University, Sejong, 30019 Republic of Korea
| | - Seungjoo Haam
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul, 03722 Republic of Korea
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14
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Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
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Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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15
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Yanagi I, Takeda KI. Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO 2sacrificial layer process. NANOTECHNOLOGY 2021; 32:415301. [PMID: 34214991 DOI: 10.1088/1361-6528/ac10e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO2. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO2sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)60passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.
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Affiliation(s)
- Itaru Yanagi
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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16
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Sethi K, Dailey GP, Zahid OK, Taylor EW, Ruzicka JA, Hall AR. Direct Detection of Conserved Viral Sequences and Other Nucleic Acid Motifs with Solid-State Nanopores. ACS NANO 2021; 15:8474-8483. [PMID: 33914524 PMCID: PMC8801185 DOI: 10.1021/acsnano.0c10887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The rapid and reliable recognition of nucleic acid sequences is essential to a broad range of fields including genotyping, gene expression analysis, and pathogen screening. For viral detection in particular, the capability is critical for optimal therapeutic response and preventing disease transmission. Here, we report an approach for detecting identifying sequence motifs within genome-scale single-strand DNA and RNA based on solid-state nanopores. By designing DNA oligonucleotide probes with complementarity to target sequences within a target genome, we establish a protocol to yield affinity-tagged duplex molecules the same length as the probe only if the target is present. The product can subsequently be bound to a protein chaperone and analyzed quantitatively with a selective solid-state nanopore assay. We first use a model DNA genome (M13mp18) to validate the approach, showing the successful isolation and detection of multiple target sequences simultaneously. We then demonstrate the protocol for the detection of RNA viruses by identifying and targeting a highly conserved sequence within human immunodeficiency virus (HIV-1B).
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Affiliation(s)
- Komal Sethi
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Gabrielle P. Dailey
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Osama K. Zahid
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Ethan W. Taylor
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jan A. Ruzicka
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC 27268, USA
| | - Adam R. Hall
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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17
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Pal S, Ramkumar B, Jugade S, Rao A, Naik A, Chakraborty B, Varma MM. Effect of single nanoparticle-nanopore interaction strength on ionic current modulation. SENSORS AND ACTUATORS. B, CHEMICAL 2020; 325:128785. [PMID: 34321714 PMCID: PMC8312308 DOI: 10.1016/j.snb.2020.128785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Solid-state nanopores are rapidly emerging as promising platforms for developing various single molecule sensing applications. The modulation of ionic current through the pore due to translocation of the target molecule has been the dominant measurement modality in nanopore sensors. Here, we focus on the dwell time, which is the duration taken by the target molecule or particle to traverse the pore and study its dependence on the strength of interaction of the target with the pore using single gold nanoparticles (NPs) as targets interacting with a silicon nitride (SiN) nanopore. The strength of interaction, which in our case is electrostatic in nature, can be controlled by coating the nanoparticles with charged polymers. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the Silicon Nitride pore which is negatively charged. Our experiments revealed how this modulation of the electrostatic force greatly affects the dwell time. Positively charged NPs with strong attractive interactions with the pore resulted in increase of dwell times by 2-3 orders of magnitude, from 0.4 ms to 75.3 ms. This extreme sensitivity of the dwell time on the strength of interaction between a target and nanopore can be exploited in emerging nanopore sensor applications.
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Affiliation(s)
- Sohini Pal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - B. Ramkumar
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sanket Jugade
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, United States
| | - Akshay Naik
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Manoj M. Varma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
- Corresponding author. (M.M. Varma)
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18
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Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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19
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Zeng S, Li S, Utterström J, Wen C, Selegård R, Zhang SL, Aili D, Zhang Z. Mechanism and Kinetics of Lipid Bilayer Formation in Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1446-1453. [PMID: 31971393 DOI: 10.1021/acs.langmuir.9b03637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores provide a highly versatile platform for rapid electrical detection and analysis of single molecules. Lipid bilayer coating of the nanopores can reduce nonspecific analyte adsorption to the nanopore sidewalls and increase the sensing selectivity by providing possibilities for tethering specific ligands in a cell-membrane mimicking environment. However, the mechanism and kinetics of lipid bilayer formation from vesicles remain unclear in the presence of nanopores. In this work, we used a silicon-based, truncated pyramidal nanopore array as the support for lipid bilayer formation. Lipid bilayer formation in the nanopores was monitored in real time by the change in ionic current through the nanopores. Statistical analysis revealed that a lipid bilayer is formed from the instantaneous rupture of individual vesicle upon adsorption in the nanopores, differing from the generally agreed mechanism that lipid bilayer forms at a high vesicle surface coverage on a planar support. The dependence of the lipid bilayer formation process on the applied bias, vesicle size, and concentration was systematically studied. In addition, the nonfouling properties of the lipid bilayer coated nanopores were demonstrated during long single-stranded DNA translocation through the nanopore array. The findings indicate that the lipid bilayer formation process can be modulated by introducing nanocavities intentionally on the planar surface to create active sites or changing the vesicle size and concentration.
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Affiliation(s)
- Shuangshuang Zeng
- Division of Solid-State Electronics, Department of Electrical Engineering , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Shiyu Li
- Division of Solid-State Electronics, Department of Electrical Engineering , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Johanna Utterström
- Laboratory of Molecular Materials, Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Chenyu Wen
- Division of Solid-State Electronics, Department of Electrical Engineering , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Robert Selegård
- Laboratory of Molecular Materials, Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Shi-Li Zhang
- Division of Solid-State Electronics, Department of Electrical Engineering , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Daniel Aili
- Laboratory of Molecular Materials, Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , SE-581 83 Linköping , Sweden
| | - Zhen Zhang
- Division of Solid-State Electronics, Department of Electrical Engineering , Uppsala University , SE-751 21 Uppsala , Sweden
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20
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Tsutsui M, Yamazaki T, Tatematsu K, Yokota K, Esaki Y, Kubo Y, Deguchi H, Arima A, Kuroda S, Kawai T. High-throughput single nanoparticle detection using a feed-through channel-integrated nanopore. NANOSCALE 2019; 11:20475-20484. [PMID: 31647092 DOI: 10.1039/c9nr07039g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The outstanding sensitivity of solid-state nanopore sensors comes at a price of low detection efficiency due to the lack of active means to transfer objects into the nanoscale sensing zone. Here we report on a key technology for high-throughput single-nanoparticle detection which exploits mutual effects of microfluidics control and multipore electrophoresis in nanopore-in-channel units integrated on a thin Si3N4 membrane. Using this novel nanostructure, we demonstrated a proof-of-concept for influenza viruses via hydropressure regulation of mass transport in the fluidic channel for continuous feeding of biosamples into the effective electric field extending out from the nanopores, wherein the feed-through mechanism allowed us to selectively detect charged objects in physiological media such as human saliva. With the versatility of nanopore sensing technologies applicable to analytes of virtually any size from cells to polynucleotides, the present integration strategy may open new avenues for practical ultrasensitive bioanalytical tools.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoko Yamazaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kenji Tatematsu
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan. and National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa 761-0395, Japan
| | - Yuko Esaki
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Yukari Kubo
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Hiroko Deguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Shun'ichi Kuroda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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21
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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22
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Miyagawa T, Hongo S, Nakamura N, Horiguchi Y, Miyahara Y, Shibata H. A Novel Diagnostic System for Infectious Diseases Using Solid-State Nanopore Devices. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:2833-2836. [PMID: 30440991 DOI: 10.1109/embc.2018.8512856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nanopore-based diagnostic systems are a promising tool for counting viruses in a specimen one by one. However, despite intensive R&D efforts, it remains difficult to recognize virus subtypes by nanopore devices. We thus propose a novel diagnostic system that combines a specialized virus recognition procedure with a nanopore detection procedure. This recognition procedure consists of three steps: 1) capture target viruses using specific probes for recognition; 2) release captured targets; and 3) detect released targets by nanopore. Proof-of-concept tests are conducted using avidin-modified fluorescent particles (as a model for viruses) and biotin-modified alkane thiol (as a model for probes). The avidin-modified particles are confirmed to be captured on electrode by biotin-modified probes and then, the particles are electrochemically released from the electrode. Consequently, the released particles are successfully detected by nanopore devices. Furthermore, the concept is also proved by using human influenza viruses (H1N1, A/PR/8/34) and sugar chain (6'-sialyllactose)-modified probes. This suggests that our concept is applicable to various infectious diseases by changing probes (ligands).
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23
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Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules. Sci Rep 2019; 9:13143. [PMID: 31511597 PMCID: PMC6739384 DOI: 10.1038/s41598-019-49622-y] [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] [Received: 06/13/2019] [Accepted: 08/28/2019] [Indexed: 01/15/2023] Open
Abstract
For nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.
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24
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Eggenberger OM, Leriche G, Koyanagi T, Ying C, Houghtaling J, Schroeder TBH, Yang J, Li J, Hall A, Mayer M. Fluid surface coatings for solid-state nanopores: comparison of phospholipid bilayers and archaea-inspired lipid monolayers. NANOTECHNOLOGY 2019; 30:325504. [PMID: 30991368 DOI: 10.1088/1361-6528/ab19e6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the context of sensing and characterizing single proteins with synthetic nanopores, lipid bilayer coatings provide at least four benefits: first, they minimize unwanted protein adhesion to the pore walls by exposing a zwitterionic, fluid surface. Second, they can slow down protein translocation and rotation by the opportunity to tether proteins with a lipid anchor to the fluid bilayer coating. Third, they provide the possibility to impart analyte specificity by including lipid anchors with a specific receptor or ligand in the coating. Fourth, they offer a method for tuning nanopore diameters by choice of the length of the lipid's acyl chains. The work presented here compares four properties of various lipid compositions with regard to their suitability as nanopore coatings for protein sensing experiments: (1) electrical noise during current recordings through solid-state nanopores before and after lipid coating, (2) long-term stability of the recorded current baseline and, by inference, of the coating, (3) viscosity of the coating as quantified by the lateral diffusion coefficient of lipids in the coating, and (4) the success rate of generating a suitable coating for quantitative nanopore-based resistive pulse recordings. We surveyed lipid coatings prepared from bolaamphiphilic, monolayer-forming lipids inspired by extremophile archaea and compared them to typical bilayer-forming phosphatidylcholine lipids containing various fractions of curvature-inducing lipids or cholesterol. We found that coatings from archaea-inspired lipids provide several advantages compared to conventional phospholipids; the stable, low noise baseline qualities and high viscosity make these membranes especially suitable for analysis that estimates physical protein parameters such as the net charge of proteins as they enable translocation events with sufficiently long duration to time-resolve dwell time distributions completely. The work presented here reveals that the ease or difficulty of coating a nanopore with lipid membranes did not depend significantly on the composition of the lipid mixture, but rather on the geometry and surface chemistry of the nanopore in the solid state substrate. In particular, annealing substrates containing the nanopore increased the success rate of generating stable lipid coatings.
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25
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Lu Y, Wu XY, Ying YL, Long YT. Simultaneous single-molecule discrimination of cysteine and homocysteine with a protein nanopore. Chem Commun (Camb) 2019; 55:9311-9314. [PMID: 31310244 DOI: 10.1039/c9cc04077c] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Discrimination between cysteine and homocysteine at the single-molecule level is achieved within a K238Q mutant aerolysin nanopore, which provides a confined space for high spatial resolution to identify the amino acid difference with a 5'-benzaldehyde poly(dA)4 probe. Our strategy allows potential detection and characterization of various amino acids and their modifications, and provides a crucial step towards developing nanopore protein sequencing devices.
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Affiliation(s)
- Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Xue-Yuan Wu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China. and State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China. and State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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de Vreede LJ, Ying C, Houghtaling J, Figueiredo Da Silva J, Hall AR, Lovera A, Mayer M. Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores. NANOTECHNOLOGY 2019; 30:265301. [PMID: 30849769 DOI: 10.1088/1361-6528/ab0e2a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This paper presents a maskless method to manufacture fused silica chips for low-noise resistive-pulse sensing. The fabrication includes wafer-scale density modification of fused silica with a femtosecond-pulsed laser, low-pressure chemical vapor deposition (LPVCD) of silicon nitride (SiN x ) and accelerated chemical wet etching of the laser-exposed regions. This procedure leads to a freestanding SiN x window, which is permanently attached to a fused silica support chip and the resulting chips are robust towards Piranha cleaning at ∼80 °C. After parallel chip manufacturing, we created a single nanopore in each chip by focused helium-ion beam or by controlled breakdown. Compared to silicon chips, the resulting fused silica nanopore chips resulted in a four-fold improvement of both the signal-to-noise ratio and the capture rate for signals from the translocation of IgG1 proteins at a recording bandwidth of 50 kHz. At a bandwidth of ∼1 MHz, the noise from the fused silica nanopore chips was three- to six-fold reduced compared to silicon chips. In contrast to silicon chips, fused silica chips showed no laser-induced current noise-a significant benefit for experiments that strive to combine nanopore-based electrical and optical measurements.
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Affiliation(s)
- Lennart J de Vreede
- Biophysics group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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McNamee CE. Effect of a liquid flow on the forces between charged solid surfaces and the non-equilibrium electric double layer. Adv Colloid Interface Sci 2019; 266:21-33. [PMID: 30831437 DOI: 10.1016/j.cis.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 01/05/2023]
Abstract
The physical properties of fluids can change as they flow through confined charged solid areas, such as a charged pore or channel, allowing the transport of fluid through the channels to be controlled. The liquid flow is influenced by the electrical double layer (EDL) that is next to the charged surface. The overlap of the EDL of two nearby charged solid surfaces results in the formation of an electrostatic force. A flow will change the EDL from an equilibrium state to a non-equilibrium state, causing the forces to also change from an equilibrium (static) state to a non-equilibrium (dynamic) state. There are numerous studies that have been performed by molecular dynamics (MD) simulations and surface force experiments which concern the equilibrium EDL and the equilibrium surface forces. However, there are significantly less studies concerning the non-equilibrium EDL and non-equilibrium surface forces, including the effect of a liquid flow on the EDL and the surface forces. This review will focus on how a liquid flow changes the EDL and the surface forces of charged hydrophilic solid surfaces in aqueous electrolyte solutions. Results obtained by MD simulations and surface force experiments are discussed in this review. A flow was seen to be able to distort the EDL, causing the surface forces to change. The EDL and surface forces were affected by the surface charge, the structuring ability of the liquid molecules and ions near the surfaces, the ion type and their specificity towards the surface, the ionic concentration, and the rate of flow of the liquid. The physical properties of the system were shown to change with a flow, e.g. the increase in the fluid viscosity next to a charged solid surface that accompanies a flow. The number of counterions adsorbed to a charged solid surface was also seen to affect the direction of flow in an EDL. The surface forces were shown to change with a flow due to changes in hydrodynamic and electrostatic forces. Information on the effect of the liquid flow on the EDL and surface forces will help improve applications that require fluid to be transported in a defined way through a charged solid vessel.
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Horiguchi Y, Goda T, Matsumoto A, Takeuchi H, Yamaoka S, Miyahara Y. Gold Nanoparticles with Ligand/Zwitterion Hybrid Layer for Individual Counting of Influenza A H1N1 Subtype Using Resistive Pulse Sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:1798-1806. [PMID: 30133291 DOI: 10.1021/acs.langmuir.8b01586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Resistive pulse sensing (RPS) is an analytical technique for detecting particles with nano- to micrometer diameters, such as proteins, viruses, and bacteria. RPS is a promising tool for diagnosis as it can analyze the characteristics of target particles individually from ion current blockades as pulse waveforms. However, it is difficult to discriminate analog targets because RPS merely provides physical information such as size, shape, concentration, and charge density of the analyte. Influenza A virus, which is 80-120 nm in diameter, has various subtypes, demonstrating the diversity of virus characteristics. For example, highly pathogenic avian influenza infections in humans are recognized as an emerging infectious disease with high mortality rates compared with human influenza viruses. Distinguishing human from avian influenza using their differing biological characteristics would be challenging using RPS. To develop a highly selective diagnostic system for infectious diseases, we combined RPS with molecular recognition. Gold nanoparticles (GNPs) that have human influenza A (H1N1 subtype) virus-specific sialic acid receptors on the surface were prepared as a virus label for RPS analysis. A sulfobetaine and sialic acid (ligand) hybrid surface was formed on the GNPs for the suppression of nonspecific interaction. The results show a size change of viruses derived from specific interactions with GNPs. In contrast, no size shift was observed when nonspecific sialic acid receptor-immobilized GNPs were used. Detection of viruses by individual particle counting could be a new facet of diagnosis.
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Affiliation(s)
- Yukichi Horiguchi
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University (TMDU) , 2-3-10 Kanda-Surugadai , Chiyoda , Tokyo 101-0062 , Japan
| | - Tatsuro Goda
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University (TMDU) , 2-3-10 Kanda-Surugadai , Chiyoda , Tokyo 101-0062 , Japan
| | - Akira Matsumoto
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University (TMDU) , 2-3-10 Kanda-Surugadai , Chiyoda , Tokyo 101-0062 , Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University (TMDU) , 1-5-45 Yushima , Bunkyo , Tokyo 113-8510 , Japan
| | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences , Tokyo Medical and Dental University (TMDU) , 1-5-45 Yushima , Bunkyo , Tokyo 113-8510 , Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering , Tokyo Medical and Dental University (TMDU) , 2-3-10 Kanda-Surugadai , Chiyoda , Tokyo 101-0062 , Japan
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Kondylis P, Schlicksup CJ, Zlotnick A, Jacobson SC. Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids. Anal Chem 2019; 91:622-636. [PMID: 30383361 PMCID: PMC6472978 DOI: 10.1021/acs.analchem.8b04824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
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Arima A, Harlisa IH, Yoshida T, Tsutsui M, Tanaka M, Yokota K, Tonomura W, Yasuda J, Taniguchi M, Washio T, Okochi M, Kawai T. Identifying Single Viruses Using Biorecognition Solid-State Nanopores. J Am Chem Soc 2018; 140:16834-16841. [DOI: 10.1021/jacs.8b10854] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Akihide Arima
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Ilva Hanun Harlisa
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takeshi Yoshida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kazumichi Yokota
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Wataru Tonomura
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Disease, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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Houghtaling J, List J, Mayer M. Nanopore-Based, Rapid Characterization of Individual Amyloid Particles in Solution: Concepts, Challenges, and Prospects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802412. [PMID: 30225962 DOI: 10.1002/smll.201802412] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Aggregates of misfolded proteins are associated with several devastating neurodegenerative diseases. These so-called amyloids are therefore explored as biomarkers for the diagnosis of dementia and other disorders, as well as for monitoring disease progression and assessment of the efficacy of therapeutic interventions. Quantification and characterization of amyloids as biomarkers is particularly demanding because the same amyloid-forming protein can exist in different states of assembly, ranging from nanometer-sized monomers to micrometer-long fibrils that interchange dynamically both in vivo and in samples from body fluids ex vivo. Soluble oligomeric amyloid aggregates, in particular, are associated with neurotoxic effects, and their molecular organization, size, and shape appear to determine their toxicity. This concept article proposes that the emerging field of nanopore-based analytics on a single molecule and single aggregate level holds the potential to account for the heterogeneity of amyloid samples and to characterize these particles-rapidly, label-free, and in aqueous solution-with regard to their size, shape, and abundance. The article describes the concept of nanopore-based resistive pulse sensing, reviews previous work in amyloid analysis, and discusses limitations and challenges that will need to be overcome to realize the full potential of amyloid characterization on a single-particle level.
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Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
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32
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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33
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Chae H, Kwak DK, Lee MK, Chi SW, Kim KB. Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction. NANOSCALE 2018; 10:17227-17235. [PMID: 30191243 DOI: 10.1039/c8nr06423g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although protein-protein interactions (PPIs) are emerging therapeutic targets for human diseases, development of high-throughput screening (HTS) technologies against PPI targets remains challenging. In this study, we propose a protein complex structure to effectively detect conformational changes of protein resulting from PPI using solid-state nanopore for a novel, widely-applicable drug screening method against various PPI targets. To effectively detect conformational changes resulting from PPI, we designed a fusion protein MLP (MDM2-linker-p53TAD), where p53TAD and MDM2 are connected by a 16 amino acid linker. The globular conformation of MLP exhibited a single-peak translocation event, whereas the dumbbell-like conformation of nutlin-3-bound MLP revealed as a double-peak signal. The proportion of double-peak to single-peak signals increased from 9.3% to 23.0% as nutlin-3 concentration increased. The translocation kinetics of the two different MLP conformations with varied applied voltage were analyzed. Further, the fractional current of the intra-peak of the double-peak signal was analyzed, probing the structure of our designed protein complex. This approach of nanopore sensing may be extendedly employed in screening of PPI inhibitors and protein conformation studies.
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Affiliation(s)
- Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea.
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34
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Mamad-Hemouch H, Bacri L, Huin C, Przybylski C, Thiébot B, Patriarche G, Jarroux N, Pelta J. Versatile cyclodextrin nanotube synthesis with functional anchors for efficient ion channel formation: design, characterization and ion conductance. NANOSCALE 2018; 10:15303-15316. [PMID: 30069556 DOI: 10.1039/c8nr02623h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biomimetic ion channels with different materials have been extensively designed to study the dynamics in a confined medium. These channels allow the development of several applications, such as ultra-fast sequencing and biomarker detection. When considering their synthesis, the use of cheap, non-cytotoxic and readily available materials is an increasing priority. Cyclodextrins, in supramolecular architectures, are widely utilized for pharmaceutical and biotechnological applications. Recent work has shown that short nanotubes (NTs) based on alpha-cyclodextrin (α-CD) assemble transient ion channels into membranes without cytotoxicity. In this study, we probe the influence of new cyclodextrin NT structural parameters and chemical modifications on channel formation, stability and electrical conductance. We report the successful synthesis of β- and γ-cyclodextrin nanotubes (β-CDNTs and γ-CDNTs), as evidenced by mass-spectrometry and high-resolution transmission electron microscopy. CDNTs were characterized by their length, diameter and number of CDs. Two hydrophobic groups, silylated or vinylated, were attached along the γ-CDNTs, improving the insertion time into the membrane. All NTs synthesized form spontaneous biomimetic ion channels. The hydrophobic NTs exhibit higher stability in membranes. Electrophysiological measurements show that ion transport is the main contribution of NT conductance and that the ion energy penalty for the entry into these NTs is similar to that of biological channels.
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Affiliation(s)
- Hajar Mamad-Hemouch
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.
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Szakács Z, Mészáros T, de Jonge MI, Gyurcsányi RE. Selective counting and sizing of single virus particles using fluorescent aptamer-based nanoparticle tracking analysis. NANOSCALE 2018; 10:13942-13948. [PMID: 29845157 DOI: 10.1039/c8nr01310a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Detection and counting of single virus particles in liquid samples are largely limited to narrow size distribution of viruses and purified formulations. To address these limitations, here we propose a calibration-free method that enables concurrently the selective recognition, counting and sizing of virus particles as demonstrated through the detection of human respiratory syncytial virus (RSV), an enveloped virus with a broad size distribution, in throat swab samples. RSV viruses were selectively labeled through their attachment glycoproteins (G) with fluorescent aptamers, which further enabled their identification, sizing and counting at the single particle level by fluorescent nanoparticle tracking analysis. The proposed approach seems to be generally applicable to virus detection and quantification. Moreover, it could be successfully applied to detect single RSV particles in swab samples of diagnostic relevance. Since the selective recognition is associated with the sizing of each detected particle, this method enables to discriminate viral elements linked to the virus as well as various virus forms and associations.
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Affiliation(s)
- Zoltán Szakács
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellert tér 4, H-1111 Budapest, Hungary.
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Marien I de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Róbert E Gyurcsányi
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellert tér 4, H-1111 Budapest, Hungary.
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36
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Bioinspired, nanoscale approaches in contemporary bioanalytics (Review). Biointerphases 2018; 13:040801. [DOI: 10.1116/1.5037582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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37
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Liu F, Ni L, Zhe J. Lab-on-a-chip electrical multiplexing techniques for cellular and molecular biomarker detection. BIOMICROFLUIDICS 2018; 12:021501. [PMID: 29682143 PMCID: PMC5893332 DOI: 10.1063/1.5022168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Signal multiplexing is vital to develop lab-on-a-chip devices that can detect and quantify multiple cellular and molecular biomarkers with high throughput, short analysis time, and low cost. Electrical detection of biomarkers has been widely used in lab-on-a-chip devices because it requires less external equipment and simple signal processing and provides higher scalability. Various electrical multiplexing for lab-on-a-chip devices have been developed for comprehensive, high throughput, and rapid analysis of biomarkers. In this paper, we first briefly introduce the widely used electrochemical and electrical impedance sensing methods. Next, we focus on reviewing various electrical multiplexing techniques that had achieved certain successes on rapid cellular and molecular biomarker detection, including direct methods (spatial and time multiplexing), and emerging technologies (frequency, codes, particle-based multiplexing). Lastly, the future opportunities and challenges on electrical multiplexing techniques are also discussed.
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Affiliation(s)
- Fan Liu
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
| | - Liwei Ni
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
| | - Jiang Zhe
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
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YANG J, LI S, WU XY, LONG YT. Development of Biological Nanopore Technique in Non-gene Sequencing Application. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61053-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lin X, Ivanov AP, Edel JB. Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles. Chem Sci 2017; 8:3905-3912. [PMID: 28626560 PMCID: PMC5465561 DOI: 10.1039/c7sc00415j] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023] Open
Abstract
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
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Affiliation(s)
- Xiaoyan Lin
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Aleksandar P Ivanov
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
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Yang L, Yamamoto T. Quantification of Virus Particles Using Nanopore-Based Resistive-Pulse Sensing Techniques. Front Microbiol 2016; 7:1500. [PMID: 27713738 PMCID: PMC5031608 DOI: 10.3389/fmicb.2016.01500] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 09/08/2016] [Indexed: 11/13/2022] Open
Abstract
Viruses have drawn much attention in recent years due to increased recognition of their important roles in virology, immunology, clinical diagnosis, and therapy. Because the biological and physical properties of viruses significantly impact their applications, quantitative detection of individual virus particles has become a critical issue. However, due to various inherent limitations of conventional enumeration techniques such as infectious titer assays, immunological assays, and electron microscopic observation, this issue remains challenging. Thanks to significant advances in nanotechnology, nanostructure-based electrical sensors have emerged as promising platforms for real-time, sensitive detection of numerous bioanalytes. In this paper, we review recent progress in nanopore-based electrical sensing, with particular emphasis on the application of this technique to the quantification of virus particles. Our aim is to provide insights into this novel nanosensor technology, and highlight its ability to enhance current understanding of a variety of viruses.
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Affiliation(s)
| | - Takatoki Yamamoto
- Department of Mechanical Engineering, School of Engineering, Tokyo Institute of TechnologyTokyo, Japan
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Darvish A, Goyal G, Aneja R, Sundaram RVK, Lee K, Ahn CW, Kim KB, Vlahovska PM, Kim MJ. Nanoparticle mechanics: deformation detection via nanopore resistive pulse sensing. NANOSCALE 2016; 8:14420-14431. [PMID: 27321911 DOI: 10.1039/c6nr03371g] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Solid-state nanopores have been widely used in the past for single-particle analysis of nanoparticles, liposomes, exosomes and viruses. The shape of soft particles, particularly liposomes with a bilayer membrane, can greatly differ inside the nanopore compared to bulk solution as the electric field inside the nanopores can cause liposome electrodeformation. Such deformations can compromise size measurement and characterization of particles, but are often neglected in nanopore resistive pulse sensing. In this paper, we investigated the deformation of various liposomes inside nanopores. We observed a significant difference in resistive pulse characteristics between soft liposomes and rigid polystyrene nanoparticles especially at higher applied voltages. We used theoretical simulations to demonstrate that the difference can be explained by shape deformation of liposomes as they translocate through the nanopores. Comparing our results with the findings from electrodeformation experiments, we demonstrated that the rigidity of liposomes can be qualitatively compared using resistive pulse characteristics. This application of nanopores can provide new opportunities to study the mechanics at the nanoscale, to investigate properties of great value in fundamental biophysics and cellular mechanobiology, such as virus deformability and fusogenicity, and in applied sciences for designing novel drug/gene delivery systems.
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Affiliation(s)
- Armin Darvish
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA.
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Wu H, Chen Y, Zhou Q, Wang R, Xia B, Ma D, Luo K, Liu Q. Translocation of Rigid Rod-Shaped Virus through Various Solid-State Nanopores. Anal Chem 2016; 88:2502-10. [DOI: 10.1021/acs.analchem.5b04905] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hongwen Wu
- State
Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yuhao Chen
- CAS
Key Laboratory of Soft Matter Chemistry and Department of Polymer
Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qizhao Zhou
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510000, China
| | - Rongliang Wang
- State
Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China
| | - Baicheng Xia
- CAS
Key Laboratory of Soft Matter Chemistry and Department of Polymer
Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dejun Ma
- State
Key Laboratory of Elemento-Organic Chemistry and Department of Chemical
Biology, National Pesticide Engineering Research Center (Tianjin), Nankai University, Tianjin, 300071, China
| | - Kaifu Luo
- CAS
Key Laboratory of Soft Matter Chemistry and Department of Polymer
Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Quanjun Liu
- State
Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China
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Ferrier DC, Shaver MP, Hands PJW. Micro- and nano-structure based oligonucleotide sensors. Biosens Bioelectron 2015; 68:798-810. [PMID: 25655465 DOI: 10.1016/j.bios.2015.01.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 12/26/2022]
Abstract
This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.
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Affiliation(s)
- David C Ferrier
- School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK
| | - Michael P Shaver
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Philip J W Hands
- School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK.
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Harms Z, Haywood DG, Kneller AR, Selzer L, Zlotnick A, Jacobson SC. Single-particle electrophoresis in nanochannels. Anal Chem 2015; 87:699-705. [PMID: 25489919 PMCID: PMC4287839 DOI: 10.1021/ac503527d] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/28/2014] [Indexed: 02/05/2023]
Abstract
Electrophoretic mobilities and particle sizes of individual Hepatitis B Virus (HBV) capsids were measured in nanofluidic channels with two nanopores in series. The channels and pores had three-dimensional topography and were milled directly in glass substrates with a focused ion beam instrument assisted by an electron flood gun. The nanochannel between the two pores was 300 nm wide, 100 nm deep, and 2.5 μm long, and the nanopores at each end had dimensions 45 nm wide, 45 nm deep, and 400 nm long. With resistive-pulse sensing, the nanopores fully resolved pulse amplitude distributions of T = 3 HBV capsids (32 nm outer diameter) and T = 4 HBV capsids (35 nm outer diameter) and had sufficient peak capacity to discriminate intermediate species from the T = 3 and T = 4 capsid distributions in an assembly reaction. Because the T = 3 and T = 4 capsids have a wiffle-ball geometry with a hollow core, the observed change in current due to the capsid transiting the nanopore is proportional to the volume of electrolyte displaced by the volume of capsid protein, not the volume of the entire capsid. Both the signal-to-noise ratio of the pulse amplitude and resolution between the T = 3 and T = 4 distributions of the pulse amplitudes increase as the electric field strength is increased. At low field strengths, transport of the larger T = 4 capsid through the nanopores is hindered relative to the smaller T = 3 capsid due to interaction with the pores, but at sufficiently high field strengths, the T = 3 and T = 4 capsids had the same electrophoretic mobilities (7.4 × 10(-5) cm(2) V(-1) s(-1)) in the nanopores and in the nanochannel with the larger cross-sectional area.
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Affiliation(s)
- Zachary
D. Harms
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel G. Haywood
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Andrew R. Kneller
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lisa Selzer
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Stephen C. Jacobson
- Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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Youn Y, Han S. Investigation of field effects in a solid-state nanopore transistor. Phys Chem Chem Phys 2015; 17:27806-11. [DOI: 10.1039/c5cp03125g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In order to calculate ion currents through solid-state nanopore transistors realistically, we propose a computational model based on the Poisson–Nernst–Plank equation.
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Affiliation(s)
- Yong Youn
- Department of materials Science and Engineering and Research Institute of Advanced Materials
- Seoul National University
- Seoul 151-744
- Korea
| | - Seungwu Han
- Department of materials Science and Engineering and Research Institute of Advanced Materials
- Seoul National University
- Seoul 151-744
- Korea
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Abstract
This Review focusses on the recent surge in applied research using tunable resistive pulse sensing, a technique used to analyse submicron colloids in aqueous solutions on a particle-by-particle basis.
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Affiliation(s)
- Eva Weatherall
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- New Zealand
- Callaghan Innovation
| | - Geoff R. Willmott
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
- School of Chemical and Physical Sciences
- Victoria University of Wellington
- New Zealand
- The Departments of Physics and Chemistry
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Agrawal KL, Shtein M. Self-powered ion detectors based on dye-sensitized photovoltaics. NANOSCALE 2014; 6:11019-11023. [PMID: 25135606 DOI: 10.1039/c4nr03417a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Autonomous sensing of metal ion contamination in remote environments with high reproducibility and sensitivity could unlock many new applications, but involves trade-offs between compactness, sensitivity, and power provisioning. In prior demonstrations of semi-autonomous sensors, the power source (e.g. a solar cell) was an additional component. Here, we demonstrate a concept, wherein a dye-sensitized solar cell is used for both power generation and sensitive detection of ionic analytes, unlocking a new pathway for ultra-miniaturization and integration.
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Affiliation(s)
- Kanika L Agrawal
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Stiff filamentous virus translocations through solid-state nanopores. Nat Commun 2014; 5:4171. [DOI: 10.1038/ncomms5171] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/20/2014] [Indexed: 11/08/2022] Open
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Luo L, German SR, Lan WJ, Holden DA, Mega TL, White HS. Resistive-pulse analysis of nanoparticles. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:513-35. [PMID: 24896310 DOI: 10.1146/annurev-anchem-071213-020107] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The development of nanopore fabrication methods during the past decade has led to the resurgence of resistive-pulse analysis of nanoparticles. The newly developed resistive-pulse methods enable researchers to simultaneously study properties of a single nanoparticle and statistics of a large ensemble of nanoparticles. This review covers the basic theory and recent advances in applying resistive-pulse analysis and extends to more complex transport motion (e.g., stochastic thermal motion of a single nanoparticle) and unusual electrical responses (e.g., resistive-pulse response sensitive to surface charge), followed by a brief summary of numerical simulations performed in this field. We emphasize the forces within a nanopore governing translocation of low-aspect-ratio, nondeformable particles but conclude by also considering soft materials such as liposomes and microgels.
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Affiliation(s)
- Long Luo
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112;
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