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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [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: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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2
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Trojanowicz M. Impact of nanotechnology on progress of flow methods in chemical analysis: A review. Anal Chim Acta 2023; 1276:341643. [PMID: 37573121 DOI: 10.1016/j.aca.2023.341643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
In evolution of instrumentation for analytical chemistry as crucial technological breakthroughs should be considered a common introduction of electronics with all its progress in integration, and then microprocessors which was followed by a widespread computerization. It is seems that a similar role can be attributed to the introduction of various elements of modern nanotechnology, observed with a fast progress since beginning of this century. It concerns all areas of the applications of analytical chemistry, including also progress in flow analysis, which are being developed since the middle of 20th century. Obviously, it should not be omitted the developed earlier and analytically applied planar structures like lipid membranes or self-assembled monolayers They had essential impact prior to discoveries of numerous extraordinary nanoparticles such as fullerenes, carbon nanotubes and graphene, or nanocrystalline semiconductors (quantum dots). Mostly, due to catalytic effects, significantly developed surface and the possibility of easy functionalization, their application in various stages of flow analytical procedures can significantly improve them. The application of new nanomaterials may be used for the development of new detection methods for flow analytical systems in macro-flow setups as well as in microfluidics and lateral flow immunoassay tests. It is also advantageous that quick flow conditions of measurements may be helpful in preventing unfavorable agglomeration of nanoparticles. A vast literature published already on this subject (e.g. almost 1000 papers about carbon nanotubes and flow-injection analytical systems) implies that for this reviews it was necessary to make an arbitrary selection of reported examples of this trend, focused mainly on achievements reported in the recent decade.
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Affiliation(s)
- Marek Trojanowicz
- Laboratory of Nuclear Analytical Techniques, Institute of Nuclear Chemistry and Technology, Warsaw, Poland; Department of Chemistry, University of Warsaw, Poland.
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3
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Wibowo YG, Ramadan BS, Taher T, Khairurrijal K. Advancements of Nanotechnology and Nanomaterials in Environmental and Human Protection for Combatting the COVID-19 During and Post-pandemic Era: A Comprehensive Scientific Review. BIOMEDICAL MATERIALS & DEVICES (NEW YORK, N.Y.) 2023:1-24. [PMID: 37363141 PMCID: PMC10171735 DOI: 10.1007/s44174-023-00086-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 06/28/2023]
Abstract
In December 2019, an outbreak of unknown pneumonia emerged in Wuhan City, Hubei Province, China. It was later identified as the SARS-CoV-2 virus and has since infected over 9 million people in more than 213 countries worldwide. Massive papers on the topic of SARS-CoV-2 that have already been published are necessary to be analyzed and discussed. This paper used the combination of systematic literature network analysis and content analysis to develop a comprehensive discussion related to the use of nanotechnology and materials in environmental and human protection. Its is shown that various efforts have been made to control the transmission of this pandemic. Nanotechnology plays a crucial role in modern vaccine design, as nanomaterials are essential tools for antigen delivery, adjuvants, and mimics of viral structures. In addition, nanomaterials and nanotechnology also reported a crucial role in environmental protection for defence and treating the pandemic. To eradicate pandemics now and in the future, successful treatments must enable rapid discovery, scalable manufacturing, and global distribution. In this review, we discuss the current approaches to COVID-19 development and highlight the critical role of nanotechnology and nanomaterials in combating the virus in the human body and the environment.
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Affiliation(s)
- Yudha Gusti Wibowo
- Department of Mining Engineering, Institut Teknologi Sumatrea, Lampung, 35365 Indonesia
| | | | - Tarmizi Taher
- Department of Environmental Engineering, Institut Teknologi Sumatera, Lampung, 35365 Indonesia
| | - Khairurrijal Khairurrijal
- Department of Physics, Institut Teknologi Sumatera, Lampung, 35365 Indonesia
- Department of Physics, Institut Teknologi Bandung, Bandung, 40132 Indonesia
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Wang J, Zhou Y, Jiang L. Bio-inspired Track-Etched Polymeric Nanochannels: Steady-State Biosensors for Detection of Analytes. ACS NANO 2021; 15:18974-19013. [PMID: 34846138 DOI: 10.1021/acsnano.1c08582] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bio-inspired polymeric nanochannel (also referred as nanopore)-based biosensors have attracted considerable attention on account of their controllable channel size and shape, multi-functional surface chemistry, unique ionic transport properties, and good robustness for applications. There are already very informative reviews on the latest developments in solid-state artificial nanochannel-based biosensors, however, which concentrated on the resistive-pulse sensing-based sensors for practical applications. The steady-state sensing-based nanochannel biosensors, in principle, have significant advantages over their counterparts in term of high sensitivity, fast response, target analytes with no size limit, and extensive suitable range. Furthermore, among the diverse materials, nanochannels based on polymeric materials perform outstandingly, due to flexible fabrication and wide application. This compressive Review summarizes the recent advances in bio-inspired polymeric nanochannels as sensing platforms for detection of important analytes in living organisms, to meet the high demand for high-performance biosensors for analysis of target analytes, and the potential for development of smart sensing devices. In the future, research efforts can be focused on transport mechanisms in the field of steady-state or resistive-pulse nanochannel-based sensors and on developing precisely size-controlled, robust, miniature and reusable, multi-functional, and high-throughput biosensors for practical applications. Future efforts should aim at a deeper understanding of the principles at the molecular level and incorporating these diverse pore architectures into homogeneous and defect-free multi-channel membrane systems. With the rapid advancement of nanoscience and biotechnology, we believe that many more achievements in nanochannel-based biosensors could be achieved in the near future, serving people in a better way.
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Affiliation(s)
- Jian Wang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, People's Republic of China
| | - Yahong Zhou
- Key Laboratory of Bio-inspired Materials and Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, People's Republic of China
| | - Lei Jiang
- Key Laboratory of Bio-inspired Materials and Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, People's Republic of China
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5
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Song Y, Zhou T, Liu Q, Liu Z, Li D. Nanoparticle and microorganism detection with a side-micron-orifice-based resistive pulse sensor. Analyst 2020; 145:5466-5474. [PMID: 32578584 DOI: 10.1039/d0an00679c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This paper presents the detection of nanoparticles and microorganisms using a recently developed side-orifice-based resistive pulse sensor (SO-RPS). By decreasing the channel height of the detection section of the SO-RPS, the detection sensitivity was increased and an average signal to noise ratio (S/N) of about 3 was achieved for 100 nm polystyrene particles. It was also found that spherical particles generate symmetrical signals. Algae with irregular shapes generate signals with more complex patterns. A scatter plot of signal magnitude versus signal width was proven to be reliable for differentiating bacteria from the nanoparticles and two types of algae. The side orifice for detecting heterogeneous nanoparticles and microorganisms is advantageous to avoid orifice clogging and the large flow resistance.
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Affiliation(s)
- Yongxin Song
- Department of Marine Engineering, Dalian Maritime University, Dalian, 116026, China
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6
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Hagan JT, Sheetz BS, Bandara YMNDY, Karawdeniya BI, Morris MA, Chevalier RB, Dwyer JR. Chemically tailoring nanopores for single-molecule sensing and glycomics. Anal Bioanal Chem 2020; 412:6639-6654. [PMID: 32488384 DOI: 10.1007/s00216-020-02717-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Brian S Sheetz
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Buddini I Karawdeniya
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Melissa A Morris
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Robert B Chevalier
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA.
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7
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Yuan Z, Liu Y, Dai M, Yi X, Wang C. Controlling DNA Translocation Through Solid-state Nanopores. NANOSCALE RESEARCH LETTERS 2020; 15:80. [PMID: 32297032 PMCID: PMC7158975 DOI: 10.1186/s11671-020-03308-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/24/2020] [Indexed: 05/14/2023]
Abstract
Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.
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Affiliation(s)
- Zhishan Yuan
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Youming Liu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Min Dai
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Xin Yi
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Chengyong Wang
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
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8
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Tshwenya L, Marken F, Mathwig K, Arotiba OA. Switching Anionic and Cationic Semipermeability in Partially Hydrolyzed Polyacrylonitrile: A pH-Tunable Ionic Rectifier. ACS APPLIED MATERIALS & INTERFACES 2020; 12:3214-3224. [PMID: 31850740 DOI: 10.1021/acsami.9b18583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane materials with semipermeability for anions or for cations are of interest in electrochemical and nanofluidic separation and purification technologies. In this study, partially hydrolyzed polyacrylonitrile (phPAN) is investigated as a pH-switchable anion/cation conductor. When switching from anionic to cationic semipermeability, also the ionic current rectification effect switches for phPAN materials deposited asymmetrically onto a 5, 10, 20, or 40 μm diameter microhole in a 6 μm thick polyethylene-terephthalate (PET) film substrate. Therefore, ionic rectifier behavior can be tuned and used to monitor and characterize semipermeability. Effects of electrolyte type and concentration and pH (relative to the zeta potential at approximately 3.1) are investigated by voltammetry, chronoamperometry, and impedance spectroscopy. A computational model provides good qualitative agreement with the observed electrolyte concentration data. High rectification effects are observed for both cations (pH > 3.1) and anions (pH < 3.1) but only at relatively low ionic strengths.
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Affiliation(s)
- Luthando Tshwenya
- Department of Chemical Sciences Formerly known as the Department of Applied Chemistry, University of Johannesburg , Doornfontein 2028 , South Africa
| | - Frank Marken
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| | - Klaus Mathwig
- Groningen Institute of Pharmacy, Pharmaceutical Analysis , The University of Groningen , P.O. Box 196, AD Groningen 9700 , The Netherlands
| | - Omotayo A Arotiba
- Department of Chemical Sciences Formerly known as the Department of Applied Chemistry, University of Johannesburg , Doornfontein 2028 , South Africa
- Centre for Nanomaterials Science Research , University of Johannesburg , Doornfontein 2028 , Johannesburg , South Africa
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9
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Bandara YMNDY, Karawdeniya BI, Hagan JT, Chevalier RB, Dwyer JR. Chemically Functionalizing Controlled Dielectric Breakdown Silicon Nitride Nanopores by Direct Photohydrosilylation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:30411-30420. [PMID: 31347369 DOI: 10.1021/acsami.9b08004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanopores are a prominent enabling tool for single-molecule applications such as DNA sequencing, protein profiling, and glycomics, and the construction of ionic circuit elements. Silicon nitride (SiNx) is a leading scaffold for these <100 nm-diameter nanofluidic ion-conducting channels, but frequently challenging surface chemistry remains an obstacle to their use. We functionalized more than 100 SiNx nanopores with different surface terminations-acidic (Si-R-OH, Si-R-CO2H), basic (Si-R-NH2), and nonionizable (Si-R-C6H3(CF3)2)-to chemically tune the nanopore size, surface charge polarity, and subsequent chemical reactivity and to change their conductance by changes of solution pH. The initial one-reaction-step covalent chemical film formation was by hydrosilylation and could be followed by straightforward condensation and click reactions. The hydrosilylation reaction step used neat reagents with no special precautions such as guarding against water content. A key feature of the approach was to combine controlled dielectric breakdown (CDB) with hydrosilylation to create and functionalize SiNx nanopores. CDB thus replaced the detrimental but conventionally necessary surface pretreatment with hydrofluoric acid. Proof-of-principle detection of the canonical test molecule, λ-DNA, yielded signals that showed that the functionalized pores were not obstructed by chemical treatments but could translocate the biopolymer. The characteristics were tuned by the surface coating character. This robust and flexible surface coating method, freed by CDB from HF etching, portends the development of nanopores with surface chemistry tuned to match the application, extending even to the creation of biomimetic nanopores.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Buddini I Karawdeniya
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - James T Hagan
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Robert B Chevalier
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
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10
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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11
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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: 21] [Impact Index Per Article: 4.2] [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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12
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Ghosal S, Sherwood JD, Chang HC. Solid-state nanopore hydrodynamics and transport. BIOMICROFLUIDICS 2019; 13:011301. [PMID: 30867871 PMCID: PMC6404949 DOI: 10.1063/1.5083913] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/31/2018] [Indexed: 05/08/2023]
Abstract
The resistive pulse method based on measuring the ion current trace as a biomolecule passing through a nanopore has become an important tool in biotechnology for characterizing molecules. A detailed physical understanding of the translocation process is essential if one is to extract the relevant molecular properties from the current signal. In this Perspective, we review some recent progress in our understanding of hydrodynamic flow and transport through nanometer sized pores. We assume that the problems of interest can be addressed through the use of the continuum version of the equations of hydrodynamic and ion transport. Thus, our discussion is restricted to pores of diameter greater than about ten nanometers: such pores are usually synthetic. We address the fundamental nanopore hydrodynamics and ion transport mechanisms and review the wealth of observed phenomena due to these mechanisms. We also suggest future ionic circuits that can be synthesized from different ionic modules based on these phenomena and their applications.
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Affiliation(s)
- Sandip Ghosal
- Department of Mechanical Engineering and Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
| | - John D Sherwood
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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13
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Kondylis P, Schlicksup CJ, Brunk NE, Zhou J, Zlotnick A, Jacobson SC. Competition between Normative and Drug-Induced Virus Self-Assembly Observed with Single-Particle Methods. J Am Chem Soc 2018; 141:1251-1260. [PMID: 30537810 DOI: 10.1021/jacs.8b10131] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Disruption of virus capsid assembly has compelling antiviral potential that has been applied to hepatitis B virus (HBV). HBV core protein assembly can be modulated by heteroaryldihydropyrimidines (HAPs), and such molecules are collectively termed core protein allosteric modulators (CpAMs). Although the antiviral effects of CpAMs are acknowledged, the mechanism of action remains an open question. Challenging aspects of characterizing misdirected assembly are the large size and nonuniform nature of the final particles. In this study of HBV assembly, we observed a competition between normative and CpAM-induced aberrant assembly with electron microscopy and resistive-pulse sensing on nanofluidic devices. This competition was a function of the strength of the association energy between individual core proteins, which is proportional to ionic strength. At strong association energy, assembly reactions primarily yielded morphologically normal HBV capsids, despite the presence of HAP-TAMRA. At weak association energy, HAP-TAMRA led to increased assembly product size and disrupted morphology. The smallest particles were T = 4 icosahedra, whereas the larger particles were defective spheres, ellipsoids, and bacilliform cylinders, with regions of T = 4 geometry interspersed with flat regions. Deviation from spherical geometry progressively increased with particle size, which is consistent with the interpretation of a competition between two alternative assembly pathways.
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14
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Hsu JP, Chen YM, Yang ST, Lin CY, Tseng S. Influence of salt valence on the rectification behavior of nanochannels. J Colloid Interface Sci 2018; 531:483-492. [PMID: 30055443 DOI: 10.1016/j.jcis.2018.07.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 01/18/2023]
Abstract
Taking account of the influence of electroosmotic flow, the behavior of the ion current rectification of a charged conical nanochannel is studied theoretically focusing on the effect of ionic valence. A continuum-based model comprising coupled Poisson-Nernst-Planck (PNP) equations for the ionic mass transport and Navier-Stokes equations for the hydrodynamic field is adopted. We show that if the bulk salt concentration is fixed, the behavior of the current-voltage curve depends highly on the ionic valence, which arises from the difference in ionic strength and ion diffusivity. As the bulk salt concentration varies, the rectification factor shows a local maximum, and the bulk salt concentration at which it occurs depends upon the salt valence: the higher the valence the lower that concentration. However, regardless of the salt valence, the ionic strength at which that local maximum occurs is essentially the same, implying that the thickness of electric double layer is the key factor. Due to the difference in ionic diffusivity, the magnitude of the rectification factor depends upon the type of salt. For example, the rectification factor of KCl is larger than that of KNO3. The qualitative behavior of the ion current rectification of a positively charged conical nanochannel is similar to that of a negatively charged nanochannel.
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Affiliation(s)
- Jyh-Ping Hsu
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Yu-Min Chen
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shu-Tuan Yang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chih-Yuan Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shiojenn Tseng
- Department of Mathematics, Tamkang University, New Taipei City 25137, Taiwan.
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15
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Zhou J, Kondylis P, Haywood DG, Harms ZD, Lee LS, Zlotnick A, Jacobson SC. Characterization of Virus Capsids and Their Assembly Intermediates by Multicycle Resistive-Pulse Sensing with Four Pores in Series. Anal Chem 2018; 90:7267-7274. [PMID: 29708733 PMCID: PMC6039186 DOI: 10.1021/acs.analchem.8b00452] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Virus self-assembly is a critical step in the virus lifecycle. Understanding how viruses assemble and disassemble provides needed insight into developing antiviral pharmaceuticals. Few tools offer sufficient resolution to study assembly intermediates that differ in size by a few dimers. Our goal is to improve resistive-pulse sensing on nanofluidic devices to offer better particle-size and temporal resolution to study intermediates and capsids generated along the assembly pathway. To increase the particle-size resolution of the resistive-pulse technique, we measured the same, single virus particles up to a thousand times, cycling them back and forth across a series of nanopores by switching the polarity of the applied potential, i.e., virus ping-pong. Multiple pores in series provide a unique multipulse signature during each cycle that improves particle tracking and, therefore, identification of a single particle and reduces the number of cycles needed to make the requisite number of measurements. With T = 3 and T = 4 hepatitis B virus (HBV) capsids, we showed the standard deviation of the particle-size distribution decreased with the square root of the number of measurements and approached discriminating particles differing in size by single dimers. We then studied in vitro assembly of HBV capsids and observed that the ensemble of intermediates shift to larger sizes over 2 days of annealing. On the contrary, assembly reactions diluted to lower dimer concentrations an hour after initiation had fewer intermediates that persisted after the 2 day incubation and had a higher ratio of T = 4 to T = 3 capsids. These reactions indicate that labile T = 4 intermediates are formed rapidly, and dependent on conditions, intermediates may be trapped as metastable species or progress to yield complete capsids.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | | | | | - Zachary D. Harms
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - Lye Siang Lee
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405
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16
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Apel PY, Blonskaya IV, Lizunov NE, Olejniczak K, Orelovitch OL, Toimil-Molares ME, Trautmann C. Osmotic Effects in Track-Etched Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703327. [PMID: 29573553 DOI: 10.1002/smll.201703327] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/05/2018] [Indexed: 06/08/2023]
Abstract
Asymmetrically etched ion-track membranes attract great interest for both fundamental and technical reasons because of a large variety of applications. So far, conductometric measurements during track etching provide only limited information about the complicated asymmetric etching process. In this paper, monitoring of osmotic phenomena is used to elucidate the initial phase of nanopore formation. It is shown that strong alkaline solutions generate a considerable osmotic flow of water through newborn conical pores. The interplay between diffusion and convection in the pore channel results in a substantially nonlinear alkali concentration gradient and a rapid change in the pore geometry after breakthrough. Similar phenomena are observed in experiments with cylindrical track-etched pores of 15-30 nm in radius. A theoretical description of the diffusion-convection processes in the pores is provided.
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Affiliation(s)
- Pavel Y Apel
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980, Dubna, Russia
- Department of Chemistry, New Technologies and Materials, Dubna State University, Universitetskaya str. 19, 141980, Dubna, Russia
| | - Irina V Blonskaya
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980, Dubna, Russia
| | - Nikolay E Lizunov
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980, Dubna, Russia
| | - Katarzyna Olejniczak
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980, Dubna, Russia
- Department of Chemistry, Nicolaus Copernicus University, Gagarina str. 7, 87-100, Torun, Poland
| | - Oleg L Orelovitch
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Joliot-Curie str. 6, 141980, Dubna, Russia
| | | | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291, Darmstadt, Germany
- Materialwissenschaft, Technische Universität Darmstadt, Alarich-Weiss-Straße 2, 64287, Darmstadt, Germany
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17
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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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18
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Xu Y. Nanofluidics: A New Arena for Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1702419. [PMID: 29094401 DOI: 10.1002/adma.201702419] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/04/2017] [Indexed: 06/07/2023]
Abstract
A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.
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Affiliation(s)
- Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
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19
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Bandara YMNDY, Nichols JW, Iroshika Karawdeniya B, Dwyer JR. Conductance‐based profiling of nanopores: Accommodating fabrication irregularities. Electrophoresis 2017; 39:626-634. [DOI: 10.1002/elps.201700299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Jason R. Dwyer
- Department of Chemistry University of Rhode Island Kingston RI USA
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20
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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21
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Apel PY, Blonskaya IV, Lizunov NE, Olejniczak K, Orelovitch OL, Sartowska BA, Dmitriev SN. Asymmetrical nanopores in track membranes: Fabrication, the effect of nanopore shape and electric charge of pore walls, promising applications. RUSS J ELECTROCHEM+ 2017. [DOI: 10.1134/s1023193517010037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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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: 53] [Impact Index Per Article: 6.6] [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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