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Hopfes T, Tahvildari R, de Wijs K, Dang C, Fondu J, Lagae L, Libbrecht S. Durability of the bubble-jet sorter enables high performance bio sample isolation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39175464 DOI: 10.1039/d4ay01168f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Sorting cells while maintaining their viability for further processing or analysis is an essential step in a variety of biological processes ranging from early diagnostics to cell therapy. Sorting techniques such as fluorescence-activated cell sorting (FACS) have evolved considerably and provide standard ways of sorting. Nevertheless, the search for compact, integrated, efficient, and high throughput microfluidic sorting platforms continues due to challenges such as cost, cell viability, and biosafety. In our previous work, we introduced a technology with the potential to become such a platform: the bubble-jet sorter. It is a silicon-based sorter chip relying on cell deflection through micro vapor bubble formation. In this work, we present a new version of the sorter chip that emphasizes durability and continuous sorting operation. To characterize the sorter, we first focus on the technical performance and show a sorter lifetime that repeatedly exceeds 80 million actuation cycles. In addition, we show continuous operation at high firing rates, but also discuss limitations due to heat buildup. In a second step, we present continuous sorting runs of millions of beads and CD3 positive T cells at rates surpassing 1000 sorting events per second, while maintaining high purity (>90%) and recovery (>85%). Dedicated viability tests show that the gentle sorting process maintains cell viability in this closed, aerosol-free device. The remarkable combination of high lifetime, sorting rate, and sorting efficiency, along with the potential for on-chip parallelization show the promise of this technology to meet the growing demand for large-scale sample isolation in drug and immunotherapy development.
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Affiliation(s)
| | | | | | - Chi Dang
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
| | | | - Liesbet Lagae
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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2
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Kizer ME, R. Dwyer J. Editors' Choice-Perspective-Deciphering the Glycan Kryptos by Solid-State Nanopore Single-Molecule Sensing: A Call for Integrated Advancements Across Glyco- and Nanopore Science. ECS SENSORS PLUS 2024; 3:020604. [PMID: 38799647 PMCID: PMC11125560 DOI: 10.1149/2754-2726/ad49b0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Glycans, or complex carbohydrates, are information-rich biopolymers critical to many biological processes and with considerable importance in pharmaceutical therapeutics. Our understanding, though, is limited compared to other biomolecules such as DNA and proteins. The greater complexity of glycan structure and the limitations of conventional chemical analysis methods hinder glycan studies. Auspiciously, nanopore single-molecule sensors-commercially available for DNA sequencing-hold great promise as a tool for enabling and advancing glycan analysis. We focus on two key areas to advance nanopore glycan characterization: molecular surface coatings to enhance nanopore performance including by molecular recognition, and high-quality glycan chemical standards for training.
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Affiliation(s)
- Megan E. Kizer
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States of America
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island, 02881, United States of America
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3
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. MICROMACHINES 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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4
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Xu X, Valavanis D, Ciocci P, Confederat S, Marcuccio F, Lemineur JF, Actis P, Kanoufi F, Unwin PR. The New Era of High-Throughput Nanoelectrochemistry. Anal Chem 2023; 95:319-356. [PMID: 36625121 PMCID: PMC9835065 DOI: 10.1021/acs.analchem.2c05105] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Xiangdong Xu
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Paolo Ciocci
- Université
Paris Cité, ITODYS, CNRS, F-75013 Paris, France
| | - Samuel Confederat
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,Faculty
of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,
| | | | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,
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5
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [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: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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6
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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7
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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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8
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He L, Tessier DR, Briggs K, Tsangaris M, Charron M, McConnell EM, Lomovtsev D, Tabard-Cossa V. Digital immunoassay for biomarker concentration quantification using solid-state nanopores. Nat Commun 2021; 12:5348. [PMID: 34504071 PMCID: PMC8429538 DOI: 10.1038/s41467-021-25566-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/12/2021] [Indexed: 12/05/2022] Open
Abstract
Single-molecule counting is the most accurate and precise method for determining the concentration of a biomarker in solution and is leading to the emergence of digital diagnostic platforms enabling precision medicine. In principle, solid-state nanopores—fully electronic sensors with single-molecule sensitivity—are well suited to the task. Here we present a digital immunoassay scheme capable of reliably quantifying the concentration of a target protein in complex biofluids that overcomes specificity, sensitivity, and consistency challenges associated with the use of solid-state nanopores for protein sensing. This is achieved by employing easily-identifiable DNA nanostructures as proxies for the presence (“1”) or absence (“0”) of the target protein captured via a magnetic bead-based sandwich immunoassay. As a proof-of-concept, we demonstrate quantification of the concentration of thyroid-stimulating hormone from human serum samples down to the high femtomolar range. Further optimization to the method will push sensitivity and dynamic range, allowing for development of precision diagnostic tools compatible with point-of-care format. The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Canada
| | | | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Canada
| | | | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Canada
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9
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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10
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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11
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Tilahun M, Tatek YB. End‐Pulled Translocation of a Star Polymer Out of a Confining Cylindrical Cavity. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mesay Tilahun
- Department of Physics Addis Ababa University Addis Ababa 1176 Ethiopia
| | - Yergou B. Tatek
- Department of Physics Addis Ababa University Addis Ababa 1176 Ethiopia
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12
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Beamish E, Tabard-Cossa V, Godin M. Digital counting of nucleic acid targets using solid-state nanopores. NANOSCALE 2020; 12:17833-17840. [PMID: 32832949 DOI: 10.1039/d0nr03878d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Assays targeting biomarkers for the early diagnosis of disease demand a sensing platform with a high degree of specificity and sensitivity. In this work, we developed and characterized a solid-state nanopore-based sensing assay for the detection of short nucleic acid targets with readily customizable nanostructured DNA probe sets. We explored the electrical signatures of three DNA nanostructures to determine their performance as probe sets in a digital counting scheme to quantify the concentration of targets. With these probes, we demonstrate the specific, simultaneous detection of two different DNA targets in a 2-plex assay, and separately that of microRNA-155, a biomarker linked to various human cancers. In addition to specific target detection, our scheme demonstrated the ability to quantify at least six different microRNA concentrations. These results highlight the potential for solid-state nanopores as single-molecule counters for future digital diagnostic technologies.
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Affiliation(s)
- Eric Beamish
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
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13
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Hu R, Tong X, Zhao Q. Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability. Adv Healthc Mater 2020; 9:e2000933. [PMID: 32734703 DOI: 10.1002/adhm.202000933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Xin Tong
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
- Peking University Yangtze Delta Institute of Optoelectronics Nantong Jiangsu 226010 China
- Collaborative Innovation Center of Quantum Matter Beijing 100084 China
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14
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Islam MF, Yap YC, Li F, Guijt RM, Breadmore MC. The influence of electrolyte concentration on nanofractures fabricated in a 3D-printed microfluidic device by controlled dielectric breakdown. Electrophoresis 2020; 41:2007-2014. [PMID: 32776330 DOI: 10.1002/elps.202000050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/15/2020] [Accepted: 08/04/2020] [Indexed: 11/08/2022]
Abstract
A three-dimensional-printed microfluidic device made of a thermoplastic material was used to study the creation of molecular filters by controlled dielectric breakdown. The device was made from acrylonitrile butadiene styrene by a fused deposition modeling three-dimensional printer and consisted of two V-shaped sample compartments separated by 750 µm of extruded plastic gap. Nanofractures were formed in the thin piece of acrylonitrile butadiene styrene by controlled dielectric breakdown by application voltage of 15-20 kV with the voltage terminated when reaching a defined current threshold. Variation of the size of the nanofractures was achieved by both variation of the current threshold and by variation of the ionic strength of the electrolyte used for breakdown. Electrophoretic transport of two proteins, R-phycoerythrin (RPE; <10 nm in size) and fluorescamine-labeled BSA (f-BSA; 2-4 nm), was used to monitor the size and transport properties of the nanofractures. Using 1 mM phosphate buffer, both RPE and f-BSA passed through the nanofractures when the current threshold was set to 25 µA. However, when the threshold was lowered to 10 µA or lower, RPE was restricted from moving through the nanofractures. When we increased the electrolyte concentration during breakdown from 1 to 10 mM phosphate buffer, BSA passed but RPE was blocked when the threshold was equal to, or lower than, 25 µA. This demonstrates that nanofracture size (pore area) is directly related to the breakdown current threshold but inversely related to the concentration of the electrolyte used for the breakdown process.
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Affiliation(s)
- Md Fokhrul Islam
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Science, University of Tasmania, Tasmania, Australia
| | - Yiing C Yap
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Science, University of Tasmania, Tasmania, Australia.,Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Feng Li
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Science, University of Tasmania, Tasmania, Australia
| | - Rosanne M Guijt
- Centre for Rural and Regional Futures, Deakin University, Geelong, Australia
| | - Michael C Breadmore
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Science, University of Tasmania, Tasmania, Australia
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15
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Matsui K, Goto Y, Yanagi I, Akahori R, Fujioka M, Ishida T, Yokoi T, Nakagawa T, Takeda KI. Low-frequency noise induced by cation exchange fluctuation on the wall of silicon nitride nanopore. Sci Rep 2020; 10:8662. [PMID: 32457511 PMCID: PMC7250840 DOI: 10.1038/s41598-020-65530-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/06/2020] [Indexed: 01/14/2023] Open
Abstract
Nanopore-based biosensors have attracted attention as highly sensitive microscopes for detecting single molecules in aqueous solutions. However, the ionic current noise through a nanopore degrades the measurement accuracy. In this study, the magnitude of the low-frequency noise in the ionic current through a silicon nitride nanopore was found to change depending on the metal ion species in the aqueous solution. The order of the low-frequency noise magnitudes of the alkali metal ionic current was consistent with the order of the adsorption affinities of the metal ions for the silanol surface of the nanopore (Li <Na <K < Rb <Cs). For the more adsorptive alkaline earth metal ions (Mg and Ca), the low-frequency noise magnitudes were as low as those for Li ions. This tendency, i.e., metal ions having a very high or low adsorption affinity causing a reduction in low-frequency noise, suggests that the low-frequency noise was induced by the exchange reactions between protons and metal ions occurring on the silanol surface. In addition, the low-frequency noise in the ionic current remained low even after replacing the CaCl2 aqueous solution with a CsCl aqueous solution, indicating that Ca ions continued being adsorbed onto silanol groups even after removing the aqueous solution.
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Affiliation(s)
- Kazuma Matsui
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan. .,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan.
| | - Yusuke Goto
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Michiru Fujioka
- Bio Systems Design Department, Hitachi High-Tech Corporation, 882 Ichige, Hitachinaka, Ibaraki, 312-8504, Japan
| | - Takeshi Ishida
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Takahide Yokoi
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Tatsuo Nakagawa
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research and Development Group, Hitachi, Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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16
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Sohi AN, Beamish E, Tabard-Cossa V, Godin M. DNA Capture by Nanopore Sensors under Flow. Anal Chem 2020; 92:8108-8116. [DOI: 10.1021/acs.analchem.9b05778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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18
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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19
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Waugh M, Briggs K, Gunn D, Gibeault M, King S, Ingram Q, Jimenez AM, Berryman S, Lomovtsev D, Andrzejewski L, Tabard-Cossa V. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 2019; 15:122-143. [DOI: 10.1038/s41596-019-0255-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
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20
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St-Denis T, Yazda K, Capaldi X, Bustamante J, Safari M, Miyahara Y, Zhang Y, Grutter P, Reisner W. An apparatus based on an atomic force microscope for implementing tip-controlled local breakdown. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:123703. [PMID: 31893796 DOI: 10.1063/1.5129665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores are powerful tools for sensing of single biomolecules in solution. Fabrication of solid-state nanopores is still challenging, however; in particular, new methods are needed to facilitate the integration of pores with larger nanofluidic and electronic device architectures. We have developed the tip-controlled local breakdown (TCLB) approach, in which an atomic force microscope (AFM) tip is brought into contact with a silicon nitride membrane that is placed onto an electrolyte reservoir. The application of a voltage bias at the AFM tip induces a dielectric breakdown that leads to the formation of a nanopore at the tip position. In this work, we report on the details of the apparatus used to fabricate nanopores using the TCLB method, and we demonstrate the formation of nanopores with smaller, more controlled diameters using a current limiting circuit that zeroes the voltage upon pore formation. Additionally, we demonstrate the capability of TCLB to fabricate pores aligned to embedded topographical features on the membranes.
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Affiliation(s)
- T St-Denis
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - K Yazda
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - X Capaldi
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - J Bustamante
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - M Safari
- Norcada, 4548-99 Street NW, Edmonton, Alberta T6E 5H5, Canada
| | - Y Miyahara
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Y Zhang
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - P Grutter
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - W Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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21
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Beamish E, Tabard-Cossa V, Godin M. Programmable DNA Nanoswitch Sensing with Solid-State Nanopores. ACS Sens 2019; 4:2458-2464. [PMID: 31449750 DOI: 10.1021/acssensors.9b01053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sensing performance of solid-state nanopores is limited by the fast kinetics of small molecular targets. To address this challenge, we translate the presence of a small target to a large conformational change of a long polymer. In this work, we explore the performance of solid-state nanopores for sensing the conformational states of molecular nanoswitches assembled using the principles of DNA origami. These programmable single-molecule switches show great potential in molecular diagnostics and long-term information storage. We investigate the translocation properties of linear and looped nanoswitch topologies using nanopores fabricated in thin membranes, ultimately comparing the performance of our nanopore platform for detecting the presence of a DNA analogue to a sequence found in a Zika virus biomarker gene with that of conventional gel electrophoresis. We found that our system provides a high-throughput method for quantifying several target concentrations within an order of magnitude by sensing only several hundred molecules using electronics of moderate bandwidth that are conventionally used in nanopore sensing systems.
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22
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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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23
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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24
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019; 65:69-77. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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25
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Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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26
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Roshan KA, Tang Z, Guan W. High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore. NANOTECHNOLOGY 2019; 30:095502. [PMID: 30523901 DOI: 10.1088/1361-6528/aaf48e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigate the current transport characteristics in the electrolyte-dielectric-electrolyte structure commonly used in the in situ controlled breakdown (CBD) fabrication of solid-state nanopores. It is found that the stochastic breakdown process could lead to fidelity issues of false positives (an incorrect indication of a true nanopore formation) and false negatives (inability to detect initial nanopore formation). Robust and deterministic detection of initial physical breakdown to alleviate false positives and false negatives is critical for precise nanopore size control. To this end, we report a high fidelity moving Z-score method based CBD fabrication of solid-state nanopore. We demonstrate 100% success rate of realizing the initial nanopore conductance of 3 ± 1 nS (corresponds to size of 1.7 ± 0.6 nm) regardless of the dielectric membrane characteristics. Our study also elucidates the Joule heating is the dominant mechanism for electric field-based nanopore enlargement. Single DNA molecule sensing using nanopores fabricated by this method was successfully demonstrated. We anticipate the moving Z-score based CBD method could enable broader access to the solid state nanopore-based single molecule analysis.
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Affiliation(s)
- Kamyar Akbari Roshan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, United States of America
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27
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Han M, Li J, He G, Lin M, Xiao W, Li X, Wu X, Jiang X. Tailored 3D printed micro-crystallization chip for versatile and high-efficiency droplet evaporative crystallization. LAB ON A CHIP 2019; 19:767-777. [PMID: 30730524 DOI: 10.1039/c8lc01319e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Droplet evaporative crystallization on a micro-structured platform with limited interfacial area has potential applications in crystallization theory, bioengineering, and particle drug preparation. Here, an efficient and versatile approach is discussed for multiple drop-evaporative crystallization processes on a micro-crystallization chip fabricated via three-dimensional printing. A chip with limited interfacial area could be fabricated on a highly controlled crystallizer interface. During liquid injection, various drop locations and evaporative conditions can be used, which enables flexible and distinct crystallization processes. This reveals controlling mechanisms and identifies nucleation locations and growth paths. Various classic crystallization systems were introduced to evaluate the chip performance. Controlled nucleation and growth mechanisms at stable evaporative rates were revealed. From the final crystal morphologies, particle locations, and distributions, the effects of the initial concentration and droplet contact conditions at the triple-phase interface could be investigated with high adjustability. Moreover, the results can provide insights into the 'coffee ring' formation during evaporative crystallization, dendritic crystal growth, and hydrate crystallization mechanisms. In the limited microstructure, the capillary flow of a liquid drop can spontaneously drive the crystal distribution and morphology. Finally, incorrect liquid drop locations that led to unpredictable crystal formation and distributions were discussed to improve repeatability and efficiency. Applications include the manufacture of particle drugs and flow chemistry.
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Affiliation(s)
- Mingguang Han
- State Key Laboratory of Fine Chemicals, Engineering Laboratory for Petrochemical Energy-efficient Separation Technology of Liaoning Province, School of Chemical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China.
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28
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Varongchayakul N, Hersey J, Squires A, Meller A, Grinstaff M. A Solid-State Hard Microfluidic-Nanopore Biosensor with Multilayer Fluidics and On-Chip Bioassay/Purification Chamber. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1804182. [PMID: 31632230 PMCID: PMC6800661 DOI: 10.1002/adfm.201804182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 05/21/2023]
Abstract
Solid-state nanopores are an emerging biosensor for nucleic acid and protein characterization. For use in a clinical setting, solid-state nanopore sensing requires sample preparation and purification, fluid handling, a heating element, electrical noise insulators, and an electrical readout detector, all of which hamper its translation to a point-of-care diagnostic device. A stand-alone microfluidic-based nanopore device is described that combines a bioassay reaction/purification chamber with a solid-state nanopore sensor. The microfluidic device is composed of the high-temperature/solvent resistance Zeonex plastic, formed via micro-machining and heat bonding, enabling the use of both a heat regulator and a magnetic controller. Fluid control through the microfluidic channels and chambers is controlled via fluid port selector valves and allows up-to eight different solutions. Electrical noise measurements and DNA translocation experiments demonstrate the integrity of the device, with performance comparable to a conventional stand-alone nanopore setup. However, the microfluidic-nanopore setup is superior in terms of ease of use. To showcase the utility of the device, single molecule detection of a DNA PCR product, after magnetic bead DNA separation, is accomplished on chip.
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Affiliation(s)
- Nitinun Varongchayakul
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Joseph Hersey
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Allison Squires
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Amit Meller
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Mark Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
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29
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Liao Z, Wang J, Zhang P, Zhang Y, Miao Y, Gao S, Deng Y, Geng L. Recent advances in microfluidic chip integrated electronic biosensors for multiplexed detection. Biosens Bioelectron 2018; 121:272-280. [DOI: 10.1016/j.bios.2018.08.061] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/13/2018] [Accepted: 08/25/2018] [Indexed: 12/11/2022]
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30
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Ying C, Houghtaling J, Eggenberger OM, Guha A, Nirmalraj P, Awasthi S, Tian J, Mayer M. Formation of Single Nanopores with Diameters of 20-50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown. ACS NANO 2018; 12:11458-11470. [PMID: 30335956 DOI: 10.1021/acsnano.8b06489] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanopores with diameters from 20 to 50 nm in silicon nitride (SiN x) windows are useful for single-molecule studies of globular macromolecules. While controlled breakdown (CBD) is gaining popularity as a method for fabricating nanopores with reproducible size control and broad accessibility, attempts to fabricate large nanopores with diameters exceeding ∼20 nm via breakdown often result in undesirable formation of multiple nanopores in SiN x membranes. To reduce the probability of producing multiple pores, we combined two strategies: laser-assisted breakdown and controlled pore enlargement by limiting the applied voltage. Based on laser power-dependent increases in nanopore conductance upon illumination and on the absence of an effect of ionic strength on the ratio between the nanopore conductance before and after laser illumination, we suggest that the increased rate of controlled breakdown results from laser-induced heating. Moreover, we demonstrate that conductance values before and after coating the nanopores with a fluid lipid bilayer can indicate fabrication of a single nanopore versus multiple nanopores. Complementary flux measurements of Ca2+ through the nanopore typically confirmed assessments of single or multiple nanopores that we obtained using the coating method. Finally, we show that thermal annealing of CBD pores significantly increased the success rate of coating and reduced the current noise before and after lipid coating. We characterize the geometry of these nanopores by analyzing individual resistive pulses produced by translocations of spherical proteins and demonstrate the usefulness of these nanopores for estimating the approximate molecular shape of IgG proteins.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jared Houghtaling
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
- Department of Biomedical Engineering , University of Michigan , 2200 Bonisteel Boulevard , Ann Arbor , Michigan 48109 , United States
| | - Olivia M Eggenberger
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Anirvan Guha
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Peter Nirmalraj
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Saurabh Awasthi
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics , Nankai University , Tianjin 300071 , China
| | - Michael Mayer
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
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31
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Wasfi A, Awwad F, Ayesh AI. Graphene-based nanopore approaches for DNA sequencing: A literature review. Biosens Bioelectron 2018; 119:191-203. [DOI: 10.1016/j.bios.2018.07.072] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
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32
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Roman J, Français O, Jarroux N, Patriarche G, Pelta J, Bacri L, Le Pioufle B. Solid-State Nanopore Easy Chip Integration in a Cheap and Reusable Microfluidic Device for Ion Transport and Polymer Conformation Sensing. ACS Sens 2018; 3:2129-2137. [PMID: 30284814 DOI: 10.1021/acssensors.8b00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores have a huge potential in upcoming societal challenging applications in biotechnologies, environment, health, and energy. Nowadays, these sensors are often used within bulky fluidic devices that can cause cross-contaminations and risky nanopore chips manipulations, leading to a short experimental lifetime. We describe the easy, fast, and cheap innovative 3D-printer-helped protocol to manufacture a microfluidic device permitting the reversible integration of a silicon based chip containing a single nanopore. We show the relevance of the shape of the obtained channels thanks to finite elements simulations. We use this device to thoroughly investigate the ionic transport through the solid-state nanopore as a function of applied voltage, salt nature, and concentration. Furthermore, its reliability is proved through the characterization of a polymer-based model of protein-urea interactions on the nanometric scale thanks to a hairy nanopore.
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Affiliation(s)
- Jean Roman
- ENS Paris-Saclay, CNRS, Institut d’Alembert, SATIE, Université Paris-Saclay, Cachan F-94230, France
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Olivier Français
- ESIEE-Paris, ESYCOM, Université Paris Est, Noisy-Le-Grand F-93160, France
| | - Nathalie Jarroux
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Gilles Patriarche
- C2N, CNRS, Université Paris-Sud, Université Paris-Saclay, C2N-Marcoussis, Marcoussis F-91460, France
| | - Juan Pelta
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Laurent Bacri
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Bruno Le Pioufle
- ENS Paris-Saclay, CNRS, Institut d’Alembert, SATIE, Université Paris-Saclay, Cachan F-94230, France
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33
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Abstract
Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.
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34
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Uhl C, Shi W, Liu Y. Organ-on-Chip Devices Toward Applications in Drug Development and Screening. J Med Device 2018. [DOI: 10.1115/1.4040272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As a necessary pathway to man-made organs, organ-on-chips (OOC), which simulate the activities, mechanics, and physiological responses of real organs, have attracted plenty of attention over the past decade. As the maturity of three-dimensional (3D) cell-culture models and microfluidics advances, the study of OOCs has made significant progress. This review article provides a comprehensive overview and classification of OOC microfluidics. Specifically, the review focuses on OOC systems capable of being used in preclinical drug screening and development. Additionally, the review highlights the strengths and weaknesses of each OOC system toward the goal of improved drug development and screening. The various OOC systems investigated throughout the review include, blood vessel, lung, liver, and tumor systems and the potential benefits, which each provides to the growing challenge of high-throughput drug screening. Published OOC systems have been reviewed over the past decade (2007–2018) with focus given mainly to more recent advances and improvements within each organ system. Each OOC system has been reviewed on how closely and realistically it is able to mimic its physiological counterpart, the degree of information provided by the system toward the ultimate goal of drug development and screening, how easily each system would be able to transition to large scale high-throughput drug screening, and what further improvements to each system would help to improve the functionality, realistic nature of the platform, and throughput capacity. Finally, a summary is provided of where the broad field of OOCs appears to be headed in the near future along with suggestions on where future efforts should be focused for optimized performance of OOC systems in general.
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Affiliation(s)
- Christopher Uhl
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015
| | - Wentao Shi
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015
| | - Yaling Liu
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA 18015 e-mail:
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35
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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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36
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de Haan HW, Sean D, Slater GW. Reducing the variance in the translocation times by prestretching the polymer. Phys Rev E 2018; 98:022501. [PMID: 30253469 DOI: 10.1103/physreve.98.022501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Indexed: 11/07/2022]
Abstract
Langevin dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the trans side. Under the influence of stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields a reduced variation in translocation times relative to the mean translocation time. This effect is explored for different ratios of the amplitude of thermal fluctuations to driving forces to control for the relative influence of the thermal path sampled by the polymer. Since the variance in translocation times is due to contributions coming from sampling both thermal noise and initial conformations, our simulations offer independent control over the two main sources of noise and allow us to shed light on how they both contribute to translocation dynamics. Simulation parameter space corresponding to experimentally relevant conditions is highlighted and shown to correspond to a significant decrease in the spread of translocation times, thus indicating that stretching DNA prior to translocation could assist nanopore-based sequencing and sizing applications.
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Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada, L1H 7K4
| | - David Sean
- Physics Department, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5.,Institut für Computerphysik, Universität Stuttgart, 70569 Stuttgart, Germany
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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37
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Yanagi I, Hamamura H, Akahori R, Takeda KI. Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration. Sci Rep 2018; 8:10129. [PMID: 29973672 PMCID: PMC6031669 DOI: 10.1038/s41598-018-28524-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
For the nanopore sensing of various large molecules, such as probe-labelled DNA and antigen-antibody complexes, the nanopore size has to be customized for each target molecule. The recently developed nanopore fabrication method utilizing dielectric breakdown of a membrane is simple and quite inexpensive, but it is somewhat unsuitable for the stable fabrication of a single large nanopore due to the risk of generating multiple nanopores. To overcome this bottleneck, we propose a new technique called “two-step breakdown” (TSB). In the first step of TSB, a local conductive thin portion (not a nanopore) is formed in the membrane by dielectric breakdown. In the second step, the created thin portion is penetrated by voltage pulses whose polarity is opposite to the polarity of the voltage used in the first step. By applying TSB to a 20-nm-thick SiN membrane, a single nanopore with a diameter of 21–26 nm could be fabricated with a high yield of 83%.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan.
| | - Hirotaka Hamamura
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Rena Akahori
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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38
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Fabrication of multiple nanopores in a SiN x membrane via controlled breakdown. Sci Rep 2018; 8:1234. [PMID: 29352158 PMCID: PMC5775244 DOI: 10.1038/s41598-018-19450-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022] Open
Abstract
This paper reports a controlled breakdown (CBD) method to fabricate multiple nanopores in a silicon nitride (SiNx) membrane with control over both nanopore count and nanopore diameter. Despite the stochastic process of the breakdown, we found that the nanopores created via CBD, tend to be of the same diameter. We propose a membrane resistance model to explain and control the multiple nanopores forming in the membrane. We prove that the membrane resistance can reflect the number of nanopores in the membrane and that the diameter of the nanopores is controlled by the exposure time and strength of the electric field. This controllable multiple nanopore formation via CBD avoids the utilization of complicated instruments and time-intensive manufacturing. We anticipate CBD has the potential to become a nanopore fabrication technique which, integrated into an optical setup, could be used as a high-throughput and multichannel characterization technique.
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39
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Beamish E, Tabard-Cossa V, Godin M. Identifying Structure in Short DNA Scaffolds Using Solid-State Nanopores. ACS Sens 2017; 2:1814-1820. [PMID: 29182276 DOI: 10.1021/acssensors.7b00628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of molecular tags along nucleic acid sequences has many potential applications in bionanotechnology, disease biomarker detection, and DNA sequencing. An attractive approach to this end is the use of solid-state nanopores, which can electrically detect molecular substructure and can be integrated into portable lab-on-a-chip sensors. We present here a DNA origami-based approach of molecular assembly in which solid-state nanopores are capable of differentiating 165 bp scaffolds containing zero, one, and two dsDNA protrusions. This highly scalable technique requires minimal sample preparation and is customizable for a wide range of targets and applications. As a proof-of-concept, an aptamer-based DNA displacement reaction is performed in which a dsDNA protrusion is formed along a 255 bp scaffold in the presence of ATP. While ATP is too small to be directly sensed using conventional nanopore methods, our approach allows us to detect ATP by identifying molecular substructure along the DNA scaffold.
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Affiliation(s)
- Eric Beamish
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Vincent Tabard-Cossa
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michel Godin
- Department
of Physics, ‡Department of Mechanical Engineering, and §Ottawa-Carleton
Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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40
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Tadaki D, Yamaura D, Araki S, Yoshida M, Arata K, Ohori T, Ishibashi KI, Kato M, Ma T, Miyata R, Tozawa Y, Yamamoto H, Niwano M, Hirano-Iwata A. Mechanically stable solvent-free lipid bilayers in nano- and micro-tapered apertures for reconstitution of cell-free synthesized hERG channels. Sci Rep 2017; 7:17736. [PMID: 29255199 PMCID: PMC5735097 DOI: 10.1038/s41598-017-17905-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/01/2017] [Indexed: 01/08/2023] Open
Abstract
The self-assembled bilayer lipid membrane (BLM) is the basic component of the cell membrane. The reconstitution of ion channel proteins in artificially formed BLMs represents a well-defined system for the functional analysis of ion channels and screening the effects of drugs that act on them. However, because BLMs are unstable, this limits the experimental throughput of BLM reconstitution systems. Here we report on the formation of mechanically stable solvent-free BLMs in microfabricated apertures with defined nano- and micro-tapered edge structures. The role of such nano- and micro-tapered structures on the stability of the BLMs was also investigated. Finally, this BLM system was combined with a cell-free synthesized human ether-a-go-go-related gene channel, a cardiac potassium channel whose relation to arrhythmic side effects following drug treatment is well recognized. Such stable BLMs as these, when combined with a cell-free system, represent a potential platform for screening the effects of drugs that act on various ion-channel genotypes.
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Affiliation(s)
- Daisuke Tadaki
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Daichi Yamaura
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Shun Araki
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Miyu Yoshida
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Kohei Arata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Takeshi Ohori
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ken-Ichi Ishibashi
- Hang-Ichi Corporation, 1-7-315 Honcho, Naka-ku, Yokohama, Kanagawa, 231-0005, Japan
| | - Miki Kato
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Teng Ma
- Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ryusuke Miyata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yuzuru Tozawa
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Hideaki Yamamoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Michio Niwano
- Kansei Fukushi Research Institute, Tohoku Fukushi University, 6-149-1 Kunimi-ga-oka, Aoba-ku, Sendai, Miyagi, 989-3201, Japan
| | - Ayumi Hirano-Iwata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. .,Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
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41
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Roman J, Jarroux N, Patriarche G, Français O, Pelta J, Le Pioufle B, Bacri L. Functionalized Solid-State Nanopore Integrated in a Reusable Microfluidic Device for a Better Stability and Nanoparticle Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:41634-41640. [PMID: 29144721 DOI: 10.1021/acsami.7b14717] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Electrical detection based on single nanopores is an efficient tool to detect biomolecules, particles and study their morphology. Nevertheless the surface of the solid-state membrane supporting the nanopore should be better controlled. Moreover, nanopore should be integrated within microfluidic architecture to facilitate control fluid exchanges. We built a reusable microfluidic system integrating a decorated membran, rendering the drain and refill of analytes and buffers easier. This process enhances strongly ionic conductance of the nanopore and its lifetime. We highlight the reliability of this device by detecting gold nanorods and spherical proteins.
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Affiliation(s)
- Jean Roman
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay , Evry F-91025, France
| | - Nathalie Jarroux
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay , Evry F-91025, France
| | - Gilles Patriarche
- Centre de Nanosciences et de Nanotechnologies, CNRS, Université Paris-Sud, Université Paris-Saclay, C2N-Marcoussis , Marcoussis 91460, France
| | - Olivier Français
- ESIEE-Paris, ESYCOM, University Paris Est , Cité Descartes BP99, Noisy-Le-Grand F-93160, France
| | - Juan Pelta
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay , Evry F-91025, France
| | | | - Laurent Bacri
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay , Evry F-91025, France
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42
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Jain T, Rasera BC, Guerrero RJS, Lim JM, Karnik R. Microfluidic multiplexing of solid-state nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:484001. [PMID: 29116942 DOI: 10.1088/1361-648x/aa9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although solid-state nanopores enable electronic analysis of many clinically and biologically relevant molecular structures, there are few existing device architectures that enable high-throughput measurement of solid-state nanopores. Herein, we report a method for microfluidic integration of multiple solid-state nanopores at a high density of one nanopore per (35 µm2). By configuring microfluidic devices with microfluidic valves, the nanopores can be rinsed from a single fluid input while retaining compatibility for multichannel electrical measurements. The microfluidic valves serve the dual purpose of fluidic switching and electric switching, enabling serial multiplexing of the eight nanopores with a single pair of electrodes. Furthermore, the device architecture exhibits low noise and is compatible with electroporation-based in situ nanopore fabrication, providing a scalable platform for automated electronic measurement of a large number of integrated solid-state nanopores.
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Affiliation(s)
- Tarun Jain
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, United States of America
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43
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Chen K, Juhasz M, Gularek F, Weinhold E, Tian Y, Keyser UF, Bell NAW. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores. NANO LETTERS 2017; 17:5199-5205. [PMID: 28829136 PMCID: PMC5599873 DOI: 10.1021/acs.nanolett.7b01009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Yu Tian
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail:
| | - Nicholas A. W. Bell
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail: . Fax: +44 (0)1223 337000
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44
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45
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Fu K, Han D, Ma C, Bohn PW. Ion selective redox cycling in zero-dimensional nanopore electrode arrays at low ionic strength. NANOSCALE 2017; 9:5164-5171. [PMID: 28393950 DOI: 10.1039/c7nr00206h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Surface charge characteristics and the electrical double layer (EDL) effect govern the transport of ions into and out of nanopores, producing a permselective concentration polarization, which dominates the electrochemical response of nanoelectrodes in solutions of low ionic strength. In this study, highly ordered, zero-dimensional nanopore electrode arrays (NEAs), with each nanopore presenting a pair of recessed electrodes, were fabricated to couple EDL effects with redox cycling, thereby achieving electrochemical detection with improved sensitivity and selectivity. These NEAs exhibit current amplification as high as 55-fold due to the redox cycling effect, which can be further increased by ∼500-fold upon the removal of the supporting electrolyte. The effect of nanopore geometry, which is a key factor determining the magnitude of the EDL effect, is fully characterized, as is the effect of the magnitude and sign of the charge of the redox-active species. The observed changes in limiting current with the concentration of the supporting electrolyte confirm the accumulation of cations and repulsion of anions in NEAs presenting negative surface charge. Exploiting this principle, dopamine was selectively determined in the presence of a 3000-fold excess of ascorbic acid within the NEA.
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Affiliation(s)
- Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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46
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Hood RL, Hood GD, Ferrari M, Grattoni A. Pioneering medical advances through nanofluidic implantable technologies. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 9. [DOI: 10.1002/wnan.1455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/27/2016] [Accepted: 12/17/2016] [Indexed: 12/11/2022]
Affiliation(s)
- R. Lyle Hood
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX USA
- Department of Mechanical Engineering; University of Texas San Antonio; San Antonio TX USA
| | - Gold Darr Hood
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX USA
| | - Mauro Ferrari
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX USA
| | - Alessandro Grattoni
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX USA
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47
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Tahvildari R, Beamish E, Briggs K, Chagnon-Lessard S, Sohi AN, Han S, Watts B, Tabard-Cossa V, Godin M. Manipulating Electrical and Fluidic Access in Integrated Nanopore-Microfluidic Arrays Using Microvalves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602601. [PMID: 28026148 DOI: 10.1002/smll.201602601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
On-chip microvalves regulate electrical and fluidic access to an array of nanopores integrated within microfluidic networks. This configuration allows for on-chip sequestration of biomolecular samples in various flow channels and analysis by independent nanopores.
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Affiliation(s)
- Radin Tahvildari
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Eric Beamish
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Ali Najafi Sohi
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shuo Han
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Benjamin Watts
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Michel Godin
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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48
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Carlsen AT, Briggs K, Hall AR, Tabard-Cossa V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. NANOTECHNOLOGY 2017; 28:085304-85304. [PMID: 28045003 PMCID: PMC5408306 DOI: 10.1088/1361-6528/aa564d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate precise positioning of nanopores fabricated by controlled breakdown (CBD) on solid-state membranes by spatially varying the electric field strength with localized membrane thinning. We show 100 × 100 nm2 precision in standard SiN x membranes (30-100 nm thick) after selective thinning by as little as 25% with a helium ion beam. Control over nanopore position is achieved through the strong dependence of the electric field-driven CBD mechanism on membrane thickness. Confinement of pore formation to the thinned region of the membrane is confirmed by TEM imaging and by analysis of DNA translocations. These results enhance the functionality of CBD as a fabrication approach and enable the production of advanced nanopore devices for single-molecule sensing applications.
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Affiliation(s)
- Autumn T. Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Adam R. Hall
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston Salem, North Carolina 27101, United States
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Sean D, Slater GW. Highly driven polymer translocation from a cylindrical cavity with a finite length. J Chem Phys 2017; 146:054903. [DOI: 10.1063/1.4975091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- David Sean
- University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Bassu M, Holik P, Schmitz S, Steltenkamp S, Burg TP. Continuous high throughput nanofluidic separation through tangential-flow vertical nanoslit arrays. LAB ON A CHIP 2016; 16:4546-4553. [PMID: 27766330 DOI: 10.1039/c6lc01089j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanofluidic devices exhibit unique, tunable transport properties that may lead to breakthroughs in molecular separations and sensing. However, the throughput of these devices is orders of magnitude too small for the processing of macroscopic samples. Here we overcome this problem by combining two technological innovations. First, nanofluidic channels are made as vertical slits connecting the two sides of a silicon nitride membrane. Arbitrary arrays of such nanoslits down to 15 nm wide with <6 Å uniformity were made by merging the idea of templating with chemical mechanical polishing to create a scalable, nanolithography-free wafer level process. Second, we provide for efficient solute transport to and from the openings of the nanoslits by incorporating the nanofluidic membrane into a microfluidic tangential-flow system, which is also fabricated at wafer level. As an exemplary application, we demonstrate charge-based continuous flow separation of small molecules with a selectivity of 100 and constant flux over more than 100 hours of operation. This proves the exciting possibility of exploiting transport phenomena governed by precision-engineered nanofluidic devices at a macroscopic scale.
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Affiliation(s)
- Margherita Bassu
- Biological Micro- and Nanotechnology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Peter Holik
- Micro System Technology (MST), Centre of Advanced European Studies and Research (caesar), 53175 Bonn, Germany
| | - Sam Schmitz
- Micro System Technology (MST), Centre of Advanced European Studies and Research (caesar), 53175 Bonn, Germany
| | - Siegfried Steltenkamp
- Micro System Technology (MST), Centre of Advanced European Studies and Research (caesar), 53175 Bonn, Germany
| | - Thomas P Burg
- Biological Micro- and Nanotechnology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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