1
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Jena MK, Mittal S, Manna SS, Pathak B. Deciphering DNA nucleotide sequences and their rotation dynamics with interpretable machine learning integrated C 3N nanopores. NANOSCALE 2023; 15:18080-18092. [PMID: 37916991 DOI: 10.1039/d3nr03771a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
A solid-state nanopore combined with the quantum transport method has garnered substantial attention and intrigue for DNA sequencing due to its potential for providing rapid and accurate sequencing results, which could have numerous applications in disease diagnosis and personalized medicine. However, the intricate and multifaceted nature of the experimental protocol poses a formidable challenge in attaining precise single nucleotide analysis. Here, we report a machine learning (ML) framework combined with the quantum transport method to accelerate high-throughput single nucleotide recognition with C3N nanopores. The optimized eXtreme Gradient Boosting Regression (XGBR) algorithm has predicted the fingerprint transmission of each unknown nucleotide and their rotation dynamics with root mean square error scores as low as 0.07. Interpretability of ML black box models with the game theory-based SHapley Additive exPlanation method has provided a quasi-explanation for the model working principle and the complex relationship between electrode-nucleotide coupling and transmission. Moreover, a comprehensive ML classification of nucleotides based on binary, ternary, and quaternary combinations shows maximum accuracy and F1 scores of 100%. The results suggest that ML in tandem with a nanopore device can potentially alleviate the experimental hurdles associated with quantum tunneling and facilitate fast and high-precision DNA sequencing.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Surya Sekhar Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India.
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2
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Murakami K, Kubota SI, Tanaka K, Tanaka H, Akabane K, Suzuki R, Shinohara Y, Takei H, Hashimoto S, Tanaka Y, Hojyo S, Sakamoto O, Naono N, Takaai T, Sato K, Kojima Y, Harada T, Hattori T, Fuke S, Yokota I, Konno S, Washio T, Fukuhara T, Teshima T, Taniguchi M, Murakami M. High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore. LAB ON A CHIP 2023; 23:4909-4918. [PMID: 37877206 DOI: 10.1039/d3lc00572k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
A digital platform that can rapidly and accurately diagnose pathogenic viral variants, including SARS-CoV-2, will minimize pandemics, public anxiety, and economic losses. We recently reported an artificial intelligence (AI)-nanopore platform that enables testing for Wuhan SARS-CoV-2 with high sensitivity and specificity within five minutes. However, which parts of the virus are recognized by the platform are unknown. Similarly, whether the platform can detect SARS-CoV-2 variants or the presence of the virus in clinical samples needs further study. Here, we demonstrated the platform can distinguish SARS-CoV-2 variants. Further, it identified mutated Wuhan SARS-CoV-2 expressing spike proteins of the delta and omicron variants, indicating it discriminates spike proteins. Finally, we used the platform to identify omicron variants with a sensitivity and specificity of 100% and 94%, respectively, in saliva specimens from COVID-19 patients. Thus, our results demonstrate the AI-nanopore platform is an effective diagnostic tool for SARS-CoV-2 variants.
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Affiliation(s)
- Kaoru Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shimpei I Kubota
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Kumiko Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroki Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Keiichiroh Akabane
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Yuta Shinohara
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Shigeru Hashimoto
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Yuki Tanaka
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shintaro Hojyo
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Takayui Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Kazuki Sato
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Yuichi Kojima
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Toshiyuki Harada
- Department of Respiratory Medicine, Japan Community Healthcare Organization Hokkaido Hospital, Sapporo, 062-8618, Japan
| | - Takeshi Hattori
- Department of Respiratory Medicine, Hokkaido Medical Center, National Hospital Organization, Sapporo, 063-0005, Japan
| | - Satoshi Fuke
- Department of Respiratory Medicine, KKR Sapporo Medical Center, Sapporo, 062-0931, Japan
| | - Isao Yokota
- Department of Biostatistics, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, 060-8638, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0020, Japan
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3
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Review of the use of nanodevices to detect single molecules. Anal Biochem 2022; 654:114645. [DOI: 10.1016/j.ab.2022.114645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
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Hagan JT, Sheetz BS, Bandara YMNDY, Karawdeniya BI, Morris MA, Chevalier RB, Dwyer JR. Chemically tailoring nanopores for single-molecule sensing and glycomics. Anal Bioanal Chem 2020; 412:6639-6654. [PMID: 32488384 DOI: 10.1007/s00216-020-02717-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Brian S Sheetz
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Buddini I Karawdeniya
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Melissa A Morris
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Robert B Chevalier
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA.
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5
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Taniguchi M. Analysis Method of the Ion Current-Time Waveform Obtained from Low Aspect Ratio Solid-state Nanopores. ANAL SCI 2020; 36:161-165. [PMID: 31813895 DOI: 10.2116/analsci.19r009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Low aspect ratio nanopores are expected to be applied to the detection of viruses and bacteria because of their high spatial resolution. Multiphysics simulations have revealed that the ion current-time waveform obtained from low aspect ratio nanopores contains information on not only the volume of viruses and bacteria, but also the structure, surface charge, and flow dynamics. Analysis using machine learning extracts information about these analytes from the ion current-time waveform. The combination of low aspect ratio nanopores, multiphysics simulation, and machine learning has made it possible to distinguish different types of viruses and bacteria with high accuracy.
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6
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Aso R, Ogawa Y, Tamaoka T, Yoshida H, Takeda S. Visualizing Progressive Atomic Change in the Metal Surface Structure Made by Ultrafast Electronic Interactions in an Ambient Environment. Angew Chem Int Ed Engl 2019; 58:16028-16032. [PMID: 31486177 DOI: 10.1002/anie.201907679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/28/2019] [Indexed: 11/07/2022]
Abstract
Understanding the atomic and molecular phenomena occurring in working catalysts and nanodevices requires the elucidation of atomic migration originating from electronic excitations. The progressive atomic dynamics on metal surface under controlled electronic stimulus in real time, space, and gas environments are visualized for the first time. By in situ environmental transmission electron microscopy, the gas molecules introduced into the biased metal nanogap could be activated by electron tunneling and caused the unpredicted atomic dynamics. The typically inactive gold was oxidized locally on the positive tip and field-evaporated to the negative tip, resulting in the atomic reconstruction on the negative tip surface. This finding of a tunneling-electron-attached-gas process will bring new insights into the design of nanostructures such as nanoparticle catalysts and quantum nanodots and will stimulate syntheses of novel nanomaterials not seen in the ambient environment.
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Affiliation(s)
- Ryotaro Aso
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yohei Ogawa
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
- Department of Materials and Manufacturing Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takehiro Tamaoka
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
- Department of Materials and Manufacturing Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hideto Yoshida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Seiji Takeda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
- Institute for NanoScience Design, Osaka University, 1-3 machikaneyama, Toyonaka, Osaka, 560-8531, Japan
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7
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Aso R, Ogawa Y, Tamaoka T, Yoshida H, Takeda S. Visualizing Progressive Atomic Change in the Metal Surface Structure Made by Ultrafast Electronic Interactions in an Ambient Environment. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryotaro Aso
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Yohei Ogawa
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
- Department of Materials and Manufacturing ScienceGraduate School of EngineeringOsaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Takehiro Tamaoka
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
- Department of Materials and Manufacturing ScienceGraduate School of EngineeringOsaka University 2-1 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Hideto Yoshida
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
| | - Seiji Takeda
- The Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka, Ibaraki Osaka 567-0047 Japan
- Institute for NanoScience DesignOsaka University 1–3 machikaneyama, Toyonaka Osaka 560-8531 Japan
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8
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Birkin PR, Linfield S, Denuault G, Jones R, Youngs JJ, Wain E. An Analytical Differential Resistance Pulse System Relying on a Time Shift Signal Analysis-Applications in Coulter Counting. ACS Sens 2019; 4:2190-2195. [PMID: 31290312 DOI: 10.1021/acssensors.9b01087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Improving the sensitivity and ultimately the range of particle sizes that can be detected with a single pore extends the versatility of the Coulter counting technique. Here, to enable a pore to have greater sensitivity, we have developed and tested a novel differential resistive pulse sensing (DiS) system for sizing particles. To do this, the response was generated through a time shift approach utilizing a "self-servoing regime" to enable the final signal to operate with a zero background in the absence of particle translocation. The detection and characterization of a series of polystyrene particles, forced to translocate through a cylindrical glass microchannel (GMC) by a suitable static pressure difference using this approach, is demonstrated. An analytical response, which scales with the size of the particles employed, was verified. Parasitic capacitive effects are discussed; however, translocations on the millisecond time scale can be detected with high sensitivity and accuracy using the approach described.
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Affiliation(s)
- Peter R. Birkin
- Department of Chemistry, University of Southampton, Southampton, SO171BJ, United Kingdom
| | - Steven Linfield
- Department of Chemistry, University of Southampton, Southampton, SO171BJ, United Kingdom
| | - Guy Denuault
- Department of Chemistry, University of Southampton, Southampton, SO171BJ, United Kingdom
| | - Ronald Jones
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jack J. Youngs
- Department of Chemistry, University of Southampton, Southampton, SO171BJ, United Kingdom
| | - Emily Wain
- Department of Chemistry, University of Southampton, Southampton, SO171BJ, United Kingdom
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9
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Bandara YMNDY, Karawdeniya BI, Hagan JT, Chevalier RB, Dwyer JR. Chemically Functionalizing Controlled Dielectric Breakdown Silicon Nitride Nanopores by Direct Photohydrosilylation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:30411-30420. [PMID: 31347369 DOI: 10.1021/acsami.9b08004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanopores are a prominent enabling tool for single-molecule applications such as DNA sequencing, protein profiling, and glycomics, and the construction of ionic circuit elements. Silicon nitride (SiNx) is a leading scaffold for these <100 nm-diameter nanofluidic ion-conducting channels, but frequently challenging surface chemistry remains an obstacle to their use. We functionalized more than 100 SiNx nanopores with different surface terminations-acidic (Si-R-OH, Si-R-CO2H), basic (Si-R-NH2), and nonionizable (Si-R-C6H3(CF3)2)-to chemically tune the nanopore size, surface charge polarity, and subsequent chemical reactivity and to change their conductance by changes of solution pH. The initial one-reaction-step covalent chemical film formation was by hydrosilylation and could be followed by straightforward condensation and click reactions. The hydrosilylation reaction step used neat reagents with no special precautions such as guarding against water content. A key feature of the approach was to combine controlled dielectric breakdown (CDB) with hydrosilylation to create and functionalize SiNx nanopores. CDB thus replaced the detrimental but conventionally necessary surface pretreatment with hydrofluoric acid. Proof-of-principle detection of the canonical test molecule, λ-DNA, yielded signals that showed that the functionalized pores were not obstructed by chemical treatments but could translocate the biopolymer. The characteristics were tuned by the surface coating character. This robust and flexible surface coating method, freed by CDB from HF etching, portends the development of nanopores with surface chemistry tuned to match the application, extending even to the creation of biomimetic nanopores.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Buddini I Karawdeniya
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - James T Hagan
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Robert B Chevalier
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
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10
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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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11
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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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12
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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13
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Bandara YMDY, Karawdeniya BI, Dwyer JR. Push-Button Method To Create Nanopores Using a Tesla-Coil Lighter. ACS OMEGA 2019; 4:226-230. [PMID: 31459326 PMCID: PMC6649298 DOI: 10.1021/acsomega.8b02660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/13/2018] [Indexed: 05/30/2023]
Abstract
Controlled dielectric breakdown (CDB) of silicon nitride thin films immersed in electrolyte solution has been used to fabricate single nanofluidic channels with ∼10 nm and smaller diameters, nanopores, useful in single-molecule sensing and ionic circuit construction. A hand-held Tesla-coil lighter was used to form nanofluidic ionic conductors through a ∼10 nm thick silicon nitride membrane. Modifications to the conventional approach were required by the low-overhead Tesla-coil-assisted method (TCAM): increased circuit resistance by including water in place of electrolyte and discrete rather than continuous voltage applications. The resulting ionic conductance could be tuned with the number of voltage applications. TCAM and conventional CDB produced nanopores with different conductance versus pH curves, suggesting different surface chemistry. Nevertheless, sensing experiments using the canonical test molecule, λ-DNA, produced signals comparable to translocation results through solid-state nanopores fabricated by other methods. Thus, the TCAM method offers flexibility in fabrication and in the properties and function of the nanoscale ionic conductors that it can generate.
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14
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Ghosal S, Sherwood JD, Chang HC. Solid-state nanopore hydrodynamics and transport. BIOMICROFLUIDICS 2019; 13:011301. [PMID: 30867871 PMCID: PMC6404949 DOI: 10.1063/1.5083913] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/31/2018] [Indexed: 05/08/2023]
Abstract
The resistive pulse method based on measuring the ion current trace as a biomolecule passing through a nanopore has become an important tool in biotechnology for characterizing molecules. A detailed physical understanding of the translocation process is essential if one is to extract the relevant molecular properties from the current signal. In this Perspective, we review some recent progress in our understanding of hydrodynamic flow and transport through nanometer sized pores. We assume that the problems of interest can be addressed through the use of the continuum version of the equations of hydrodynamic and ion transport. Thus, our discussion is restricted to pores of diameter greater than about ten nanometers: such pores are usually synthetic. We address the fundamental nanopore hydrodynamics and ion transport mechanisms and review the wealth of observed phenomena due to these mechanisms. We also suggest future ionic circuits that can be synthesized from different ionic modules based on these phenomena and their applications.
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Affiliation(s)
- Sandip Ghosal
- Department of Mechanical Engineering and Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
| | - John D Sherwood
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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15
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Wongkaew N, Simsek M, Griesche C, Baeumner AJ. Functional Nanomaterials and Nanostructures Enhancing Electrochemical Biosensors and Lab-on-a-Chip Performances: Recent Progress, Applications, and Future Perspective. Chem Rev 2018; 119:120-194. [DOI: 10.1021/acs.chemrev.8b00172] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Nongnoot Wongkaew
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Marcel Simsek
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Griesche
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93053 Regensburg, Germany
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16
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Surveying silicon nitride nanopores for glycomics and heparin quality assurance. Nat Commun 2018; 9:3278. [PMID: 30115917 PMCID: PMC6095881 DOI: 10.1038/s41467-018-05751-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/17/2018] [Indexed: 12/26/2022] Open
Abstract
Polysaccharides have key biological functions and can be harnessed for therapeutic roles, such as the anticoagulant heparin. Their complexity—e.g., >100 monosaccharides with variety in linkage and branching structure—significantly complicates analysis compared to other biopolymers such as DNA and proteins. More, and improved, analysis tools have been called for, and here we demonstrate that solid-state silicon nitride nanopore sensors and tuned sensing conditions can be used to reliably detect native polysaccharides and enzymatic digestion products, differentiate between different polysaccharides in straightforward assays, provide new experimental insights into nanopore electrokinetics, and uncover polysaccharide properties. We show that nanopore sensing allows us to easily differentiate between a clinical heparin sample and one spiked with the contaminant that caused deaths in 2008 when its presence went undetected by conventional assays. The work reported here lays a foundation to further explore polysaccharide characterization and develop assays using thin-film solid-state nanopore sensors. The complexity of polysaccharides significantly complicates their analysis in comparison to other biopolymers. Here, the authors demonstrate that solid-state silicon nitride nanopore sensors can be used to reliably detect native polysaccharides and to perform a simple quality assurance assay on a polysaccharide therapeutic, heparin.
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17
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Yuan Z, Wang C, Yi X, Ni Z, Chen Y, Li T. Solid-State Nanopore. NANOSCALE RESEARCH LETTERS 2018; 13:56. [PMID: 29460116 PMCID: PMC5818388 DOI: 10.1186/s11671-018-2463-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/28/2018] [Indexed: 05/23/2023]
Abstract
Solid-state nanopore has captured the attention of many researchers due to its characteristic of nanoscale. Now, different fabrication methods have been reported, which can be summarized into two broad categories: "top-down" etching technology and "bottom-up" shrinkage technology. Ion track etching method, mask etching method chemical solution etching method, and high-energy particle etching and shrinkage method are exhibited in this report. Besides, we also discussed applications of solid-state nanopore fabrication technology in DNA sequencing, protein detection, and energy conversion.
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Affiliation(s)
- Zhishan Yuan
- School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Chengyong Wang
- School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xin Yi
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Tie Li
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
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18
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Bandara YMNDY, Nichols JW, Iroshika Karawdeniya B, Dwyer JR. Conductance‐based profiling of nanopores: Accommodating fabrication irregularities. Electrophoresis 2017; 39:626-634. [DOI: 10.1002/elps.201700299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Jason R. Dwyer
- Department of Chemistry University of Rhode Island Kingston RI USA
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19
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Park KB, Kim HJ, Kang YH, Yu JS, Chae H, Lee K, Kim HM, Kim KB. Highly reliable and low-noise solid-state nanopores with an atomic layer deposited ZnO membrane on a quartz substrate. NANOSCALE 2017; 9:18772-18780. [PMID: 29168535 DOI: 10.1039/c7nr05755e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a fabrication scheme for a solid-state ZnO nanopore membrane directly deposited on top of a quartz substrate by atomic layer deposition (ALD) and investigate the characteristics of DNA translocation through the nanopores. We chose a ZnO membrane owing to its high isoelectric point (∼9.5) as well as its chemical and mechanical stability. Aside from the extremely low noise level exhibited by this device on a highly insulating and low dielectric quartz substrate, it also slows down the translocation speed of DNA by more than one order of magnitude as compared to that of a SiNx nanopore device. We propose that the electrostatic interaction between the positively charged ZnO nanopore wall, resulting from the high isoelectric point of ZnO, and the negatively charged phosphate backbone of DNA provides an additional frictional force that slows down the DNA translocation.
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Affiliation(s)
- Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea.
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20
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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21
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Hiratani M, Ohara M, Kawano R. Amplification and Quantification of an Antisense Oligonucleotide from Target microRNA Using Programmable DNA and a Biological Nanopore. Anal Chem 2017; 89:2312-2317. [PMID: 28192937 DOI: 10.1021/acs.analchem.6b03830] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This paper describes a strategy for autonomous diagnoses of cancers using microRNA (miRNA) and therapy for tumor cells by DNA computing techniques and nanopore measurement. Theranostics, which involves the combination of diagnosis and therapy, has emerged as an approach for personalized medicine or point-of-care cancer diagnostics. DNA computing will become a potent tool for theranostics because it functions completely autonomously without the need for external regulations. However, conventional theranostics using DNA computing involves a one-to-one reaction in which a single input molecule generates a single output molecule; the concentration of the antisense drug is insufficient for the therapy in this type of reaction. Herein we developed an amplification system involving an isothermal reaction in which a large amount of the antisense DNA drug was autonomously generated after detecting miRNA from small cell lung cancer. In addition, we successfully quantified the amount of the generated drug molecule by nanopore measurement with high accuracy, which was more accurate than conventional gel electrophoresis. This autonomous amplification strategy is a potent candidate for a broad range of theranostics using DNA computing.
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Affiliation(s)
- Moe Hiratani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT) , 2-24-16 Naka-cho Koganei-shi, Tokyo 184-8588, Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT) , 2-24-16 Naka-cho Koganei-shi, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT) , 2-24-16 Naka-cho Koganei-shi, Tokyo 184-8588, Japan
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22
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Bandara YMNDY, Karawdeniya BI, Whelan JC, Ginsberg LDS, Dwyer JR. Solution-Based Photo-Patterned Gold Film Formation on Silicon Nitride. ACS APPLIED MATERIALS & INTERFACES 2016; 8:34964-34969. [PMID: 27936582 DOI: 10.1021/acsami.6b12720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silicon nitride fabricated by low-pressure chemical vapor deposition (LPCVD) to be silicon-rich (SiNx), is a ubiquitous insulating thin film in the microelectronics industry, and an exceptional structural material for nanofabrication. Free-standing <100 nm thick SiNx membranes are especially compelling, particularly when used to deliver forefront molecular sensing capabilities in nanofluidic devices. We developed an accessible, gentle, and solution-based photodirected surface metallization approach well-suited to forming patterned metal films as integral structural and functional features in thin-membrane-based SiNx devices-for use as electrodes or surface chemical functionalization platforms, for example-augmenting existing device capabilities and properties for a wide range of applications.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Buddini Iroshika Karawdeniya
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Julie C Whelan
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Lucas D S Ginsberg
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
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23
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Dwyer JR, Bandara YMNDY, Whelan JC, Karawdeniya BI, Nichols JW. Silicon Nitride Thin Films for Nanofluidic Device Fabrication. NANOFLUIDICS 2016. [DOI: 10.1039/9781849735230-00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
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Affiliation(s)
- J. R. Dwyer
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | | | - J. C. Whelan
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - B. I. Karawdeniya
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - J. W. Nichols
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
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24
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Bandara YMNDY, Karawdeniya BI, Dwyer JR. Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication. ACS APPLIED MATERIALS & INTERFACES 2016; 8:30583-30589. [PMID: 27709879 DOI: 10.1021/acsami.6b10045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a method for simply characterizing the size and shape of a nanopore during solution-based fabrication and surface modification, using only low-overhead approaches native to conventional nanopore measurements. Solution-based nanopore fabrication methods are democratizing nanopore science by supplanting the traditional use of charged-particle microscopes for fabrication, but nanopore profiling has customarily depended on microscopic examination. Our approach exploits the dependence of nanopore conductance in solution on nanopore size, shape, and surface chemistry in order to characterize nanopores. Measurements of the changing nanopore conductance during formation by etching or deposition can be analyzed using our method to characterize the nascent nanopore size and shape, beyond the typical cylindrical approximation, in real-time. Our approach thus accords with ongoing efforts to broaden the accessibility of nanopore science from fabrication through use: it is compatible with conventional instrumentation and offers straightforward nanoscale characterization of the core tool of the field.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Buddini Iroshika Karawdeniya
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
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25
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Hsu WL, Daiguji H. Manipulation of Protein Translocation through Nanopores by Flow Field Control and Application to Nanopore Sensors. Anal Chem 2016; 88:9251-8. [PMID: 27571138 DOI: 10.1021/acs.analchem.6b02513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.
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Affiliation(s)
- Wei-Lun Hsu
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
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26
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Yanagi I, Akahori R, Aoki M, Harada K, Takeda KI. Multichannel detection of ionic currents through two nanopores fabricated on integrated Si3N4 membranes. LAB ON A CHIP 2016; 16:3340-3350. [PMID: 27440476 DOI: 10.1039/c6lc00639f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Integration of solid-state nanopores and multichannel detection of signals from each nanopore are effective measures for realizing high-throughput nanopore sensors. In the present study, we demonstrated fabrication of Si3N4 membrane arrays and the simultaneous measurement of ionic currents through two nanopores formed in two adjacent membranes. Membranes with thicknesses as low as 6.4 nm and small nanopores with diameters of less than 2 nm could be fabricated using the poly-Si sacrificial-layer process and multilevel pulse-voltage injection. Using the fabricated nanopore membranes, we successfully achieved simultaneous detection of clear ionic-current blockades when single-stranded short homopolymers (poly(dA)60) passed through two nanopores. In addition, we investigated the signal crosstalk and leakage current among separated chambers. When two nanopores were isolated on the front surface of the membrane, there was no signal crosstalk or leakage current between the chambers. However, when two nanopores were isolated on the backside of the Si substrate, signal crosstalk and leakage current were observed owing to high-capacitance coupling between the chambers and electrolysis of water on the surface of the Si substrate. The signal crosstalk and leakage current could be suppressed by oxidizing the exposed Si surface in the membrane chip. Finally, the observed ionic-current blockade when poly(dA)60 passed through the nanopore in the oxidized chip was approximately half of that observed in the non-oxidized chip.
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Affiliation(s)
- Itaru Yanagi
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Rena Akahori
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Mayu Aoki
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Kunio Harada
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Ken-Ichi Takeda
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
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27
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He Y, Tsutsui M, Scheicher RH, Miao XS, Taniguchi M. Salt-Gradient Approach for Regulating Capture-to-Translocation Dynamics of DNA with Nanochannel Sensors. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhui He
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Makusu Tsutsui
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Ralph H. Scheicher
- Division
of Materials Theory, Department of Physics and Astronomy, Angström
Laboratory, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Xiang Shui Miao
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Masateru Taniguchi
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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28
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Yanagi I, Oura T, Haga T, Ando M, Yamamoto J, Mine T, Ishida T, Hatano T, Akahori R, Yokoi T, Anazawa T. Side-gated ultrathin-channel nanopore FET sensors. NANOTECHNOLOGY 2016; 27:115501. [PMID: 26876025 DOI: 10.1088/0957-4484/27/11/115501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.
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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
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29
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Prasongkit J, Feliciano GT, Rocha AR, He Y, Osotchan T, Ahuja R, Scheicher RH. Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene. Sci Rep 2015; 5:17560. [PMID: 26634811 PMCID: PMC4669446 DOI: 10.1038/srep17560] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023] Open
Abstract
Fast, cost effective, single-shot DNA sequencing could be the prelude of a new era in genetics. As DNA encodes the information for the production of proteins in all known living beings on Earth, determining the nucleobase sequences is the first and necessary step in that direction. Graphene-based nanopore devices hold great promise for next-generation DNA sequencing. In this work, we develop a novel approach for sequencing DNA using bilayer graphene to read the interlayer conductance through the layers in the presence of target nucleobases. Classical molecular dynamics simulations of DNA translocation through the pore were performed to trace the nucleobase trajectories and evaluate the interaction between the nucleobases and the nanopore. This interaction stabilizes the bases in different orientations, resulting in smaller fluctuations of the nucleobases inside the pore. We assessed the performance of a bilayer graphene nanopore setup for the purpose of DNA sequencing by employing density functional theory and non-equilibrium Green’s function method to investigate the interlayer conductance of nucleobases coupling simultaneously to the top and bottom graphene layers. The obtained conductance is significantly affected by the presence of DNA in the bilayer graphene nanopore, allowing us to analyze DNA sequences.
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Affiliation(s)
- Jariyanee Prasongkit
- Division of Physics, Faculty of Science, Nakhon Phanom University, Nakhon Phanom 48000, Thailand.,Nanotec-KKU Center of Excellence on Advanced Nanomaterials for Energy Production and Storage, Khon Kaen 40002, Thailand
| | - Gustavo T Feliciano
- Institute of Chemistry, Physical Chemistry Department, Universidade Estadual Paulista (UNESP), Araraquara, SP, Brazil
| | - Alexandre R Rocha
- Instituto de Física Téorica, Universidade Estadual Paulista (UNESP), São Paulo, SP, Brazil
| | - Yuhui He
- School of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Tanakorn Osotchan
- Department of Physics, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Rajeev Ahuja
- Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.,Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ralph H Scheicher
- Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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30
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He Y, Tsutsui M, Miao XS, Taniguchi M. Impact of Water-Depletion Layer on Transport in Hydrophobic Nanochannels. Anal Chem 2015; 87:12040-50. [DOI: 10.1021/acs.analchem.5b03061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhui He
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makusu Tsutsui
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Xiang Shui Miao
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Masateru Taniguchi
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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31
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Yanagi I, Ishida T, Fujisaki K, Takeda KI. Fabrication of 3-nm-thick Si3N4 membranes for solid-state nanopores using the poly-Si sacrificial layer process. Sci Rep 2015; 5:14656. [PMID: 26424588 PMCID: PMC4589763 DOI: 10.1038/srep14656] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022] Open
Abstract
To improve the spatial resolution of solid-state nanopores, thinning the membrane is a very important issue. The most commonly used membrane material for solid-state nanopores is silicon nitride (Si3N4). However, until now, stable wafer-scale fabrication of Si3N4 membranes with a thickness of less than 5 nm has not been reported, although a further reduction in thickness is desired to improve spatial resolution. In the present study, to fabricate thinner Si3N4 membranes with a thickness of less than 5 nm in a wafer, a new fabrication process that employs a polycrystalline-Si (poly-Si) sacrificial layer was developed. This process enables the stable fabrication of Si3N4 membranes with thicknesses of 3 nm. Nanopores were fabricated in the membrane using a transmission electron microscope (TEM) beam. Based on the relationship between the ionic current through the nanopores and their diameter, the effective thickness of the nanopores was estimated to range from 0.6 to 2.2 nm. Moreover, DNA translocation through the nanopores was observed.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Takeshi Ishida
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Koji Fujisaki
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Ken-Ichi Takeda
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
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Liu N, Yang Z, Ou X, Wei B, Zhang J, Jia Y, Xia F. Nanopore-based analysis of biochemical species. Mikrochim Acta 2015; 183:955-963. [PMID: 27013767 PMCID: PMC4778144 DOI: 10.1007/s00604-015-1560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/30/2015] [Indexed: 12/11/2022]
Abstract
Biological nanochannels or nanopores play a crucial role in basic biochemical processes in cells. Artificial nanopores possessing dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels are of particular interest with respect to the design of biosensors with a sensitivity that can go down to the fM level and even to single molecule detection. Nanopore-based analysis (NPA) is currently a new research field with fascinating prospects. This review (with 118 refs.) summarizes the progress made in this field in the recent 10 years. Following an introduction into the fundamentals of NPA, we demonstrate its potential by describing selected methods for sensing (a) proteins such as streptavidin, certain antibodies, or thrombin via aptamers; (b) oligomers, larger nucleic acids, or micro-RNA; (c) small molecules, (d) ions such as K(I) which is vital to the maintenance of life, or Hg(II) which is dangerous to health. We summarize the results and discuss the merits and limitations of the various methods at last. Graphical abstractSchematic of a signal-off system and a signal-on system in nanopore analysis. The effective diameter of nanopores decreases when targets undergo certain interactions with receptors attached on the inner surface of the nanopore. Correspondingly, the current will drop on appearance of the analyte. This is referred to as a "signal-off" system. Conversely, it is called a "signal-on" system.
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Affiliation(s)
- Nannan Liu
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Zekun Yang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Xiaowen Ou
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Benmei Wei
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Juntao Zhang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Yongmei Jia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Fan Xia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
- />National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074 China
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Liu L, Ma B. Controlled protein separation based on pressure–voltage (P–V) coupling effects in a nanopore based device. RSC Adv 2015; 5:98004-98009. [DOI: 10.1039/c5ra16952f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
A U-type device containing two cells connected by nanopore arrays was designed for controlled protein separation. By finding P–V equilibrium points for BSA and Hb, the separation ratios can be achieved as BSA : Hb = 12.5 and Hb : BSA = 14.3.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- School of Mechanical Engineering
- Southeast University
- Nanjing 210096
- People’s Republic of China
| | - Bin Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
- School of Mechanical Engineering
- Southeast University
- Nanjing 210096
- People’s Republic of China
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