1
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Zhang L, Wahab OJ, Jallow AA, O’Dell ZJ, Pungsrisai T, Sridhar S, Vernon KL, Willets KA, Baker LA. Recent Developments in Single-Entity Electrochemistry. Anal Chem 2024; 96:8036-8055. [PMID: 38727715 PMCID: PMC11112546 DOI: 10.1021/acs.analchem.4c01406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- L. Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - O. J. Wahab
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - A. A. Jallow
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - Z. J. O’Dell
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - T. Pungsrisai
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - S. Sridhar
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - K. L. Vernon
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
| | - K. A. Willets
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - L. A. Baker
- Department
of Chemistry, Texas A&M University, College Station, Texas 77845, United States
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2
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Dutt S, Karawdeniya B, Bandara YMNDY, Kluth P. Nanopore sensing and machine learning: future of biomarker analysis and disease detection. Future Sci OA 2024; 10:2340882. [PMID: 38817373 PMCID: PMC11137830 DOI: 10.2144/fsoa-2023-0226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 06/01/2024] Open
Affiliation(s)
- Shankar Dutt
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra ACT 2601, Australia
| | - Buddini Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra ACT 2601, Australia
| | - Yapa MNDY Bandara
- Research School of Chemistry, Australian National University, Canberra ACT 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra ACT 2601, Australia
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3
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Li X, Fu YH, Wei N, Yu RJ, Bhatti H, Zhang L, Yan F, Xia F, Ewing AG, Long YT, Ying YL. Emerging Data Processing Methods for Single-Entity Electrochemistry. Angew Chem Int Ed Engl 2024; 63:e202316551. [PMID: 38411372 DOI: 10.1002/anie.202316551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ying-Huan Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nannan Wei
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
| | - Huma Bhatti
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Limin Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 430034, Wuhan, P. R. China
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296, Gothenburg, Sweden
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
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4
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Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. SMALL METHODS 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
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5
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Zhou C, Cai Z, Jin B, Lin H, Xu L, Jin Z. Saliva-based detection of SARS-CoV-2: a bibliometric analysis of global research. Mol Cell Biochem 2024; 479:761-777. [PMID: 37178376 PMCID: PMC10182745 DOI: 10.1007/s11010-023-04760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Saliva has emerged as a promising noninvasive biofluid for the diagnosis of oral and systemic diseases, including viral infections. During the coronavirus disease 2019 (COVID-19) pandemic, a growing number of studies focused on saliva-based detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Taking advantage of the WoS core collection (WoSCC) and CiteSpace, we retrieved 1021 articles related to saliva-based detection of SARS-CoV-2 and conducted a comprehensive bibliometric analysis. We analyzed countries, institutions, authors, cited authors, and cited journals to summarize their contribution and influence and analyzed keywords to explore research hotspots and trends. From 2020 to 2021, research focused on viral transmission via saliva and verification of saliva as a reliable specimen, whereas from 2021 to the present, the focus of research has switched to saliva-based biosensors for SARS-CoV-2 detection. By far, saliva has been verified as a reliable specimen for SARS-CoV-2 detection, although a standardized procedure for saliva sampling and processing is needed. Studies on saliva-based detection of SARS-CoV-2 will promote the development of saliva-based diagnostics and biosensors for viral detection. Collectively, our findings could provide valuable information to help scientists perceive the basic knowledge landscapes on saliva-based detection of SARS-CoV-2, the past and current research hotspots, and future opportunities.
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Affiliation(s)
- Chun Zhou
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China
- Department of Science and Education, the Affiliated Jinhua Hospital of Wenzhou Medical University, Jinhua, 321000, Zhejiang, China
| | - Zhaopin Cai
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Boxing Jin
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Huisong Lin
- Zhejiang Institute of Medical Device Testing, Hangzhou, Zhejiang, China
| | - Lingling Xu
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China
| | - Zhigang Jin
- Jinhua People's Hospital Joint Center for Biomedical Research, Zhejiang Normal University, Jinhua, 321000, Zhejiang, China.
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua, 321000, Zhejiang, China.
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6
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Morimura A, Taniguchi M, Takei H, Sakamoto O, Naono N, Akeda Y, Onozuka D, Yoshimura J, Tomono K, Kutsuna S, Hamaguchi S. Using novel micropore technology combined with artificial intelligence to differentiate Staphylococcus aureus and Staphylococcus epidermidis. Sci Rep 2024; 14:6994. [PMID: 38523156 PMCID: PMC10961322 DOI: 10.1038/s41598-024-55773-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
Methods for identifying bacterial pathogens are broadly categorised into conventional culture-based microbiology, nucleic acid-based tests, and mass spectrometry. The conventional method requires several days to isolate and identify bacteria. Nucleic acid-based tests and mass spectrometry are relatively rapid and reliable, but they require trained technicians. Moreover, mass spectrometry requires expensive equipment. The development of a novel, inexpensive, and simple technique for identifying bacterial pathogens is needed. Through combining micropore technology and assembly machine learning, we developed a novel classifier whose receiver operating characteristic (ROC) curve showed an area under the ROC curve of 0.94, which rapidly differentiated between Staphylococcus aureus and Staphylococcus epidermidis in this proof-of-concept study. Morphologically similar bacteria belonging to an identical genus can be distinguished using our method, which requires no specific training, and may facilitate the diagnosis and treatment of patients with bacterial infections in remote areas and in developing countries.
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Affiliation(s)
- Ayumi Morimura
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuraoka-cho, Shibuya-ku, Tokyo, 150-8512, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Daisuke Onozuka
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Graduate School of Medicine, Osaka University, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazunori Tomono
- Osaka Institute of Public Health, 1-3-3 Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan
| | - Satoshi Kutsuna
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, 2-15 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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7
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Affiliation(s)
- Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Tian Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hanhan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
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8
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Shah A, Pathak S, Li K, Garaj S, Bazant MZ, Gupta A, Doyle PS. A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes. NANO LETTERS 2024. [PMID: 38437028 DOI: 10.1021/acs.nanolett.3c04997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.
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Affiliation(s)
- Arjav Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Shakul Pathak
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kun Li
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Slaven Garaj
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
- Department of Physics, National University of Singapore, Singapore 119077
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
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9
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Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. Nat Commun 2024; 15:1699. [PMID: 38402271 PMCID: PMC10894232 DOI: 10.1038/s41467-024-45968-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
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Affiliation(s)
| | - Jovan Pešović
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Marko Panić
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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10
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Zhang S, Cao Z, Fan P, Sun W, Xiao Y, Zhang P, Wang Y, Huang S. Discrimination of Disaccharide Isomers of Different Glycosidic Linkages Using a Modified MspA Nanopore. Angew Chem Int Ed Engl 2024; 63:e202316766. [PMID: 38116834 DOI: 10.1002/anie.202316766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Disaccharides are composed of two monosaccharide subunits joined by a glycosidic linkage in an α or β configuration. Different combinations of isomeric monosaccharide subunits and different glycosidic linkages result in different isomeric disaccharide products. Thus, direct discrimination of these disaccharide isomers from a mixture is extremely difficult. In this paper, a hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore conjugated with a phenylboronic acid (PBA) adapter was applied for disaccharide sensing, with which three most widely known disaccharides in nature, including sucrose, lactose and maltose, were clearly discriminated. Besides, all six isomeric α-D-glucopyranosyl-D-fructoses, differing only in their glycosidic linkages, were also well resolved. Assisted by a custom machine learning algorithm, a 0.99 discrimination accuracy is achieved. Nanopore discrimination of disaccharide isomers with different glycosidic linkages, which has never been previously demonstrated, is inspiring for nanopore saccharide sequencing. This sensing capacity was also applied in direct identification of isomaltulose additives in a commercial sucrose-free yogurt, from which isomaltulose, lactose and L-lactic acid were simultaneously detected.
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Affiliation(s)
- Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yunqi Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuqin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, Suzhou, 215163, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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11
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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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12
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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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13
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Dutt S, Shao H, Karawdeniya B, Bandara YMNDY, Daskalaki E, Suominen H, Kluth P. High Accuracy Protein Identification: Fusion of Solid-State Nanopore Sensing and Machine Learning. SMALL METHODS 2023; 7:e2300676. [PMID: 37718979 DOI: 10.1002/smtd.202300676] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analyzing biomolecules such as proteins at single-molecule level. While molecular-level information on size, shape, and charge of proteins can be assessed by nanopores, the identification of proteins with comparable sizes remains a challenge. Here, solid-state nanopore sensing is combined with machine learning to address this challenge. The translocations of four similarly sized proteins is assessed using amplifiers with bandwidths (BWs) of 100 kHz and 10 MHz, the highest bandwidth reported for protein sensing, using nanopores fabricated in <10 nm thick silicon nitride membranes. F-values of up to 65.9% and 83.2% (without clustering of the protein signals) are achieved with 100 kHz and 10 MHz BW measurements, respectively, for identification of the four proteins. The accuracy of protein identification is further enhanced by classifying the signals into different clusters based on signal attributes, with F-value and specificity of up to 88.7% and 96.4%, respectively, for combinations of four proteins. The combined use of high bandwidth instruments, advanced clustering and machine learning methods allows label-free identification of proteins with high accuracy.
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Affiliation(s)
- Shankar Dutt
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Hancheng Shao
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Buddini Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
| | - Y M Nuwan D Y Bandara
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Elena Daskalaki
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT, 2601, Australia
| | - Hanna Suominen
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT, 2601, Australia
- Eccles Institute of Neuroscience, College of Health and Medicine, Australian National University, Canberra, ACT, 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 2601, Australia
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14
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Valenzuela-Amaro HM, Aguayo-Acosta A, Meléndez-Sánchez ER, de la Rosa O, Vázquez-Ortega PG, Oyervides-Muñoz MA, Sosa-Hernández JE, Parra-Saldívar R. Emerging Applications of Nanobiosensors in Pathogen Detection in Water and Food. BIOSENSORS 2023; 13:922. [PMID: 37887115 PMCID: PMC10605657 DOI: 10.3390/bios13100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Food and waterborne illnesses are still a major concern in health and food safety areas. Every year, almost 0.42 million and 2.2 million deaths related to food and waterborne illness are reported worldwide, respectively. In foodborne pathogens, bacteria such as Salmonella, Shiga-toxin producer Escherichia coli, Campylobacter, and Listeria monocytogenes are considered to be high-concern pathogens. High-concern waterborne pathogens are Vibrio cholerae, leptospirosis, Schistosoma mansoni, and Schistosima japonicum, among others. Despite the major efforts of food and water quality control to monitor the presence of these pathogens of concern in these kinds of sources, foodborne and waterborne illness occurrence is still high globally. For these reasons, the development of novel and faster pathogen-detection methods applicable to real-time surveillance strategies are required. Methods based on biosensor devices have emerged as novel tools for faster detection of food and water pathogens, in contrast to traditional methods that are usually time-consuming and are unsuitable for large-scale monitoring. Biosensor devices can be summarized as devices that use biochemical reactions with a biorecognition section (isolated enzymes, antibodies, tissues, genetic materials, or aptamers) to detect pathogens. In most cases, biosensors are based on the correlation of electrical, thermal, or optical signals in the presence of pathogen biomarkers. The application of nano and molecular technologies allows the identification of pathogens in a faster and high-sensibility manner, at extremely low-pathogen concentrations. In fact, the integration of gold, silver, iron, and magnetic nanoparticles (NP) in biosensors has demonstrated an improvement in their detection functionality. The present review summarizes the principal application of nanomaterials and biosensor-based devices for the detection of pathogens in food and water samples. Additionally, it highlights the improvement of biosensor devices through nanomaterials. Nanomaterials offer unique advantages for pathogen detection. The nanoscale and high specific surface area allows for more effective interaction with pathogenic agents, enhancing the sensitivity and selectivity of the biosensors. Finally, biosensors' capability to functionalize with specific molecules such as antibodies or nucleic acids facilitates the specific detection of the target pathogens.
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Affiliation(s)
- Hiram Martin Valenzuela-Amaro
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Edgar Ricardo Meléndez-Sánchez
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Orlando de la Rosa
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico; (H.M.V.-A.); (A.A.-A.); (E.R.M.-S.); (O.d.l.R.); (M.A.O.-M.)
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
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15
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Zeid AM, Mostafa IM, Lou B, Xu G. Advances in miniaturized nanosensing platforms for analysis of pathogenic bacteria and viruses. LAB ON A CHIP 2023; 23:4160-4172. [PMID: 37668185 DOI: 10.1039/d3lc00674c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Pathogenic bacteria and viruses are the main causes of infectious diseases all over the world. Early diagnosis of such infectious diseases is a critical step in management of their spread and treatment of the infection in its early stages. Therefore, the innovation of smart sensing platforms for point-of-care diagnosis of life-threatening infectious diseases such as COVID-19 is a prerequisite to isolate the patients and provide them with suitable treatment strategies. The developed diagnostic sensors should be highly sensitive, specific, ultrafast, portable, cheap, label-free, and selective. In recent years, different nanosensors have been developed for the detection of bacterial and viral pathogens. We focus here on label-free miniaturized nanosensing platforms that were efficiently applied for pathogenic detection in biological matrices. Such devices include nanopore sensors and nanostructure-integrated lab-on-a-chip sensors that are characterized by portability, simplicity, cost-effectiveness, and ultrafast analysis because they avoid the time-consuming sample preparation steps. Furthermore, nanopore-based sensors could afford single-molecule counting of viruses in biological specimens, yielding high-sensitivity and high-accuracy detection. Moreover, non-invasive nanosensors that are capable of detecting volatile organic compounds emitted from the diseased organ to the skin, urine, or exhaled breath were also reviewed. The merits and applications of all these nanosensors for analysis of pathogenic bacteria and viruses in biological matrices will be discussed in detail, emphasizing the importance of artificial intelligence in advancing specific nanosensors.
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Affiliation(s)
- Abdallah M Zeid
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Islam M Mostafa
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Baohua Lou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Guobao Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
- University of Science and Technology of China, Hefei, Anhui 230026, China
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16
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Yasuura M, Tan ZL, Horiguchi Y, Ashiba H, Fukuda T. Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components. SENSORS (BASEL, SWITZERLAND) 2023; 23:6830. [PMID: 37571612 PMCID: PMC10422600 DOI: 10.3390/s23156830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.
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Affiliation(s)
- Masato Yasuura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Z.L.T.); (Y.H.); (H.A.); (T.F.)
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17
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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18
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Rahn KL, Peramune U, Zhang T, Anand RK. Label-Free Electrochemical Methods for Disease Detection. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:49-69. [PMID: 36854209 DOI: 10.1146/annurev-anchem-091622-085754] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Label-free electrochemical biosensing leverages the advantages of label-free techniques, low cost, and fewer user steps, with the sensitivity and portability of electrochemical analysis. In this review, we identify four label-free electrochemical biosensing mechanisms: (a) blocking the electrode surface, (b) allowing greater access to the electrode surface, (c) changing the intercalation or electrostatic affinity of a redox probe to a biorecognition unit, and (d) modulating ion or electron transport properties due to conformational and surface charge changes. Each mechanism is described, recent advancements are summarized, and relative advantages and disadvantages of the techniques are discussed. Furthermore, two avenues for gaining further diagnostic information from label-free electrochemical biosensors, through multiplex analysis and incorporating machine learning, are examined.
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Affiliation(s)
- Kira L Rahn
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Umesha Peramune
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Tianyi Zhang
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Robbyn K Anand
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
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19
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Satta S, Rockwood SJ, Wang K, Wang S, Mozneb M, Arzt M, Hsiai TK, Sharma A. Microfluidic Organ-Chips and Stem Cell Models in the Fight Against COVID-19. Circ Res 2023; 132:1405-1424. [PMID: 37167356 PMCID: PMC10171291 DOI: 10.1161/circresaha.122.321877] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
SARS-CoV-2, the virus underlying COVID-19, has now been recognized to cause multiorgan disease with a systemic effect on the host. To effectively combat SARS-CoV-2 and the subsequent development of COVID-19, it is critical to detect, monitor, and model viral pathogenesis. In this review, we discuss recent advancements in microfluidics, organ-on-a-chip, and human stem cell-derived models to study SARS-CoV-2 infection in the physiological organ microenvironment, together with their limitations. Microfluidic-based detection methods have greatly enhanced the rapidity, accessibility, and sensitivity of viral detection from patient samples. Engineered organ-on-a-chip models that recapitulate in vivo physiology have been developed for many organ systems to study viral pathology. Human stem cell-derived models have been utilized not only to model viral tropism and pathogenesis in a physiologically relevant context but also to screen for effective therapeutic compounds. The combination of all these platforms, along with future advancements, may aid to identify potential targets and develop novel strategies to counteract COVID-19 pathogenesis.
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Affiliation(s)
- Sandro Satta
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Sarah J Rockwood
- Stanford University Medical Scientist Training Program, Palo Alto, CA (S.J.R.)
| | - Kaidong Wang
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Shaolei Wang
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Maedeh Mozneb
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Madelyn Arzt
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Tzung K Hsiai
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Arun Sharma
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
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20
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Chen X, Zhou S, Wang Y, Zheng L, Guan S, Wang D, Wang L, Guan X. Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis. Trends Analyt Chem 2023; 162:117060. [PMID: 38106545 PMCID: PMC10722900 DOI: 10.1016/j.trac.2023.117060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.
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Affiliation(s)
- Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Ling Zheng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Sarah Guan
- Hinsdale Central High School, Hinsdale, IL 60521, USA
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
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21
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Kitta K, Sakamoto M, Hayakawa K, Nukazuka A, Kano K, Yamamoto T. Nanopore Impedance Spectroscopy Reveals Electrical Properties of Single Nanoparticles for Detecting and Identifying Pathogenic Viruses. ACS OMEGA 2023; 8:14684-14693. [PMID: 37125101 PMCID: PMC10134219 DOI: 10.1021/acsomega.3c00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
In the conventional nanopore method, direct current (DC) is used to study molecules and nanoparticles; however, it cannot easily discriminate between materials with similarly sized particles. Herein, we developed an alternating current (AC)-based nanopore method to measure the impedance of a single nanoparticle and distinguish between particles of the same size based on their material characteristics. We demonstrated the performance of this method using impedance measurements to determine the size and frequency characteristics of various particles, ranging in diameter from 200 nm to 1 μm. Furthermore, the alternating current method exhibited high accuracy for biosensing applications, identifying viruses with over 85% accuracy using single-particle measurement and machine learning. Therefore, this novel nanopore method is useful for applications in materials science, biology, and medicine.
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Affiliation(s)
- Kazuki Kitta
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Maami Sakamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kei Hayakawa
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Akira Nukazuka
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Kazuhiko Kano
- Material
Research and Innovation Division, DENSO
CORPORATION, 1-1 Showa-cho, Kariya, Aichi 448-8661, Japan
| | - Takatoki Yamamoto
- Mechanical
Engineering, Tokyo Institute of Technology, Ishikawadai 1-314, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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22
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Jena MK, Pathak B. Development of an Artificially Intelligent Nanopore for High-Throughput DNA Sequencing with a Machine-Learning-Aided Quantum-Tunneling Approach. NANO LETTERS 2023; 23:2511-2521. [PMID: 36799480 DOI: 10.1021/acs.nanolett.2c04062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Solid-state nanopore-based single-molecule DNA sequencing with quantum tunneling technology poses formidable challenges to achieve long-read sequencing and high-throughput analysis. Here, we propose a method for developing an artificially intelligent (AI) nanopore that does not require extraction of the signature transmission function for each nucleotide of the whole DNA strand by integrating supervised machine learning (ML) and transverse quantum transport technology with a graphene nanopore. The optimized ML model can predict the transmission function of all other nucleotides after training with data sets of all the orientations of any nucleotide inside the nanopore with a root-mean-square error (RMSE) of as low as 0.062. Further, up to 96.01% accuracy is achieved in classifying the unlabeled nucleotides with their transmission readouts. We envision that an AI nanopore can alleviate the experimental challenges of the quantum-tunneling method and pave the way for rapid and high-precision DNA sequencing by predicting their signature transmission functions.
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Affiliation(s)
- Milan Kumar Jena
- 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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23
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Ramalingam M, Jaisankar A, Cheng L, Krishnan S, Lan L, Hassan A, Sasmazel HT, Kaji H, Deigner HP, Pedraz JL, Kim HW, Shi Z, Marrazza G. Impact of nanotechnology on conventional and artificial intelligence-based biosensing strategies for the detection of viruses. DISCOVER NANO 2023; 18:58. [PMID: 37032711 PMCID: PMC10066940 DOI: 10.1186/s11671-023-03842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Recent years have witnessed the emergence of several viruses and other pathogens. Some of these infectious diseases have spread globally, resulting in pandemics. Although biosensors of various types have been utilized for virus detection, their limited sensitivity remains an issue. Therefore, the development of better diagnostic tools that facilitate the more efficient detection of viruses and other pathogens has become important. Nanotechnology has been recognized as a powerful tool for the detection of viruses, and it is expected to change the landscape of virus detection and analysis. Recently, nanomaterials have gained enormous attention for their value in improving biosensor performance owing to their high surface-to-volume ratio and quantum size effects. This article reviews the impact of nanotechnology on the design, development, and performance of sensors for the detection of viruses. Special attention has been paid to nanoscale materials, various types of nanobiosensors, the internet of medical things, and artificial intelligence-based viral diagnostic techniques.
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Affiliation(s)
- Murugan Ramalingam
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
- grid.411982.70000 0001 0705 4288Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Department of Nanobiomedical Science, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116 South Korea
- grid.440424.20000 0004 0595 4604Department of Metallurgical and Materials Engineering, Faculty of Engineering, Atilim University, 06836 Ankara, Turkey
| | - Abinaya Jaisankar
- grid.412813.d0000 0001 0687 4946Centre for Biomaterials, Cellular and Molecular Theranostics, School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632014 India
| | - Lijia Cheng
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Sasirekha Krishnan
- grid.412813.d0000 0001 0687 4946Centre for Biomaterials, Cellular and Molecular Theranostics, School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632014 India
| | - Liang Lan
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Anwarul Hassan
- grid.412603.20000 0004 0634 1084Department of Mechanical and Industrial Engineering, Biomedical Research Center, Qatar University, 2713, Doha, Qatar
| | - Hilal Turkoglu Sasmazel
- grid.440424.20000 0004 0595 4604Department of Metallurgical and Materials Engineering, Faculty of Engineering, Atilim University, 06836 Ankara, Turkey
| | - Hirokazu Kaji
- grid.265073.50000 0001 1014 9130Department of Biomechanics, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, 101-0062 Japan
| | - Hans-Peter Deigner
- grid.21051.370000 0001 0601 6589Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, 78054 Villingen-Schwenningen, Germany
| | - Jose Luis Pedraz
- grid.11480.3c0000000121671098NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine, 28029 Madrid, Spain
| | - Hae-Won Kim
- grid.411982.70000 0001 0705 4288Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Department of Nanobiomedical Science, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116 South Korea
| | - Zheng Shi
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Giovanna Marrazza
- grid.8404.80000 0004 1757 2304Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Florence, Italy
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24
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Li M, Xiong Y, Cao Y, Zhang C, Li Y, Ning H, Liu F, Zhou H, Li X, Ye X, Pang Y, Zhang J, Liang X, Qing G. Identification of tagged glycans with a protein nanopore. Nat Commun 2023; 14:1737. [PMID: 36977665 PMCID: PMC10050315 DOI: 10.1038/s41467-023-37348-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Structural complexity of glycans derived from the diversities in composition, linage, configuration, and branching considerably complicates structural analysis. Nanopore-based single-molecule sensing offers the potential to elucidate glycan structure and even sequence glycan. However, the small molecular size and low charge density of glycans have restricted direct nanopore detection of glycan. Here we show that glycan sensing can be achieved using a wild-type aerolysin nanopore by introducing a facile glycan derivatization strategy. The glycan molecule can induce impressive current blockages when moving through the nanopore after being connected with an aromatic group-containing tag (plus a carrier group for the neutral glycan). The obtained nanopore data permit the identification of glycan regio- and stereoisomers, glycans with variable monosaccharide numbers, and distinct branched glycans, either independently or with the use of machine learning methods. The presented nanopore sensing strategy for glycans paves the way towards nanopore glycan profiling and potentially sequencing.
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Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Hanwen Ning
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Fan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Han Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Jiaming Zhang
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China.
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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25
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Siwy ZS, Bruening ML, Howorka S. Nanopores: synergy from DNA sequencing to industrial filtration - small holes with big impact. Chem Soc Rev 2023; 52:1983-1994. [PMID: 36794856 DOI: 10.1039/d2cs00894g] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications.
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Affiliation(s)
- Zuzanna S Siwy
- Department of Physics and Astronomy, University of California, Irvine, USA.
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, USA.
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, UK.
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26
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Bošković F, Zhu J, Tivony R, Ohmann A, Chen K, Alawami MF, Đorđević M, Ermann N, Pereira-Dias J, Fairhead M, Howarth M, Baker S, Keyser UF. Simultaneous identification of viruses and viral variants with programmable DNA nanobait. NATURE NANOTECHNOLOGY 2023; 18:290-298. [PMID: 36646828 PMCID: PMC10020084 DOI: 10.1038/s41565-022-01287-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/07/2022] [Indexed: 05/31/2023]
Abstract
Respiratory infections are the major cause of death from infectious disease worldwide. Multiplexed diagnostic approaches are essential as many respiratory viruses have indistinguishable symptoms. We created self-assembled DNA nanobait that can simultaneously identify multiple short RNA targets. The nanobait approach relies on specific target selection via toehold-mediated strand displacement and rapid readout via nanopore sensing. Here we show that this platform can concurrently identify several common respiratory viruses, detecting a panel of short targets of viral nucleic acids from multiple viruses. Our nanobait can be easily reprogrammed to discriminate viral variants with single-nucleotide resolution, as we demonstrated for several key SARS-CoV-2 variants. Last, we show that the nanobait discriminates between samples extracted from oropharyngeal swabs from negative- and positive-SARS-CoV-2 patients without preamplification. Our system allows for the multiplexed identification of native RNA molecules, providing a new scalable approach for the diagnostics of multiple respiratory viruses in a single assay.
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Affiliation(s)
- Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Milan Đorđević
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Niklas Ermann
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | | | - Mark Howarth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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27
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Stierlen A, Greive SJ, Bacri L, Manivet P, Cressiot B, Pelta J. Nanopore Discrimination of Coagulation Biomarker Derivatives and Characterization of a Post-Translational Modification. ACS CENTRAL SCIENCE 2023; 9:228-238. [PMID: 36844502 PMCID: PMC9951287 DOI: 10.1021/acscentsci.2c01256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Indexed: 06/18/2023]
Abstract
One of the most important health challenges is the early and ongoing detection of disease for prevention, as well as personalized treatment management. Development of new sensitive analytical point-of-care tests are, therefore, necessary for direct biomarker detection from biofluids as critical tools to address the healthcare needs of an aging global population. Coagulation disorders associated with stroke, heart attack, or cancer are defined by an increased level of the fibrinopeptide A (FPA) biomarker, among others. This biomarker exists in more than one form: it can be post-translationally modified with a phosphate and also cleaved to form shorter peptides. Current assays are long and have difficulties in discriminating between these derivatives; hence, this is an underutilized biomarker for routine clinical practice. We use nanopore sensing to identify FPA, the phosphorylated FPA, and two derivatives. Each of these peptides is characterized by unique electrical signals for both dwell time and blockade level. We also show that the phosphorylated form of FPA can adopt two different conformations, each of which have different values for each electrical parameter. We were able to use these parameters to discriminate these peptides from a mix, thereby opening the way for the potential development of new point-of-care tests.
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Affiliation(s)
- Aïcha Stierlen
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
| | | | - Laurent Bacri
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Philippe Manivet
- Centre
de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75475 Paris, France
- Université
Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
| | | | - Juan Pelta
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
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28
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Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
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Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
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29
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Takashima Y, Komoto Y, Ohshiro T, Nakatani K, Taniguchi M. Quantitative Microscopic Observation of Base-Ligand Interactions via Hydrogen Bonds by Single-Molecule Counting. J Am Chem Soc 2023; 145:1310-1318. [PMID: 36597667 DOI: 10.1021/jacs.2c11260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chemical properties have been based on statistical averages since the introduction of Avogadro's number. The lack of suitable methods for counting identified single molecules has posed challenges to counting statistics. The selectivity, affinity, and mode of hydrogen bonding between base and small molecules that make up DNA, which is vital for living organisms, have not yet been revealed at the single molecule level. Here, we show the quantitation of the above-mentioned parameters via single-molecule counting based on the combination of single-molecule electrical measurements and AI. The binding selectivity values of five ligands to four different base molecules were evaluated quantitatively by determining the ratio of the number of aggregates in a solution mixture of base molecules and a ligand. In addition, we show the ligand dependence of the mode and number of microscopic hydrogen bonds via single-molecule counting and quantum chemical calculations.
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Affiliation(s)
- Yusuke Takashima
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Yuki Komoto
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan.,Artificial Intelligence Research Center, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), OsakaUniversity, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Takahito Ohshiro
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
| | - Kazuhiko Nakatani
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka567-0047, Japan
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30
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Dastres E, Bijani F, Naderi R, Zamani A, Edalat M. Evaluating the habitat suitability modeling of Aceria alhagi and Alhagi maurorum in their native range using machine learning techniques.. [DOI: 10.21203/rs.3.rs-2441475/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abstract
Spatial locational modeling techniques are increasingly used in species distribution modeling. However, the implemented techniques differ in their modeling performance. In this study, we tested the predictive accuracy of three algorithms, namely "random forest (RF)," "support vector machine (SVM)," and "boosted regression trees (BRT)" to prepare habitat suitability mapping of an invasive species, Alhagi maurorum, and its potential biological control agent, Aceria alhagi. Location of this study was in Fars Province, southwest of Iran. The spatial distributions of the species were forecasted using GPS devices and GIS software. The probability values of occurrence were then checked using three algorithms. The predictive accuracy of the machine learning (ML) techniques was assessed by computing the “area under the curve (AUC)” of the “receiver-operating characteristic” plot. When the Aceria alhagi was modeled, the AUC values of RF, BRT and SVM were 0.89, 0.81, and 0.79, respectively. However, in habitat suitability models (HSMs) of Alhagi maurorum the AUC values of RF, BRT and SVM were 0.89, 0.80, and 0.73, respectively. The RF model provided significantly more accurate predictions than other algorithms. The importance of factors on the growth and development of Alhagi maurorum and Aceria alhagi was also determined using the partial least squares (PLS) algorithm, and the most crucial factors were the road and slope. Habitat suitability modeling based on algorithms may significantly increase the accuracy of species distribution forecasts, and thus it shows considerable promise for different conservation biological and biogeographical applications.
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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: 31] [Impact Index Per Article: 31.0] [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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Fyta M. Functionalized electrodes embedded in nanopores: read-out enhancement? Chem Asian J 2023; 18:e202200916. [PMID: 36372991 PMCID: PMC10107472 DOI: 10.1002/asia.202200916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
In this review, functionalized nanogaps embedded in nanopores are discussed in view of their high biosensitivity in detecting biomolecules, their length, type, and sequence. Specific focus is given on nanoelectrodes functionalized with tiny nanometer-sized diamond-like particles offering vast functionalization possibilities for gold junction electrodes. This choice of the functionalization, in turn, offers nucleotide-specific binding possibilities improving the detection signals arising from such functionalized electrodes potentially embedded in a nanopore. The review sheds light onto the use and enhancement of the tunnelling recognition in functionalized nanogaps towards sensing DNA nucleotides and mutation detection, providing important input for a practical realization.
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Affiliation(s)
- Maria Fyta
- Computational Biotechnology, RWTH-Aachen University, Worringerweg 3, 52072, Aachen, Germany
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33
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Jena MK, Roy D, Pathak B. Machine Learning Aided Interpretable Approach for Single Nucleotide-Based DNA Sequencing using a Model Nanopore. J Phys Chem Lett 2022; 13:11818-11830. [PMID: 36520020 DOI: 10.1021/acs.jpclett.2c02824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore-based electrical detection of DNA nucleotides with the quantum tunneling technique has emerged as a powerful strategy to be the next-generation sequencing technology. However, experimental complexity has been a foremost obstacle in achieving a more accurate high-throughput analysis with industrial scalability. Here, with one of the nucleotide training data sets of a model monolayer gold nanopore, we have predicted the transmission function for all other nucleotides with root-mean-square error scores as low as 0.12 using the optimized eXtreme Gradient Boosting Regression (XGBR) model. Further, the SHapley Additive exPlanations (SHAP) analysis helped in exploring the interpretability of the XGBR model prediction and revealed the complex relationship between the molecular properties of nucleotides and their transmission functions by both global and local interpretable explanations. Hence, experimental integration of our proposed machine-learning-assisted transmission function prediction method can offer a new direction for the realization of cheap, accurate, and ultrafast DNA sequencing.
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Affiliation(s)
- Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
| | - Diptendu Roy
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh453552, India
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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Alsalameh S, Alnajjar K, Makhzoum T, Al Eman N, Shakir I, Mir TA, Alkattan K, Chinnappan R, Yaqinuddin A. Advances in Biosensing Technologies for Diagnosis of COVID-19. BIOSENSORS 2022; 12:898. [PMID: 36291035 PMCID: PMC9599206 DOI: 10.3390/bios12100898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
The COVID-19 pandemic has severely impacted normal human life worldwide. Due to its rapid community spread and high mortality statistics, the development of prompt diagnostic tests for a massive number of samples is essential. Currently used traditional methods are often expensive, time-consuming, laboratory-based, and unable to handle a large number of specimens in resource-limited settings. Because of its high contagiousness, efficient identification of SARS-CoV-2 carriers is crucial. As the advantages of adopting biosensors for efficient diagnosis of COVID-19 increase, this narrative review summarizes the recent advances and the respective reasons to consider applying biosensors. Biosensors are the most sensitive, specific, rapid, user-friendly tools having the potential to deliver point-of-care diagnostics beyond traditional standards. This review provides a brief introduction to conventional methods used for COVID-19 diagnosis and summarizes their advantages and disadvantages. It also discusses the pathogenesis of COVID-19, potential diagnostic biomarkers, and rapid diagnosis using biosensor technology. The current advancements in biosensing technologies, from academic research to commercial achievements, have been emphasized in recent publications. We covered a wide range of topics, including biomarker detection, viral genomes, viral proteins, immune responses to infection, and other potential proinflammatory biomolecules. Major challenges and prospects for future application in point-of-care settings are also highlighted.
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Affiliation(s)
| | - Khalid Alnajjar
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Tariq Makhzoum
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Noor Al Eman
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ismail Shakir
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Tanveer Ahmad Mir
- Laboratory of Tissue/Organ Bioengineering and BioMEMS, Organ Transplant Centre of Excellence, Transplant Research and Innovation Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
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Song Z, Liang Y, Yang J. Nanopore Detection Assisted DNA Information Processing. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12183135. [PMID: 36144924 PMCID: PMC9504103 DOI: 10.3390/nano12183135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 05/27/2023]
Abstract
The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.
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Affiliation(s)
- Zichen Song
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yuan Liang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
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Li Y, Lin C, Peng Y, He J, Yang Y. High-sensitivity and point-of-care detection of SARS-CoV-2 from nasal and throat swabs by magnetic SERS biosensor. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 365:131974. [PMID: 35505925 PMCID: PMC9047405 DOI: 10.1016/j.snb.2022.131974] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 05/20/2023]
Abstract
The outbreak of COVID-19 caused by SARS-CoV-2 urges the development of rapidly and accurately diagnostic methods. Here, one high-sensitivity and point-of-care detection method based on magnetic SERS biosensor composed of Fe3O4-Au nanocomposite and Au nanoneedles array was developed to detect SARS-CoV-2 directly. Among, the magnetic Fe3O4-Au nanocomposite is applied to capture and separate virus from nasal and throat swabs and enhance the Raman signals of SARS-CoV-2. The magnetic SERS biosensor possessed high sensitivity by optimizing the Fe3O4-Au nanocomposite. More significantly, the on-site detection of inactivated SARS-CoV-2 virus was achieved based on the magnetic SERS biosensor with ultra-low limit of detection of 100 copies/mL during 15 mins. Furthermore, the contaminated nasal and throat swabs samples were identified by support vector machine, and the diagnostic accuracy of 100% was obtained. The magnetic SERS biosensor combined with support vector machine provides giant potential as the point-of-care detection tool for SARS-CoV-2.
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Affiliation(s)
- Yanyan Li
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenglong Lin
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusi Peng
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun He
- Anhui Provincial Center for Disease Control and Prevention, Hefei 12560, Anhui, People's Republic of China
- Public Health Research Institute of Anhui Province, Hefei 12560, Anhui, People's Republic of China
| | - Yong Yang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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38
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Kiremitler NB, Kemerli MZ, Kayaci N, Karagoz S, Pekdemir S, Sarp G, Sanduvac S, Onses MS, Yilmaz E. Nanostructures for the Prevention, Diagnosis, and Treatment of SARS-CoV-2: A Review. ACS APPLIED NANO MATERIALS 2022; 5:6029-6054. [PMID: 37552745 PMCID: PMC8905929 DOI: 10.1021/acsanm.2c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/15/2022] [Indexed: 06/17/2023]
Abstract
Scientists, doctors, engineers, and even entire societies have become aware of the seriousness of the COVID-19 infection and are taking action quickly, using all the tools from protection to treatment against coronavirus SARS-CoV-2. Especially in this sense, scientific approaches and materials using nanotechnology are frequently preferred. In this review, we focus on how nanoscience and nanotechnology approaches can be used for protective equipment, diagnostic and treatment methods, medicine, and vaccine applications to stop the coronavirus SARS-CoV-2 and prevent its spread. SARS-CoV-2, which itself can be considered as a core-shell nanoparticle, can interact with various materials around it and remain bound for variable periods of time while maintaining its bioactivity. These applications are especially critical for the controlled use of disinfection systems. One of the most important processes in the fight against coronavirus is the rapid diagnosis of the virus in humans and the initiation of isolation and treatment processes. The development of nanotechnology-based test and diagnostic kits is another important research thrust. Nanotechnological therapeutics based on antiviral drug design and nanoarchitecture vaccines have been vital. Nanotechnology plays critical roles in the production of protective film surfaces for self-cleaning and antiviral masks, gloves, and laboratory clothes. An overview of literature studies highlighting nanotechnology and nanomaterial-based approaches to combat SARS-CoV-2 is presented.
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Affiliation(s)
- Nuri Burak Kiremitler
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Department of Materials Science and Engineering,
Faculty of Engineering, Erciyes University, 38039 Kayseri,
Turkey
| | - Munteha Zeynep Kemerli
- Drug Application and Research Center,
Erciyes University, 38039 Kayseri,
Turkey
- Department of Health Services, Halil Bayraktar
Vocational College, Erciyes University, 38039 Kayseri,
Turkey
| | - Nilgun Kayaci
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Department of Materials Science and Engineering,
Faculty of Engineering, Erciyes University, 38039 Kayseri,
Turkey
| | - Sultan Karagoz
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Department of Textile Engineering, Faculty of
Engineering, Erciyes University, 38039 Kayseri,
Turkey
| | - Sami Pekdemir
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Department of Airframes and Powerplants, Erciyes
University, 38039 Kayseri, Turkey
| | - Gokhan Sarp
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Faculty of Pharmacy, Erciyes
University, 38039 Kayseri, Turkey
| | - Senem Sanduvac
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Bünyan Vocational College, Kayseri
University, 38280 Kayseri, Turkey
| | - Mustafa Serdar Onses
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Department of Materials Science and Engineering,
Faculty of Engineering, Erciyes University, 38039 Kayseri,
Turkey
| | - Erkan Yilmaz
- ERNAM-Erciyes University Nanotechnology
Application and Research Center, 38039 Kayseri,
Turkey
- Faculty of Pharmacy, Erciyes
University, 38039 Kayseri, Turkey
- Technology Research & Application
Center (TAUM), Erciyes University, 38039 Kayseri,
Turkey
- ChemicaMed Chemical Inc., Erciyes
University Technology Development Zone, 38039 Kayseri,
Turkey
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Tanimoto IMF, Cressiot B, Greive SJ, Le Pioufle B, Bacri L, Pelta J. Focus on using nanopore technology for societal health, environmental, and energy challenges. NANO RESEARCH 2022; 15:9906-9920. [PMID: 35610982 PMCID: PMC9120803 DOI: 10.1007/s12274-022-4379-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
With an increasing global population that is rapidly ageing, our society faces challenges that impact health, environment, and energy demand. With this ageing comes an accumulation of cellular changes that lead to the development of diseases and susceptibility to infections. This impacts not only the health system, but also the global economy. As the population increases, so does the demand for energy and the emission of pollutants, leading to a progressive degradation of our environment. This in turn impacts health through reduced access to arable land, clean water, and breathable air. New monitoring approaches to assist in environmental control and minimize the impact on health are urgently needed, leading to the development of new sensor technologies that are highly sensitive, rapid, and low-cost. Nanopore sensing is a new technology that helps to meet this purpose, with the potential to provide rapid point-of-care medical diagnosis, real-time on-site pollutant monitoring systems to manage environmental health, as well as integrated sensors to increase the efficiency and storage capacity of renewable energy sources. In this review we discuss how the powerful approach of nanopore based single-molecule, or particle, electrical promises to overcome existing and emerging societal challenges, providing new opportunities and tools for personalized medicine, localized environmental monitoring, and improved energy production and storage systems.
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Affiliation(s)
- Izadora Mayumi Fujinami Tanimoto
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | | | | | - Bruno Le Pioufle
- LuMIn, CNRS, Institut d’Alembert, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Laurent Bacri
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Juan Pelta
- LAMBE, CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
- LAMBE, CNRS, CY Cergy Paris Université, 95000 Cergy, France
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40
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Horiguchi Y, Naono N, Sakamoto O, Takeuchi H, Yamaoka S, Miyahara Y. Methodology to Detect Biological Particles Using a Biosensing Surface Integrated in Resistive Pulse Sensing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20168-20178. [PMID: 35446533 DOI: 10.1021/acsami.1c25006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Resistive pulse sensing (RPS) is an analytical method that can be used to individually count particles from a small sample. RPS simply monitors the physical characteristics of particles, such as size, shape, and charge density, and the integration of RPS with biosensing is an attractive theme to detect biological particles such as virus and bacteria. In this report, a methodology of biosensing on RPS was investigated. Polydopamine (PD), an adhesive component of mussels, was used as the base material to create a sensing surface. PD adheres to most materials, such as noble metals, metal oxides, semiconductors, and polymers; as a result, PD is a versatile intermediate layer for the fabrication of a biosensing surface. As an example of a biological particle, human influenza A virus (H1N1 subtype) was used to monitor translocation of particles through the pore membrane. When virus-specific ligands (6'-sialyllactose) were immobilized on the pore surface, the translocation time of the virus particles was considerably extended. The detailed translocation data suggest that the viral particles were trapped on the sensing surface by specific interactions. In addition, virus translocation processes on different pore surfaces were distinguished using machine learning. The result shows that the simple and versatile PD-based biosensor surface design was effective. This advanced RPS measurement system could be a promising analytical technique.
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Affiliation(s)
- Yukichi Horiguchi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
| | - Norihiko Naono
- Aipore Inc., Cerulean Tower 15F, 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Osamu Sakamoto
- Aipore Inc., Cerulean Tower 15F, 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan
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41
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS 2022; 12:nano12091534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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42
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Sheshanarayana R, Govind Rajan A. Tailoring Nanoporous Graphene via Machine Learning: Predicting Probabilities and Formation Times of Arbitrary Nanopore Shapes. J Chem Phys 2022; 156:204703. [DOI: 10.1063/5.0089469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanopores in graphene, a 2D material, are currently being explored for various applications, such as gas separation, water desalination, and DNA sequencing. The shapes and sizes of nanopores play a major role in determining the performance of devices made out of graphene. However, given an arbitrary nanopore shape, anticipating its creation probability and formation time are challenging inverse problems, solving which could help develop theoretical models for nanoporous graphene and guide experiments in tailoring pore sizes/shapes. In this work, we develop a machine learning (ML) framework to predict these target variables, based on data generated using kinetic Monte Carlo simulations and chemical graph theory. Thereby, we enable the rapid quantification of the ease of formation of a given nanopore shape in graphene via silicon-catalyzed electron-beam etching and provide an experimental handle to realize it in practice. We use structural features such as the number of carbon atoms removed, the number of edge atoms, the diameter of the nanopore, and its shape factor, which can be readily extracted from the nanopore shape. We show that the trained models can accurately predict nanopore probabilities and formation times with R2 values on the test set of 0.97 and 0.95, respectively. Not only that, we obtain physical insight into the working of the model and discuss the role played by the various structural features in modulating nanopore formation. Overall, our work provides a solid foundation for experimental studies to manipulate nanopore sizes/shapes and for theoretical studies to consider realistic structures of nanopores in graphene.
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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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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46
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Li N, Zhao B, Stavins R, Peinetti AS, Chauhan N, Bashir R, Cunningham BT, King WP, Lu Y, Wang X, Valera E. Overcoming the limitations of COVID-19 diagnostics with nanostructures, nucleic acid engineering, and additive manufacturing. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2022; 26:100966. [PMID: 34840515 PMCID: PMC8604633 DOI: 10.1016/j.cossms.2021.100966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/04/2023]
Abstract
The COVID-19 pandemic revealed fundamental limitations in the current model for infectious disease diagnosis and serology, based upon complex assay workflows, laboratory-based instrumentation, and expensive materials for managing samples and reagents. The lengthy time delays required to obtain test results, the high cost of gold-standard PCR tests, and poor sensitivity of rapid point-of-care tests contributed directly to society's inability to efficiently identify COVID-19-positive individuals for quarantine, which in turn continues to impact return to normal activities throughout the economy. Over the past year, enormous resources have been invested to develop more effective rapid tests and laboratory tests with greater throughput, yet the vast majority of engineering and chemistry approaches are merely incremental improvements to existing methods for nucleic acid amplification, lateral flow test strips, and enzymatic amplification assays for protein-based biomarkers. Meanwhile, widespread commercial availability of new test kits continues to be hampered by the cost and time required to develop single-use disposable microfluidic plastic cartridges manufactured by injection molding. Through development of novel technologies for sensitive, selective, rapid, and robust viral detection and more efficient approaches for scalable manufacturing of microfluidic devices, we can be much better prepared for future management of infectious pathogen outbreaks. Here, we describe how photonic metamaterials, graphene nanomaterials, designer DNA nanostructures, and polymers amenable to scalable additive manufacturing are being applied towards overcoming the fundamental limitations of currently dominant COVID-19 diagnostic approaches. In this paper, we review how several distinct classes of nanomaterials and nanochemistry enable simple assay workflows, high sensitivity, inexpensive instrumentation, point-of-care sample-to-answer virus diagnosis, and rapidly scaled manufacturing.
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Affiliation(s)
- Nantao Li
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
| | - Bin Zhao
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Ana Sol Peinetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Neha Chauhan
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Rashid Bashir
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - Brian T Cunningham
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - William P King
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Yi Lu
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Xing Wang
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Enrique Valera
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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Yang JM, Feng JD. Progress on optical measurements in single-molecule analysis with nanopores. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2021-1133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
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Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
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