1
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Pang S, Wang M, Yuan J, Yang Z, Yu H, Zhang H, Dong T, Liu A. Sensitive Dual-Signal ELISA Based on Specific Phage-Displayed Double Peptide Probes with Internal Filtering Effect to Assay Monkeypox Virus Antigen. Anal Chem 2024; 96:10064-10073. [PMID: 38842443 DOI: 10.1021/acs.analchem.4c01802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The global spread of monkeypox has become a worldwide public healthcare issue. Therefore, there is an urgent need for accurate and sensitive detection methods to effectively control its spreading. Herein, we screened by phage display two peptides M4 (sequence: DPCGERICSIAL) and M6 (sequence: SCSSFLCSLKVG) with good affinity and specificity to monkeypox virus (MPXV) B21R protein. To simulate the state of the peptide in the phage and to avoid spatial obstacles of the peptide, GGGSK was added at the C terminus of M4 and named as M4a. Molecular docking shows that peptide M4a and peptide M6 are bound to different epitopes of B21R by hydrogen bonds and salt-bridge interactions, respectively. Then, peptide M4a was selected as the capture probe, phage M6 as the detection probe, and carbonized polymer dots (CPDs) as the fluorescent probe, and a colorimetric and fluorescent double-signal capture peptide/antigen/signal peptide-displayed phage sandwich ELISA triggered by horseradish peroxidase (HRP) through a simple internal filtration effect (IFE) was constructed. HRP catalyzes H2O2 to oxidize 3,3',5,5'-tetramethylbenzidine (TMB) to generate blue oxidized TMB, which can further quench the fluorescence of CPDs through IFE, enabling to detect MPXV B21R in colorimetric and fluorescent modes. The proposed simple immunoassay platform shows good sensitivity and reliability in MPXV B21R detection. The limit of detection for colorimetric and fluorescent modes was 27.8 and 9.14 pg/mL MPXV B21R, respectively. Thus, the established double-peptide sandwich-based dual-signal immunoassay provides guidance for the development of reliable and sensitive antigen detection capable of mutual confirmation, which also has great potential for exploring various analytical strategies for other respiratory virus surveillance.
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Affiliation(s)
- Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Jinlong Yuan
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Zhonghuang Yang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Haohan Zhang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
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2
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Chau CC, Maffeo CM, Aksimentiev A, Radford SE, Hewitt EW, Actis P. Single molecule delivery into living cells. Nat Commun 2024; 15:4403. [PMID: 38782907 PMCID: PMC11116494 DOI: 10.1038/s41467-024-48608-3] [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: 02/12/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.
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Affiliation(s)
- Chalmers C Chau
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
| | - Christopher M Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK.
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK.
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3
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Ahmed SA, Liu Y, Xiong T, Zhao Y, Xie B, Pan C, Ma W, Yu P. Iontronic Sensing Based on Confined Ion Transport. Anal Chem 2024; 96:8056-8077. [PMID: 38663001 DOI: 10.1021/acs.analchem.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Saud Asif Ahmed
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yueru Zhao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Boyang Xie
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Cong Pan
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, 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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Charles-Achille S, Janot JM, Cayrol B, Balme S. Influence of Seed structure on Volume distribution of α-Synuclein Oligomer at Early Stages of Aggregation using nanopipette. Chembiochem 2024; 25:e202300748. [PMID: 38240074 DOI: 10.1002/cbic.202300748] [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: 11/01/2023] [Revised: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Understanding α-synuclein aggregation is crucial in the context of Parkinson's disease. The objective of this study was to investigate the influence of aggregation induced by preformed seeding on the volume of oligomers during the early stages, using a label-free, single-molecule characterization approach. By utilizing nanopipettes of varying sizes, the volume of the oligomers can be calculated from the amplitude of the current blockade and pipette geometry. Further investigation of the aggregates formed over time in the presence of added seeds revealed an acceleration in the formation of large aggregates and the existence of multiple distinct populations of oligomers. Additionally, we observed that spontaneously formed seeds inhibited the formation of smaller oligomers, in contrast to the effect of HNE seeds. These results suggest that the seeds play a crucial role in the formation of oligomers and their sizes during the early stages of aggregation, whereas the classical thioflavin T assay remains negative.
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Affiliation(s)
- Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Bastien Cayrol
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34000, Montpellier, France
| | - Sebastien Balme
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34000, Montpellier, France
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6
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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7
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Punia B, Chaudhury S. Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity. J Phys Chem B 2024; 128:1876-1883. [PMID: 38355410 DOI: 10.1021/acs.jpcb.3c08350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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8
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Pang S, Yu H, Zhang Y, Jiao Y, Zheng Z, Wang M, Zhang H, Liu A. Bioscreening specific peptide-expressing phage and its application in sensitive dual-mode immunoassay of SARS-CoV-2 spike antigen. Talanta 2024; 266:125093. [PMID: 37611368 DOI: 10.1016/j.talanta.2023.125093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/12/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Biorecognition components with high affinity and selectivity are vital in bioassay to diagnose and treat epidemic disease. Herein a phage display strategy of combining single-amplification-panning with non-amplification-panning was developed, by which a phage displaying cyclic heptapeptide ACLDWLFNSC (peptide J4) with good affinity and specificity to SARS-CoV-2 spike protein (SP) was identified. Molecular docking suggests that peptide J4 binds to S2 subunit by hydrogen bonding and hydrophobic interaction. Then the J4-phage was used as the capture antibody to establish phage-based chemiluminescence immunoassay (CLIA) and electrochemical impedance spectroscopy (EIS) analytical systems. The as-proposed dual-modal immunoassay platform exhibited good sensitivity and reliability in SARS-CoV-2 SP and pseudovirus assay. The limit of detection for SARS-CoV-2 SP by EIS immunoassay is 0.152 pg/mL, which is dramatically lower than that of 42 pg/mL for J4-phage based CLIA. Further, low to 40 transducing units (TU)/mL, 10 TU/mL SARS-CoV-2 pseudoviruses can be detected by the proposed J4-phage based CLIA and electrochemical immunosensor, respectively. Therefore, the as-developed dual mode immunoassays are potential methods to detect SARS-CoV-2. It is also expected to explore various phages with specific peptides to different targets for bioanalysis.
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Affiliation(s)
- Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Haipeng Yu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Yaru Zhang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Yiming Jiao
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Zongmei Zheng
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China; Qingdao Hightop Biotech Co., Ltd, 369 Hedong Road, Hi-tech Industrial Development Zone, Qingdao, 266112, China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Haohan Zhang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University, 308 Ningxia Rd, Qingdao, 266071, China.
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9
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Confederat S, Lee S, Vang D, Soulias D, Marcuccio F, Peace TI, Edwards MA, Strobbia P, Samanta D, Wälti C, Actis P. Next-Generation Nanopore Sensors Based on Conductive Pulse Sensing for Enhanced Detection of Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305186. [PMID: 37649152 DOI: 10.1002/smll.202305186] [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: 06/23/2023] [Revised: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Nanopore sensing has been successfully used to characterize biological molecules with single-molecule resolution based on the resistive pulse sensing approach. However, its use in nanoparticle characterization has been constrained by the need to tailor the nanopore aperture size to the size of the analyte, precluding the analysis of heterogeneous samples. Additionally, nanopore sensors often require the use of high salt concentrations to improve the signal-to-noise ratio, which further limits their ability to study a wide range of nanoparticles that are unstable at high ionic strength. Here, a new paradigm in nanopore research that takes advantage of a polymer electrolyte system to comprise a conductive pulse sensing approach is presented. A finite element model is developed to explain the conductive pulse signals observed and compare these results with experiments. This system enables the analytical characterization of heterogeneous nanoparticle mixtures at low ionic strength . Furthermore, the wide applicability of the method is demonstrated by characterizing metallic nanospheres of varied sizes, plasmonic nanostars with various degrees of branching, and protein-based spherical nucleic acids with different oligonucleotide loadings. This system will complement the toolbox of nanomaterials characterization techniques to enable real-time optimization workflow for engineering a wide range of nanomaterials.
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Affiliation(s)
- Samuel Confederat
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Der Vang
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Dimitrios Soulias
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ, Oxford, UK
| | - Fabio Marcuccio
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK
| | - Timotheus I Peace
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Martin Andrew Edwards
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Pietro Strobbia
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Christoph Wälti
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, LS2 9JT, Leeds, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, LS2 9JT, Leeds, UK
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10
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Lee SM, Nai YH, Doeven EH, Balakrishnan HK, Yuan D, Guijt RM. Abridged solid-phase extraction with alkaline Poly(ethylene) glycol lysis (ASAP) for direct DNA amplification. Talanta 2024; 266:125006. [PMID: 37572478 DOI: 10.1016/j.talanta.2023.125006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/14/2023]
Abstract
Complexity of sample preparation decelerate the development of sample-in-answer-out devices for point-of-need nucleic acid amplification testing. Here, we present the consolidation of alkaline poly(ethylene) glycol-based lysis and solid-phase extraction for rapid and simple sample preparation compatible with direct on-bead amplification. Simultaneous cell lysis and binding of DNA were achieved using an optimised reagent comprising 15% PEG8000, 0.5 M NaCl, and 3.5 mM KOH. This was combined with direct, on-bead amplification using 1.5 μg beads per 20 μL PCR reaction mix. The novel single reagent, 5-min method improved the detection limit by 10 and 100-fold compared with commercial DNA extraction kits and the original alkaline PEG lysis method, respectively. The sensitivity can be further enhanced by one amplification cycle with an ethanol wash or by extending the incubation to 10 min before collecting the magnetic particles. Both methods successfully detected a single copy of Escherichia coli DNA. In biological fluids (saliva, sweat, and urine), the 5-min method was delayed by about one cycle compared to the 15-min method. The proposed methods are attractive for incorporation in the workflow for point-of-need testing of biological samples by providing a practical and chemical method for simple alternative DNA sample preparation.
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Affiliation(s)
- Soo Min Lee
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia
| | - Yi H Nai
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia
| | - Egan H Doeven
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; Deakin University, School of Life and Environmental Sciences, Waurn Ponds, VIC 3216, Australia
| | - Hari Kalathil Balakrishnan
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; Department of Chemical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Dan Yuan
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia; School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Rosanne M Guijt
- Deakin University, Centre for Rural and Regional Futures (CeRRF), Waurn Ponds, VIC 3216, Australia.
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11
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [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: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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12
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Khatri S, Pandey P, Mejia G, Ghimire G, Leng F, He J. Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes. J Am Chem Soc 2023; 145:28075-28084. [PMID: 37996390 PMCID: PMC11036617 DOI: 10.1021/jacs.3c09311] [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: 11/25/2023]
Abstract
Glass nanopipettes have gained widespread use as a versatile single-entity detector in chemical and biological sensing, analysis, and imaging. Its advantages include low cost, easy accessibility, simplicity of use, and high versatility. However, conventional nanopipettes based on the volume exclusion mechanism have limitations in detecting small biomolecules due to their small volume and high mobility in aqueous solution. To overcome this challenge, we have employed a novel approach by capitalizing on the strong nanoconfinement effect of nanopipettes. This is achieved by utilizing both the hard confinement provided by the long taper nanopipette tip at the cis side and the soft confinement offered by the hydrogel at the trans side. Through this approach, we have effectively slowed down the exit motion of small molecules, allowing us to enrich and jam them at the nanopipette tip. Consequently, we have achieved high throughput detection of small biomolecules with sizes as small as 1 nm, including nucleoside triphosphates, short peptides, and small proteins with excellent signal-to-noise ratios. Furthermore, molecular complex formation through specific intermolecular interactions, such as hydrogen bonding between closely spaced nucleotides in the jam-packed nanopipette tip, has been detected based on the unique ionic current changes.
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Affiliation(s)
- Santosh Khatri
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - German Mejia
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Govinda Ghimire
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Fenfei Leng
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
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13
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Zhang A, Guo Z, Ge G, Liu Z. Insights into In Vivo Environmental Effects on Quantitative Biochemistry in Single Cells. Anal Chem 2023; 95:17246-17255. [PMID: 37963214 DOI: 10.1021/acs.analchem.3c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Biomacromolecules exist and function in a crowded and spatially confined intracellular milieu. Single-cell analysis has been an essential tool for deciphering the molecular mechanisms of cell biology and cellular heterogeneity. However, a sound understanding of in vivo environmental effects on single-cell quantification has not been well established. In this study, via cell mimicking with giant unilamellar vesicles and single-cell analysis by an approach called plasmonic immunosandwich assay (PISA) that we developed previously, we investigated the effects of two in vivo environmental factors, i.e., molecular crowding and spatial confinement, on quantitative biochemistry in the cytoplasm of single cells. We find that molecular crowding greatly affects the biomolecular interactions and immunorecognition-based detection while the effect of spatial confinement in cell-sized space is negligible. Without considering the effect of molecular crowding, the results by PISA were found to be apparently under-quantitated, being only 29.5-50.0% of those by the calibration curve considering the effect of molecular crowding. We further demonstrated that the use of a calibration curve established with standard solutions containing 20% (wt) polyethylene glycol 6000 can well offset the effect of intracellular crowding and thereby provide a simple but accurate calibration for the PISA measurement. Thus, this study not only sheds light on how intracellular environmental factors influence biomolecular interactions and immunorecognition-based single-cell quantification but also provides a simple but effective strategy to make the single-cell analysis more accurate.
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Affiliation(s)
- Anqi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Ge Ge
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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14
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Liu Y, Wang X, Campolo G, Teng X, Ying L, Edel JB, Ivanov AP. Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores. ACS NANO 2023; 17:22999-23009. [PMID: 37947369 PMCID: PMC10690843 DOI: 10.1021/acsnano.3c08456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation in the brain has been significantly implicated in Parkinson's disease (PD). Beyond the brain, oligomers of α-Synuclein are also found in cerebrospinal fluid (CSF) and blood, where the analysis of these aggregates may provide diagnostic routes and enable a better understanding of disease mechanisms. However, detecting α-Syn in CSF and blood is challenging due to its heterogeneous protein size and shape, and low abundance in clinical samples. Nanopore technology offers a promising route for the detection of single proteins in solution; however, the method often lacks the necessary selectivity in complex biofluids, where multiple background biomolecules are present. We address these limitations by developing a strategy that combines nanopore-based sensing with molecular carriers that can specifically capture α-Syn oligomers with sizes of less than 20 nm. We demonstrate that α-Synuclein oligomers can be detected directly in clinical samples, with minimal sample processing, by their ion current characteristics and successfully utilize this technology to differentiate cohorts of PD patients from healthy controls. The measurements indicate that detecting α-Syn oligomers present in CSF may potentially provide valuable insights into the progression and monitoring of Parkinson's disease.
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Affiliation(s)
- Yaxian Liu
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Giulia Campolo
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiangyu Teng
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Liming Ying
- National
Heart and Lung Institute, Imperial College
London, Molecular Sciences Research Hub, London W12 0BZ, United Kingdom
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
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15
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Stuber A, Douaki A, Hengsteler J, Buckingham D, Momotenko D, Garoli D, Nakatsuka N. Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores. ACS NANO 2023; 17:19168-19179. [PMID: 37721359 PMCID: PMC10569099 DOI: 10.1021/acsnano.3c05377] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Ali Douaki
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Denis Buckingham
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, Oldenburg D-26129, Germany
| | - Denis Garoli
- Instituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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16
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Moderne M, Abrao-Nemeir I, Meyer N, Du J, Charles-Achille S, Janot JM, Torrent J, Lepoitevin M, Balme S. Combining iontronic, chromatography and nanopipette for Aβ42 aggregates detection and separation. Anal Chim Acta 2023; 1275:341587. [PMID: 37524475 DOI: 10.1016/j.aca.2023.341587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/04/2023] [Indexed: 08/02/2023]
Abstract
In this work, we aim to capture, detect and analysis at single molecule level Aβ42 aggregates. To this end, two strategies of track-etched nanopore membranes functionalization were investigated. The first one uses an aptamer and requires only three steps, whereas the second strategy uses Lecanemab antibodies and requires six steps. Out of the two presented strategies, the second one was found to be the most suitable to detect Aβ42 aggregates using a quick current-voltage readout. The resulting single nanopore was then upscale to multipore membranes to capture the Aβ42 aggregates before analysis through them through a single-molecule approach. By comparing the species present in the retentate and filtrate, we confirmed the membrane's affinity for the larger Aβ42 aggregates present in the sample. We found that chromatographic membranes combined with an ionic diode for binary on/off readout are powerful tools for detecting rare biomarkers before single molecule analysis.
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Affiliation(s)
- Mathilde Moderne
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France; INM, University of Montpellier, INSERM, Montpellier, France
| | - Jun Du
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, France
| | - Mathilde Lepoitevin
- Institut des Matériaux Poreux de Paris (IMAP), UMR 8004 CNRS, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, 75005, Paris, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier, Cedex 5, France.
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17
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Abrao-Nemeir I, Meyer N, Nouvel A, Charles-Achille S, Janot JM, Torrent J, Balme S. Aβ42 fibril and non-fibril oligomers characterization using a nanopipette. Biophys Chem 2023; 300:107076. [PMID: 37480837 DOI: 10.1016/j.bpc.2023.107076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023]
Abstract
The Aβ42 aggregates with different structures and morphology was investigated through a single molecule label-free technique. To this end, the quartz nanopipettes were functionalized with polyethylene glycol. The set of Aβ42- epigallocatechin-3-gallate fibrils with length (from 85 nm to 250 nm) obtained by sonication was detected. The comparison of experimental and computed value of the amplitude of relative current blockade using a geometrical model show that for fibrils longer than 80 nm, the discriminating parameter is their diameter. Then, non-fibril oligomers obtain from Aβ42(Osaka) aggregation at different time seed was investigated. The analysis of the amplitude of relative current blockade shows that detected oligomers are smaller than 30 nm regardless the aggregation time. In addition, the wide distributions of the dwell time suggests the polymorph character of the sample.
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Affiliation(s)
- Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France; INM, University of Montpellier, INSERM, Montpellier, France
| | - Alexis Nouvel
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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18
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Meyer N, Bentin J, Janot JM, Abrao-Nemeir I, Charles-Achille S, Pratlong M, Aquilina A, Trinquet E, Perrier V, Picaud F, Torrent J, Balme S. Ultrasensitive Detection of Aβ42 Seeds in Cerebrospinal Fluid with a Nanopipette-Based Real-Time Fast Amyloid Seeding and Translocation Assay. Anal Chem 2023; 95:12623-12630. [PMID: 37587130 DOI: 10.1021/acs.analchem.3c00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
In this work, early-stage Aβ42 aggregates were detected using a real-time fast amyloid seeding and translocation (RT-FAST) assay. Specifically, Aβ42 monomers were incubated in buffer solution with and without preformed Aβ42 seeds in a quartz nanopipette coated with L-DOPA. Then, formed Aβ42 aggregates were analyzed on flyby resistive pulse sensing at various incubation time points. Aβ42 aggregates were detected only in the sample with Aβ42 seeds after 180 min of incubation, giving an on/off readout of the presence of preformed seeds. Moreover, this RT-FAST assay could detect preformed seeds spiked in 4% cerebrospinal fluid/buffer solution. However, in this condition, the time to detect the first aggregates was increased. Analysis of Cy3-labeled Aβ42 monomer adsorption on a quartz substrate after L-DOPA coating by confocal fluorescence spectroscopy and molecular dynamics simulation showed the huge influence of Aβ42 adsorption on the aggregation process.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Jeremy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Imad Abrao-Nemeir
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Maud Pratlong
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | | | - Eric Trinquet
- PerkinElmer, Parc Marcel Boiteux, 30200 Codolet, France
| | - Veronique Perrier
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Joan Torrent
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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19
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Zhang X, Lin M, Dai Y, Xia F. Stochastic Sensing of Dynamic Interactions and Chemical Reactions with Nanopores/Nanochannels. Anal Chem 2023. [PMID: 37413795 DOI: 10.1021/acs.analchem.3c00543] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.
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Affiliation(s)
- Xiaojin Zhang
- 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, Wuhan 430074, China
| | - Meihua Lin
- 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, Wuhan 430074, China
| | - Yu Dai
- 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, Wuhan 430074, 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, Wuhan 430074, China
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20
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Christopoulou NM, Kalogianni DP, Christopoulos TK. Multifold improvement in allergen detection capability of dipstick-type immunosensors via macromolecular crowding. Talanta 2023; 265:124899. [PMID: 37421795 DOI: 10.1016/j.talanta.2023.124899] [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: 04/18/2023] [Revised: 06/22/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
Dipstick-type lateral flow immunosensors are used widely for on-site detection of food allergens. The weakness of the immunosensors of this type, however, is their low sensitivity. Contrary to current methods, that focus on improving detection capability through the introduction of novel labels or multistep protocols, this work exploits macromolecular crowding to modify and regulate the microenvironment of the immunoassay, thus promoting the interactions that are responsible for allergen recognition and signal generation. The effect of 14 macromolecular crowding agents was explored using, as a model, commercially available and widely applied dipstick immunosensors, which are already optimized in terms of reagents and conditions for peanut allergen detection. An about 10-fold improvement in detection capability was achieved by using polyvinylpyrrolidone, Mr 29,000, as a macromolecular crowder without compromising simplicity and practicality. The proposed approach is complementary to other methods of improving the sensitivity by using novel labels. Because biomacromolecular interactions have a fundamental role in all types of biosensors, we foresee that the proposed strategy will also find applications in other biosensors and analytical devices.
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Affiliation(s)
- Natalia-Maria Christopoulou
- Analytical/Bioanalytical Chemistry & Nanotechnology Group, Department of Chemistry, University of Patras, Rio, Patras, 26504, Greece
| | - Despina P Kalogianni
- Analytical/Bioanalytical Chemistry & Nanotechnology Group, Department of Chemistry, University of Patras, Rio, Patras, 26504, Greece
| | - Theodore K Christopoulos
- Analytical/Bioanalytical Chemistry & Nanotechnology Group, Department of Chemistry, University of Patras, Rio, Patras, 26504, Greece.
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21
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Wang XY, Lv J, Wu X, Hong Q, Qian RC. The Modification and Applications of Nanopipettes in Electrochemical Analysis. Chempluschem 2023; 88:e202300100. [PMID: 37442793 DOI: 10.1002/cplu.202300100] [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: 02/21/2023] [Revised: 05/31/2023] [Indexed: 07/15/2023]
Abstract
Nanopipette, which is fabricated by glasses and possesses a nanoscale pore in the tip, has been proven to be immensely useful in electrochemical analysis. Numerous nanopipette-based sensors have emerged with improved sensitivity, selectivity, ease of use, and miniaturization. In this minireview, we provide an overview of the recent developments of nanopipette-based electrochemical sensors based on different types of nanopipettes, including single-nanopipettes, self-referenced nanopipettes, dual-nanopipettes, and double-barrel nanopipettes. Several important modification materials for nanopipette functionalization are highlighted, such as conductive materials, macromolecular materials, and functional molecules. These materials can improve the sensing performance and targeting specificities of nanopipettes. We also discuss examples of related applications and the future development of nanopipette-based strategies.
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Affiliation(s)
- Xiao-Yuan Wang
- Key Laboratory for Advanced Materials &, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Jian Lv
- Key Laboratory for Advanced Materials &, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Xue Wu
- Key Laboratory for Advanced Materials &, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Qin Hong
- Key Laboratory for Advanced Materials &, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
| | - Ruo-Can Qian
- Key Laboratory for Advanced Materials &, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, P. R. China
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22
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Punia B, Chaudhury S. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores. J Phys Chem B 2023. [PMID: 37294938 DOI: 10.1021/acs.jpcb.3c02792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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23
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Zhang X, Galenkamp NS, van der Heide NJ, Moreno J, Maglia G, Kjems J. Specific Detection of Proteins by a Nanobody-Functionalized Nanopore Sensor. ACS NANO 2023; 17:9167-9177. [PMID: 37127291 PMCID: PMC10184537 DOI: 10.1021/acsnano.2c12733] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are label-free single-molecule analytical tools that show great potential for stochastic sensing of proteins. Here, we described a ClyA nanopore functionalized with different nanobodies through a 5-6 nm DNA linker at its periphery. Ty1, 2Rs15d, 2Rb17c, and nb22 nanobodies were employed to specifically recognize the large protein SARS-CoV-2 Spike, a medium-sized HER2 receptor, and the small protein murine urokinase-type plasminogen activator (muPA), respectively. The pores modified with Ty1, 2Rs15d, and 2Rb17c were capable of stochastic sensing of Spike protein and HER2 receptor, respectively, following a model where unbound nanobodies, facilitated by a DNA linker, move inside the nanopore and provoke reversible blockade events, whereas engagement with the large- and medium-sized proteins outside of the pore leads to a reduced dynamic movement of the nanobodies and an increased current through the open pore. Exploiting the multivalent interaction between trimeric Spike protein and multimerized Ty1 nanobodies enabled the detection of picomolar concentrations of Spike protein. In comparison, detection of the smaller muPA proteins follows a different model where muPA, complexing with the nb22, moves into the pore, generating larger blockage signals. Importantly, the components in blood did not affect the sensing performance of the nanobody-functionalized nanopore, which endows the pore with great potential for clinical detection of protein biomarkers.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Julián Moreno
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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24
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Marcuccio F, Soulias D, Chau CCC, Radford SE, Hewitt E, Actis P, Edwards MA. Mechanistic Study of the Conductance and Enhanced Single-Molecule Detection in a Polymer-Electrolyte Nanopore. ACS NANOSCIENCE AU 2023; 3:172-181. [PMID: 37096230 PMCID: PMC10119975 DOI: 10.1021/acsnanoscienceau.2c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 04/26/2023]
Abstract
Solid-state nanopores have been widely employed in the detection of biomolecules, but low signal-to-noise ratios still represent a major obstacle in the discrimination of nucleic acid and protein sequences substantially smaller than the nanopore diameter. The addition of 50% poly(ethylene) glycol (PEG) to the external solution is a simple way to enhance the detection of such biomolecules. Here, we demonstrate with finite-element modeling and experiments that the addition of PEG to the external solution introduces a strong imbalance in the transport properties of cations and anions, drastically affecting the current response of the nanopore. We further show that the strong asymmetric current response is due to a polarity-dependent ion distribution and transport at the nanopipette tip region, leading to either ion depletion or enrichment for few tens of nanometers across its aperture. We provide evidence that a combination of the decreased/increased diffusion coefficients of cations/anions in the bath outside the nanopore and the interaction between a translocating molecule and the nanopore-bath interface is responsible for the increase in the translocation signals. We expect this new mechanism to contribute to further developments in nanopore sensing by suggesting that tuning the diffusion coefficients of ions could enhance the sensitivity of the system.
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Affiliation(s)
- Fabio Marcuccio
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Dimitrios Soulias
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Chalmers C. C. Chau
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, LeedsLS2 9JT, U.K.
| | - Paolo Actis
- School
of Electronic and Electrical Engineering, University of Leeds, LeedsLS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, LeedsLS2 9JT, U.K.
| | - Martin Andrew Edwards
- Department
of Chemistry and Biochemistry, University
of Arkansas, Fayetteville, Arkansas72701, United States
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25
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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26
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Guan X, Li H, Chen L, Qi G, Jin Y. Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection. ACS Sens 2023; 8:427-442. [PMID: 36670058 DOI: 10.1021/acssensors.2c02102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.
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Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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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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Xu X, Valavanis D, Ciocci P, Confederat S, Marcuccio F, Lemineur JF, Actis P, Kanoufi F, Unwin PR. The New Era of High-Throughput Nanoelectrochemistry. Anal Chem 2023; 95:319-356. [PMID: 36625121 PMCID: PMC9835065 DOI: 10.1021/acs.analchem.2c05105] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Xiangdong Xu
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Paolo Ciocci
- Université
Paris Cité, ITODYS, CNRS, F-75013 Paris, France
| | - Samuel Confederat
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,Faculty
of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,
| | | | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,
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30
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Zong W, Shao X, Li J, Chai Y, Hu X, Zhang X. Synthetic Intracellular Environments: From Basic Science to Applications. Anal Chem 2023; 95:535-549. [PMID: 36625127 DOI: 10.1021/acs.analchem.2c04199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Wei Zong
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xiaotong Shao
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Jinlong Li
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China.,Heilongjiang Provincial Key Laboratory of Catalytic Synthesis for Fine Chemicals, Qiqihar University, Qiqihar161006, China
| | - Yunhe Chai
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
| | - Xinyu Hu
- Key Laboratory of Micro-Nano Optoelectronic Devices (Wenzhou), College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou325035, China
| | - Xunan Zhang
- College of Chemistry and Chemical Engineering, Qiqihar University, No. 42 Wenhua Street, Qiqihar161006, China
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31
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Chau C, Marcuccio F, Soulias D, Edwards MA, Tuplin A, Radford SE, Hewitt E, Actis P. Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore. ACS NANO 2022; 16:20075-20085. [PMID: 36279181 PMCID: PMC9798860 DOI: 10.1021/acsnano.2c08312] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.
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Affiliation(s)
- Chalmers Chau
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
- 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.
| | - Dimitrios Soulias
- 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.
| | - Martin Andrew Edwards
- Department
of Chemistry & Biochemistry, University
of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Andrew Tuplin
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sheena E. Radford
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Eric Hewitt
- School
of Molecular and Cellular Biology and Astbury Centre for Structural
Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - 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.
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32
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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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33
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Macromolecular crowding agents enhance the sensitivity of lateral flow immunoassays. Biosens Bioelectron 2022; 218:114737. [DOI: 10.1016/j.bios.2022.114737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022]
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34
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Trivedi M, Gupta R, Nirmalkar N. Electroosmotic transport and current rectification of viscoelastic electrolyte in a conical pore nanomembrane. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2022.120755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran. ANAL SCI 2022; 38:1505-1512. [PMID: 36050568 DOI: 10.1007/s44211-022-00185-5] [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: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 11/01/2022]
Abstract
In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO4, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (CDex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO3H and ClO4- functional groups, was responsible for the J-aggregation in the HClO4 solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.
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36
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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37
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Meyer N, Janot JM, Torrent J, Balme S. Real-Time Fast Amyloid Seeding and Translocation of α-Synuclein with a Nanopipette. ACS CENTRAL SCIENCE 2022; 8:441-448. [PMID: 35505874 PMCID: PMC9052795 DOI: 10.1021/acscentsci.1c01404] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The detection to α-synuclein (αS) assemblies as a biomarker of synucleinopathies is an important challenge for further development of an early diagnosis tool. Here, we present proof of concept real-time fast amyloid seeding and translocation (RT-FAST) based on a nanopipette that combines in one unique system a reaction vessel to accelerate the seed amplification and nanopore sensor for single-molecule αS assembly detection. RT-FAST allows the detection of the presence αS seeds WT and A53T variant in a given sample in only 90 min by adding a low quantity (35 μL at 100 nM) of recombinant αS for amplification. It also shows cross-seeding aggregation by adding mixing seeds A53T with WT monomers. Finally, we establish the dependence between the capture rate of aggregates by the nanopore sensor and the initial seed concentration from 200 pM to 2 pM, which promises further development toward a quantitative analysis of the initial seed concentration.
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Affiliation(s)
- Nathan Meyer
- Institut
Européen des Membranes, UMR5635 University of Montpellier ENCSM
CNRS, Place Eugène
Bataillon, 34095 Montpellier cedex 5, France
- INM,
University of Montpellier, INSERM, 34091 Montpellier, France
| | - Jean-Marc Janot
- Institut
Européen des Membranes, UMR5635 University of Montpellier ENCSM
CNRS, Place Eugène
Bataillon, 34095 Montpellier cedex 5, France
| | - Joan Torrent
- INM,
University of Montpellier, INSERM, 34091 Montpellier, France
| | - Sébastien Balme
- Institut
Européen des Membranes, UMR5635 University of Montpellier ENCSM
CNRS, Place Eugène
Bataillon, 34095 Montpellier cedex 5, France
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38
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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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Xie ZP, Liu SM, Zhai YM. Study on the Self-assembly and Signal Amplification Ability of Nucleic Acid Nanostructure with the Nanopipette. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Meyer N, Arroyo N, Baldelli M, Coquart N, Janot JM, Perrier V, Chinappi M, Picaud F, Torrent J, Balme S. Conical nanopores highlight the pro-aggregating effects of pyrimethanil fungicide on Aβ(1-42) peptides and dimeric splitting phenomena. CHEMOSPHERE 2022; 291:132733. [PMID: 34742766 DOI: 10.1016/j.chemosphere.2021.132733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The Aβ(1-42) aggregation is a key event in the physiopathology of Alzheimer's disease (AD). Exogenous factors such as environmental pollutants, and more particularly pesticides, can corrupt Aβ(1-42) assembly and could influence the occurrence and pathophysiology of AD. However, pesticide involvement in the early stages of Aβ(1-42) aggregation is still unknown. Here, we employed conical track-etched nanopore in order to analyse the Aβ(1-42) fibril formation in the presence of pyrimethanil, a widely used fungicide belonging to the anilinopyrimidine class. Our results evidenced a pro-aggregating effect of pyrimethanil on Aβ(1-42). Aβ(1-42) assemblies were successfully detected using conical nanopore coated with PEG. Using an analytical model, the large current blockades observed (>0.7) were assigned to species with size close to the sensing pore. The long dwell times (hundreds ms scale) were interpreted by the possible interactions amyloid/PEG using molecular dynamic simulation. Such interaction could leave until splitting phenomena of the dimer structure. Our work also evidences that the pyrimethanil induce an aggregation of Aβ(1-42) mechanism in two steps including the reorganization prior the elongation phase.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Nicolas Arroyo
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 Route de Gray, 25030, Besançon, France
| | - Matteo Baldelli
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via Del Politecnico 1, 00133, Roma, Italy
| | - Nicolas Coquart
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Jean Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | | | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Via Del Politecnico 1, 00133, Roma, Italy
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 Route de Gray, 25030, Besançon, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.
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Chen J, Sun L, Wang S, Tian F, Zhu H, Zhang R, Dai L. Crowding-induced polymer trapping in a channel. Phys Rev E 2021; 104:054502. [PMID: 34942690 DOI: 10.1103/physreve.104.054502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 11/07/2022]
Abstract
In this work, we report an intriguing phenomenon: crowding-induced polymer trapping in a channel. Using Langevin dynamics simulations and analytical calculations, we find that for a polymer confined in a channel, crowding particles can push a polymer into the channel corner through inducing an effective polymer-corner attraction due to the depletion effect. This phenomenon is referred to as polymer trapping. The occurrence of polymer trapping requires a minimum volume fraction of crowders, ϕ^{*}, which scales as ϕ^{*}∼(a_{c}/L_{p})^{1/3} for a_{c}≫a_{m} and ϕ^{*}∼(a_{c}/L_{p})^{1/3}(a_{c}/a_{m})^{1/2} for a_{c}≪a_{m}, where a_{c} is the crowder diameter, a_{m} is the monomer diameter, and L_{p} is the polymer persistence length. For DNA, ϕ^{*} is estimated to be around 0.25 for crowders with a_{c}=2nm. We find that ϕ^{*} also strongly depends on the shape of the channel cross section, and ϕ^{*} is much smaller for a triangle channel than a square channel. The polymer trapping leads to a nearly fully stretched polymer conformation along a channel corner, which may have practical applications, such as full stretching of DNA for the nanochannel-based genome mapping technology.
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Affiliation(s)
- Jialu Chen
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Simin Wang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Haoqi Zhu
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong, China
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Pandey P, Sesena-Rubfiaro A, Khatri S, He J. Development of multifunctional nanopipettes for controlled intracellular delivery and single-entity detection. Faraday Discuss 2021; 233:315-335. [PMID: 34889345 DOI: 10.1039/d1fd00057h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intracellular delivery of biomolecules and nanoscale materials to individual cells has gained remarkable attention in recent years owing to its wide applications in drug delivery, clinical diagnostics, bio-imaging and single-cell analysis. It remains a challenge to control and measure the delivered amount in one cell. In this work, we developed a multifunctional nanopipette - containing both a nanopore and nanoelectrode (pyrolytic carbon) at the apex - as a facile, minimally invasive and effective platform for both controllable single-cell intracellular delivery and single-entity counting. While controlled by a micromanipulator, the baseline changes of the nanopore ionic current (I) and nanoelectrode open circuit potential (V) help to guide the nanopipette tip insertion and positioning processes. The delivery from the nanopore barrel can be facilely controlled by the applied nanopore bias. To optimize the intracellular single-entity detection during delivery, we studied the effects of the nanopipette tip geometry and solution salt concentration in controlled experiments. We have successfully delivered gold nanoparticles and biomolecules into the cell, as confirmed by the increased scattering and fluorescence signals, respectively. The delivered entities have also been detected at the single-entity level using either one or both transient I and V signals. We found that the sensitivity of the single-entity electrochemical measurement was greatly affected by the local environment of the cell and varied between cell lines.
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Affiliation(s)
- Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA.
| | | | - Santosh Khatri
- Physics Department, Florida International University, Miami, Florida, 33199, USA.
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, USA
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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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Meyer N, Arroyo N, Janot JM, Lepoitevin M, Stevenson A, Nemeir IA, Perrier V, Bougard D, Belondrade M, Cot D, Bentin J, Picaud F, Torrent J, Balme S. Detection of Amyloid-β Fibrils Using Track-Etched Nanopores: Effect of Geometry and Crowding. ACS Sens 2021; 6:3733-3743. [PMID: 34554735 DOI: 10.1021/acssensors.1c01523] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several neurodegenerative diseases have been linked to proteins or peptides that are prone to aggregate in different brain regions. Aggregation of amyloid-β (Aβ) peptides is recognized as the main cause of Alzheimer's disease (AD) progression, leading to the formation of toxic Aβ oligomers and amyloid fibrils. The molecular mechanism of Aβ aggregation is complex and still not fully understood. Nanopore technology provides a new way to obtain kinetic and morphological aspects of Aβ aggregation at a single-molecule scale without labeling by detecting the electrochemical signal of the peptides when they pass through the hole. Here, we investigate the influence of nanoscale geometry (conical and bullet-like shape) of a track-etched nanopore pore and the effect of molecular crowding (polyethylene glycol-functionalized pores) on Aβ fibril sensing and analysis. Various Aβ fibril samples that differed by their length were produced by sonication of fibrils obtained in the presence of epigallocatechin gallate. The conical nanopore functionalized with polyethylene glycol (PEG) 5 kDa is suitable for discrimination of the fibril size from relative current blockade. The bullet-like-shaped nanopore enhances the amplitude of the current and increases the dwell time, allowing us to well discern the fibrils. Finally, the nanopore crowded with PEG 20 kDa enhances the relative current blockade and increases the dwell time; however, the discrimination is not improved compared to the "bullet-shaped" nanopore.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Nicolas Arroyo
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Mathilde Lepoitevin
- Institut des Matériaux Poreux de Paris (IMAP), UMR 8004 CNRS, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, 75005 Paris, France
| | - Anna Stevenson
- Institut des Matériaux Poreux de Paris (IMAP), UMR 8004 CNRS, Ecole Normale Supérieure de Paris, Ecole Supérieure de Physique et de Chimie Industrielles de Paris, PSL Université, 75005 Paris, France
- School of Chemistry, University of St. Andrews, St. Andrews KY16 9ST, U.K
| | - Imad Abrao Nemeir
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Veronique Perrier
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Daisy Bougard
- Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, EFS, Univ Antilles, 34095 Montpellier, France
| | - Maxime Belondrade
- Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, EFS, Univ Antilles, 34095 Montpellier, France
| | - Didier Cot
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Jérémy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France
| | - Joan Torrent
- INM UM, CNRS, INSERM, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Sebastien Balme
- Institut Européen des Membranes, UMR5635 UM ENCSM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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46
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Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
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Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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47
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Nakatsuka N, Heard KJ, Faillétaz A, Momotenko D, Vörös J, Gage FH, Vadodaria KC. Sensing serotonin secreted from human serotonergic neurons using aptamer-modified nanopipettes. Mol Psychiatry 2021; 26:2753-2763. [PMID: 33767349 PMCID: PMC9997689 DOI: 10.1038/s41380-021-01066-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/17/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
The serotonergic system in the human brain modulates several physiological processes, and altered serotonergic neurotransmission has been implicated in the neuropathology of several psychiatric disorders. The study of serotonergic neurotransmission in psychiatry has long been restricted to animal models, but advances in cell reprogramming technology have enabled the generation of serotonergic neurons from patient-induced pluripotent stem cells (iPSCs). While iPSC-derived human serotonergic neurons offer the possibility to study serotonin (5-HT) release and uptake, particularly by 5-HT-modulating drugs such as selective serotonin reuptake inhibitors (SSRIs), a major limitation is the inability to reliably quantify 5-HT secreted from neurons in vitro. Herein, we address this technical gap via a novel sensing technology that couples 5-HT-specific DNA aptamers into nanopores (glass nanopipettes) with orifices of ~10 nm to detect 5-HT in complex neuronal culture medium with higher selectivity, sensitivity, and stability than existing methods. The 5-HT aptamers undergo conformational rearrangement upon target capture and serve as gatekeepers of ionic flux through the nanopipette opening. We generated human serotonergic neurons in vitro and detected secreted 5-HT using aptamer-coated nanopipettes in a low nanomolar range, with the possibility of detecting significantly lower (picomolar) concentrations. Furthermore, as a proof of concept, we treated human serotonergic neurons in vitro with the SSRI citalopram and detected a significant increase in extracellular 5-HT using the aptamer-modified nanopipettes. We demonstrate the utility of such methods for 5-HT detection, raising the possibility of fast quantification of neurotransmitters secreted from patient-derived live neuronal cells.
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Affiliation(s)
- Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Kelly J Heard
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alix Faillétaz
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Krishna C Vadodaria
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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48
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Al Sulaiman D, Gatehouse A, Ivanov AP, Edel JB, Ladame S. Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26673-26681. [PMID: 34085806 DOI: 10.1021/acsami.1c01145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fast sampling followed by sequence-independent sensing and length-dependent detection of short double-stranded DNA fragments, the size of those found in blood and other bodily fluids, is achieved using engineered molecular sensors, dubbed hydrogel-filled nanopores (HFNs). Fragments as short as 100 base pairs were blindly sampled and concentrated at the tip of an HFN before reversing the applied potential to detect and distinguish individual molecules based on fragment length as they translocate out of the nanopore. A remarkable 16-fold increase in the signal-to-noise ratio was observed in the eject configuration compared to the load configuration, enabling the resolution of fragments with a size difference of 50 nucleotides in length. This fast and versatile technology offers great tunability for both sampling and detection. While increasing sampling time leads to an increase in the local DNA concentration at the tip prior to detection, a linear correlation between the peak current and DNA fragment size enables good resolution of fragments up to 250 bp long.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alfie Gatehouse
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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49
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Cai S, Pataillot-Meakin T, Shibakawa A, Ren R, Bevan CL, Ladame S, Ivanov AP, Edel JB. Single-molecule amplification-free multiplexed detection of circulating microRNA cancer biomarkers from serum. Nat Commun 2021; 12:3515. [PMID: 34112774 PMCID: PMC8192752 DOI: 10.1038/s41467-021-23497-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) play essential roles in post-transcriptional gene expression and are also found freely circulating in bodily fluids such as blood. Dysregulated miRNA signatures have been associated with many diseases including cancer, and miRNA profiling from liquid biopsies offers a promising strategy for cancer diagnosis, prognosis and monitoring. Here, we develop size-encoded molecular probes that can be used for simultaneous electro-optical nanopore sensing of miRNAs, allowing for ultrasensitive, sequence-specific and multiplexed detection directly in unprocessed human serum, in sample volumes as small as 0.1 μl. We show that this approach allows for femtomolar sensitivity and single-base mismatch selectivity. We demonstrate the ability to simultaneously monitor miRNAs (miR-141-3p and miR-375-3p) from prostate cancer patients with active disease and in remission. This technology can pave the way for next generation of minimally invasive diagnostic and companion diagnostic tests for cancer.
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Affiliation(s)
- Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Thomas Pataillot-Meakin
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Akifumi Shibakawa
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK
| | - Charlotte L Bevan
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, London, W12 0BZ, UK.
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London, W12 0BZ, UK.
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Reynaud L, Bouchet-Spinelli A, Janot JM, Buhot A, Balme S, Raillon C. Discrimination of α-Thrombin and γ-Thrombin Using Aptamer-Functionalized Nanopore Sensing. Anal Chem 2021; 93:7889-7897. [PMID: 34038092 DOI: 10.1021/acs.analchem.1c00461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein detection and identification at the single-molecule level are major challenges in many biotechnological fields. Solid-state nanopores have raised attention as label-free biosensors with high sensitivity. Here, we use solid-state nanopore sensing to discriminate two closely related proteins, α-thrombin and γ-thrombin. We show that aptamer functionalization improves protein discrimination thanks to a significant difference in the relative current blockade amplitude. To enhance discrimination, we postprocessed the signals using machine learning and training algorithms and we were able to reach an accuracy of 98.8% using seven features and ensemble methods.
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Affiliation(s)
- Lucile Reynaud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | | | - Jean-Marc Janot
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | - Sébastien Balme
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Camille Raillon
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
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