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Koch C, Reilly-O'Donnell B, Gutierrez R, Lucarelli C, Ng FS, Gorelik J, Ivanov AP, Edel JB. Nanopore sequencing of DNA-barcoded probes for highly multiplexed detection of microRNA, proteins and small biomarkers. NATURE NANOTECHNOLOGY 2023; 18:1483-1491. [PMID: 37749222 PMCID: PMC10716039 DOI: 10.1038/s41565-023-01479-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/28/2023] [Indexed: 09/27/2023]
Abstract
There is an unmet need to develop low-cost, rapid and highly multiplexed diagnostic technology platforms for quantitatively detecting blood biomarkers to advance clinical diagnostics beyond the single biomarker model. Here we perform nanopore sequencing of DNA-barcoded molecular probes engineered to recognize a panel of analytes. This allows for highly multiplexed and simultaneous quantitative detection of at least 40 targets, such as microRNAs, proteins and neurotransmitters, on the basis of the translocation dynamics of each probe as it passes through a nanopore. Our workflow is built around a commercially available MinION sequencing device, offering a one-hour turnaround time from sample preparation to results. We also demonstrate that the strategy can directly detect cardiovascular disease-associated microRNA from human serum without extraction or amplification. Due to the modularity of barcoded probes, the number and type of targets detected can be significantly expanded.
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Affiliation(s)
- Caroline Koch
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Benedict Reilly-O'Donnell
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | | | - Carla Lucarelli
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Fu Siong Ng
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Julia Gorelik
- National Heart and Lung Institute, ICTEM, Imperial College London, London, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK.
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2
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Recent Advances in Aptamer‐Based Nanopore Sensing at Single‐Molecule Resolution. Chem Asian J 2022; 17:e202200364. [DOI: 10.1002/asia.202200364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/20/2022] [Indexed: 11/07/2022]
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Silicon Nitride-Based Micro-Apertures Coated with Parylene for the Investigation of Pore Proteins Fused in Free-Standing Lipid Bilayers. MEMBRANES 2022; 12:membranes12030309. [PMID: 35323784 PMCID: PMC8954132 DOI: 10.3390/membranes12030309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
Abstract
In this work, we present a microsystem setup for performing sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) were constructed in microfabricated silicon nitride apertures (<100 µm in diameter), conformal coated with Parylene (Parylene-C or Parylene-AF4). Within these BLMs, electrophysiological measurements were conducted to monitor the behavior of different pore proteins. Two approaches to integrate pore-forming proteins into the membrane were applied: direct reconstitution and reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. The advantage of utilizing OMVs is that the pore proteins remain in their native lipid and lipopolysaccharide (LPS) environment, representing a more natural state compared to the usage of fused purified pore proteins. Multiple aperture chips can be easily assembled in the 3d-printed holder to conduct parallel membrane transport investigations. Moreover, well defined microfabricated apertures are achievable with very high reproducibility. The presented microsystem allows the investigation of fast gating events (down to 1 ms), pore blocking by an antibiotic, and gating events of small pores (amplitude of approx. 3 pA).
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Olmos CM, Rosero G, Fernández-Cabada T, Booth R, Der M, Cabaleiro JM, Debut A, Cumbal L, Pérez MS, Lerner B. Hybrid microchannel-solid state micropore device for fast and optical cell detection. RSC Adv 2020; 10:5361-5370. [PMID: 35498312 PMCID: PMC9049143 DOI: 10.1039/c9ra09939e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/20/2020] [Indexed: 11/28/2022] Open
Abstract
This paper presents a methodology for cell detection and counting using a device that combines PDMS (polydimethylsiloxane) microfluidic multilayer channels with a single solid state micropore. Optimal conditions of solid-state micropore fabrication from crystalline silicon wafers are presented. Micropores of varying size can be obtained by directly etching using an etchant agent concentration of 50 wt% KOH, at varying temperatures (40, 60, 80 °C) and voltages (100, 500, 1000 mV). Scanning Electron Microscopy (SEM), and profilometry techniques have been used for the micropore characterization. In order to find optimal conditions for cell detection a COMSOL Multiphysics simulation was performed. Pressure drop, shear stress, fluid viscosities and flow rates parameters were evaluated. The potential viability of the device for cell detection and counting, avoiding cellular damage, is demonstrated. This paper presents a methodology for cell detection and counting using a device that combines PDMS (polydimethylsiloxane) microfluidic multilayer channels with a single solid state micropore.![]()
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Affiliation(s)
- Carol M. Olmos
- Facultad Regional Haedo
- Universidad Tecnológica Nacional (UTN)
- Haedo
- Argentina
| | - Gustavo Rosero
- Facultad Regional Haedo
- Universidad Tecnológica Nacional (UTN)
- Haedo
- Argentina
| | | | | | - Manuel Der
- Departamento de Física
- Facultad de Ciencias Exactas y Naturales
- Universidad de Buenos Aires (UBA)
- Cuidad Universitaria
- Buenos Aires
| | - Juan M. Cabaleiro
- CONICET-Fluid Dynamics Laboratory
- Facultad de ingeniería
- Universidad de Buenos Aires (UBA)
- Buenos Aires
- Argentina
| | - Alexis Debut
- Centro de Nanociencia y Nanotecnología
- Universidad de las Fuerzas Armadas ESPE
- Sangolquí
- Ecuador
| | - Luis Cumbal
- Centro de Nanociencia y Nanotecnología
- Universidad de las Fuerzas Armadas ESPE
- Sangolquí
- Ecuador
| | - Maximiliano S. Pérez
- Facultad Regional Haedo
- Universidad Tecnológica Nacional (UTN)
- Haedo
- Argentina
- Instituto de Ingeniería Biomédica
| | - Betiana Lerner
- Facultad Regional Haedo
- Universidad Tecnológica Nacional (UTN)
- Haedo
- Argentina
- Department of Electrical and Computer Engineering
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5
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Small molecule electro-optical binding assay using nanopores. Nat Commun 2019; 10:1797. [PMID: 30996223 PMCID: PMC6470146 DOI: 10.1038/s41467-019-09476-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/12/2019] [Indexed: 01/12/2023] Open
Abstract
The identification of short nucleic acids and proteins at the single molecule level is a major driving force for the development of novel detection strategies. Nanopore sensing has been gaining in prominence due to its label-free operation and single molecule sensitivity. However, it remains challenging to detect small molecules selectively. Here we propose to combine the electrical sensing modality of a nanopore with fluorescence-based detection. Selectivity is achieved by grafting either molecular beacons, complementary DNA, or proteins to a DNA molecular carrier. We show that the fraction of synchronised events between the electrical and optical channels, can be used to perform single molecule binding assays without the need to directly label the analyte. Such a strategy can be used to detect targets in complex biological fluids such as human serum and urine. Future optimisation of this technology may enable novel assays for quantitative protein detection as well as gene mutation analysis with applications in next-generation clinical sample analysis. Nanopore detection of small molecules can be improved using molecular carriers, but separating a small analyte from the carrier signal can be challenging. Here the authors address this challenge using simultaneous electrical and optical readout in nanopore sensing to detect small molecules and quantify binding affinities.
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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Zhu L, Gu D, Liu Q. Hydrogen Peroxide Sensing Based on Inner Surfaces Modification of Solid-State Nanopore. NANOSCALE RESEARCH LETTERS 2017; 12:422. [PMID: 28637348 PMCID: PMC5478554 DOI: 10.1186/s11671-017-2190-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/08/2017] [Indexed: 05/20/2023]
Abstract
There are many techniques for the detection of molecules. But detection of molecules through solid-state nanopore in a solution is one of the promising, high-throughput, and low-cost technology used these days. In the present investigation, a solid-state nanopore platform was fabricated for the detection of hydrogen peroxide (H2O2), which is not only a label free product but also a significant participant in the redox reaction. We have successfully fabricated silicon nitride (Si3N4) nanopores with diameters of ~50 nm by using a focused Ga ion beam, the inner surface of the nanopore has been modified with horseradish peroxidase (HRP) by employing carbodiimide coupling chemistry. The immobilized HRP enzymes have ability to induce redox reactions in a single nanopore channel. Moreover, a real-time single aggregated ABTS•+ molecular translocation events were monitored and investigated. The designed solid-state nanopore biosensor is reversible and can be applied to detect H2O2 multiple times.
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Affiliation(s)
- Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing, 210096, People's Republic of China
| | - Dejian Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing, 210096, People's Republic of China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing, 210096, People's Republic of China.
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Rashid JIA, Yusof NA. The strategies of DNA immobilization and hybridization detection mechanism in the construction of electrochemical DNA sensor: A review. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.09.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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9
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Ren R, Zhang Y, Nadappuram BP, Akpinar B, Klenerman D, Ivanov AP, Edel JB, Korchev Y. Nanopore extended field-effect transistor for selective single-molecule biosensing. Nat Commun 2017; 8:586. [PMID: 28928405 PMCID: PMC5605549 DOI: 10.1038/s41467-017-00549-w] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/07/2017] [Indexed: 11/21/2022] Open
Abstract
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry. We report on a polypyrrole functionalized nexFET, with controllable gate voltage that can be used to switch on/off, and slow down single-molecule DNA transport through a nanopore. This strategy enables higher molecular throughput, enhanced signal-to-noise, and even heightened selectivity via functionalization with an embedded receptor. This is shown for selective sensing of an anti-insulin antibody in the presence of its IgG isotype. Efficient detection of single molecules is vital to many biosensing technologies, which require analytical platforms with high selectivity and sensitivity. Ren et al. combine a nanopore sensor and a field-effect transistor, whereby gate voltage mediates DNA and protein transport through the nanopore.
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Affiliation(s)
- Ren Ren
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - Yanjun Zhang
- Department of Medicine, Imperial College London, London, W12 0NN, UK. .,Tianjin Neurological Institute, Tianjin Medical University General Hospital, Heping Qu, 300052, China.
| | | | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
| | - Yuri Korchev
- Department of Medicine, Imperial College London, London, W12 0NN, UK.,National University of Science & Technology MISIS, Moscow, 119049, Russia
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Quantitative differentiation of multiple virus in blood using nanoporous silicon oxide immunosensor and artificial neural network. Biosens Bioelectron 2017; 98:180-188. [PMID: 28672193 DOI: 10.1016/j.bios.2017.06.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/14/2017] [Accepted: 06/22/2017] [Indexed: 12/25/2022]
Abstract
In spite of the rapid developments in various nanosensor technologies, it still remains challenging to realize a reliable ultrasensitive electrical biosensing platform which will be able to detect multiple viruses in blood simultaneously with a fairly high reproducibility without using secondary labels. In this paper, we have reported quantitative differentiation of Hep-B and Hep-C viruses in blood using nanoporous silicon oxide immunosensor array and artificial neural network (ANN). The peak frequency output (fp) from the steady state sensitivity characteristics and the first cut off frequency (fc) from the transient characteristics have been considered as inputs to the multilayer ANN. Implementation of several classifier blocks in the ANN architecture and coupling them with both the sensor chips, functionalized with Hep-B and Hep-C antibodies have enabled the quantification of the viruses with an accuracy of around 95% in the range of 0.04fM-1pM and with an accuracy of around 90% beyond 1pM and within 25nM in blood serum. This is the most sensitive report on multiple virus quantification using label free method.
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Tan S, Gu D, Liu H, Liu Q. Detection of a single enzyme molecule based on a solid-state nanopore sensor. NANOTECHNOLOGY 2016; 27:155502. [PMID: 26937593 DOI: 10.1088/0957-4484/27/15/155502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The nanopore sensor as a high-throughput and low-cost technology can detect a single molecule in a solution. In the present study, relatively large silicon nitride (Si3N4) nanopores with diameters of ∼28 and ∼88 nm were fabricated successfully using a focused Ga ion beam. We have used solid-state nanopores with various sizes to detect the single horseradish peroxidase (HRP) molecule and for the first time analyzed single HRP molecular translocation events. In addition, a real-time monitored single enzyme molecular biochemical reaction and a translocation of the product of enzyme catalysis substrates were investigated by using a Si3N4 nanopore. Our nanopore system showed a high sensitivity in detecting single enzyme molecules and a real-time monitored single enzyme molecular biochemical reaction. This method could also be significant for studying gene expression or enzyme dynamics at the single-molecule level.
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Affiliation(s)
- ShengWei Tan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China
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