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Raja SN, Jain S, Kipen J, Jaldén J, Stemme G, Herland A, Niklaus F. Electromigrated Gold Nanogap Tunnel Junction Arrays: Fabrication and Electrical Behavior in Liquid and Gaseous Media. ACS APPLIED MATERIALS & INTERFACES 2024; 16:37131-37146. [PMID: 38954436 PMCID: PMC11261569 DOI: 10.1021/acsami.4c03282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Tunnel junctions have been suggested as high-throughput electronic single molecule sensors in liquids with several seminal experiments conducted using break junctions with reconfigurable gaps. For practical single molecule sensing applications, arrays of on-chip integrated fixed-gap tunnel junctions that can be built into compact systems are preferable. Fabricating nanogaps by electromigration is one of the most promising approaches to realize on-chip integrated tunnel junction sensors. However, the electrical behavior of fixed-gap tunnel junctions immersed in liquid media has not been systematically studied to date, and the formation of electromigrated nanogap tunnel junctions in liquid media has not yet been demonstrated. In this work, we perform a comparative study of the formation and electrical behavior of arrays of gold nanogap tunnel junctions made by feedback-controlled electromigration immersed in various liquid and gaseous media (deionized water, mesitylene, ethanol, nitrogen, and air). We demonstrate that tunnel junctions can be obtained from microfabricated gold nanoconstrictions inside liquid media. Electromigration of junctions in air produces the highest yield (61-67%), electromigration in deionized water and mesitylene results in a lower yield than in air (44-48%), whereas electromigration in ethanol fails to produce viable tunnel junctions due to interfering electrochemical processes. We map out the stability of the conductance characteristics of the resulting tunnel junctions and identify medium-specific operational conditions that have an impact on the yield of forming stable junctions. Furthermore, we highlight the unique challenges associated with working with arrays of large numbers of tunnel junctions in batches. Our findings will inform future efforts to build single molecule sensors using on-chip integrated tunnel junctions.
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Affiliation(s)
- Shyamprasad N. Raja
- Division
of Micro and Nanosystems (MST), School of Electrical Engineering and
Computer Science (EECS), KTH Royal Institute
of Technology, SE-10044 Stockholm, Sweden
| | - Saumey Jain
- Division
of Micro and Nanosystems (MST), School of Electrical Engineering and
Computer Science (EECS), KTH Royal Institute
of Technology, SE-10044 Stockholm, Sweden
- Division
of Nanobiotechnology, SciLifeLab, Department of Protein Science, School
of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Javier Kipen
- Division
of Information Science and Engineering (ISE), School of Electrical
Engineering and Computer Science (EECS), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Joakim Jaldén
- Division
of Information Science and Engineering (ISE), School of Electrical
Engineering and Computer Science (EECS), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Göran Stemme
- Division
of Micro and Nanosystems (MST), School of Electrical Engineering and
Computer Science (EECS), KTH Royal Institute
of Technology, SE-10044 Stockholm, Sweden
| | - Anna Herland
- Division
of Nanobiotechnology, SciLifeLab, Department of Protein Science, School
of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
- AIMES-Center
for the Advancement of Integrated Medical and Engineering Sciences,
Department of Neuroscience, Karolinska Institute, SE-17177 Solna, Sweden
| | - Frank Niklaus
- Division
of Micro and Nanosystems (MST), School of Electrical Engineering and
Computer Science (EECS), KTH Royal Institute
of Technology, SE-10044 Stockholm, Sweden
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2
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Raja SN, Jain S, Kipen J, Jaldén J, Stemme G, Herland A, Niklaus F. High-bandwidth low-current measurement system for automated and scalable probing of tunnel junctions in liquids. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:074710. [PMID: 39037302 DOI: 10.1063/5.0204188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/06/2024] [Indexed: 07/23/2024]
Abstract
Tunnel junctions have long been used to immobilize and study the electronic transport properties of single molecules. The sensitivity of tunneling currents to entities in the tunneling gap has generated interest in developing electronic biosensors with single molecule resolution. Tunnel junctions can, for example, be used for sensing bound or unbound DNA, RNA, amino acids, and proteins in liquids. However, manufacturing technologies for on-chip integrated arrays of tunnel junction sensors are still in their infancy, and scalable measurement strategies that allow the measurement of large numbers of tunneling junctions are required to facilitate progress. Here, we describe an experimental setup to perform scalable, high-bandwidth (>10 kHz) measurements of low currents (pA-nA) in arrays of on-chip integrated tunnel junctions immersed in various liquid media. Leveraging a commercially available compact 100 kHz bandwidth low-current measurement instrument, we developed a custom two-terminal probe on which the amplifier is directly mounted to decrease parasitic probe capacitances to sub-pF levels. We also integrated a motorized three-axis stage, which could be powered down using software control, inside the Faraday cage of the setup. This enabled automated data acquisition on arrays of tunnel junctions without worsening the noise floor despite being inside the Faraday cage. A deliberately positioned air gap in the fluidic path ensured liquid perfusion to the chip from outside the Faraday cage without coupling in additional noise. We demonstrate the performance of our setup using rapid current switching observed in electromigrated gold tunnel junctions immersed in deionized water.
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Affiliation(s)
- Shyamprasad N Raja
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Saumey Jain
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
- Division of Nanobiotechnology, SciLife Lab, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Javier Kipen
- Division of Information Science and Engineering, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Joakim Jaldén
- Division of Information Science and Engineering, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Göran Stemme
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Anna Herland
- Division of Nanobiotechnology, SciLife Lab, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
- AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences, Department of Neuroscience, Karolinska Institute, SE-171 77 Solna, Sweden
| | - Frank Niklaus
- Division of Micro and Nanosystems, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
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Jiang T, Yi L, Liu X, Ivanov AP, Edel JB, Tang L. Fabrication of electron tunneling probes for measuring single-protein conductance. Nat Protoc 2023; 18:2579-2599. [PMID: 37420088 DOI: 10.1038/s41596-023-00846-3] [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: 11/09/2022] [Accepted: 04/21/2023] [Indexed: 07/09/2023]
Abstract
Studying the electrical properties of individual proteins is a prominent research area in the field of bioelectronics. Electron tunnelling or quantum mechanical tunnelling (QMT) probes can act as powerful tools for investigating the electrical properties of proteins. However, current fabrication methods for these probes often have limited reproducibility, unreliable contact or inadequate binding of proteins onto the electrodes, so better solutions are required. Here, we detail a generalizable and straightforward set of instructions for fabricating simple, nanopipette-based, tunnelling probes, suitable for measuring conductance in single proteins. Our QMT probe is based on a high-aspect-ratio dual-channel nanopipette that integrates a pair of gold tunneling electrodes with a gap of less than 5 nm, fabricated via the pyrolytic deposition of carbon followed by the electrochemical deposition of gold. The gold tunneling electrodes can be functionalized using an extensive library of available surface modifications to achieve single-protein-electrode contact. We use a biotinylated thiol modification, in which a biotin-streptavidin-biotin bridge is used to form the single-protein junction. The resulting protein-coupled QMT probes enable the stable electrical measurement of the same single protein in solution for up to several hours. We also describe the analysis method used to interpret time-dependent single-protein conductance measurements, which can provide essential information for understanding electron transport and exploring protein dynamics. The total time required to complete the protocol is ~33 h and it can be carried out by users trained in less than 24 h.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China
| | - Long Yi
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China
| | - 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
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China.
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He Q, Tang L. Sub-5 nm nanogap electrodes towards single-molecular biosensing. Biosens Bioelectron 2022; 213:114486. [PMID: 35749816 DOI: 10.1016/j.bios.2022.114486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/02/2022]
Abstract
Nanogap electrodes (NGEs) with sub-5 nm gap has been widely used in single-molecule sensing and sequencing, with the characteristics of label-free, high sensitivity, rapid detection and low-cost. However, the fabrication of sub-5 nm gap electrodes with high controllability and reproducibility still remains a great challenge that impedes the experimental research and the commercialization of the nanogap device. Here, we review the common currently used fabrication methods of nanogap electrodes, such as gap narrowing deposition, mechanical controllable break junctions and the fabrication methods combined with nanopore or nanochannel. We then highlight the typical applications of nanogap electrodes in biological/chemical sensing fields, including single molecule recognition, single molecule sequencing and chemical kinetics analysis. Finally, the challenges of nanogap electrodes in single molecule sensing/sequencing are outlined and the future directions for sensing perspectives are suggested.
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Affiliation(s)
- Qiuxiang He
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China.
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Wang Y, Sadar J, Tsao CW, Mukherjee S, Qing Q. Nanopore chip with self-aligned transverse tunneling junction for DNA detection. Biosens Bioelectron 2021; 193:113552. [PMID: 34416434 DOI: 10.1016/j.bios.2021.113552] [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: 04/04/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
To achieve better signal quality and resolution in nanopore sequencing, there has been strong interest in quantum tunneling based detection which requires integration of tunneling junctions in nanopores. However, there has been very limited success due to precision and reproducibility issues. Here we report a new strategy based on feedback-controlled electrochemical processes in a confined nanoscale space to construct nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip. We demonstrate high-yield (>93%) correlated detection of translocating DNAs from both the ionic channel and the tunneling junction with enriched event rate. We also observed events attributed to non-translocating DNA making contact with the transverse electrodes. Existing challenges for precise sequencing are discussed, including fast translocation speed, and interference from transient electrostatic signals from fast-moving DNAs. Our work can serve as a first step to provide an accessible, and reproducible platform enabling further optimizations for tunneling-based DNA detection, and potentially sequencing.
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Affiliation(s)
- Yuan Wang
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Joshua Sadar
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Ching-Wei Tsao
- School for Engineering of Matter, Transport & Energy, And Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States
| | - Sanjana Mukherjee
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States
| | - Quan Qing
- Department of Physics, Arizona State University, Tempe, Arizona, 85287, United States; Biodesign Institute, Arizona State University, Tempe, Arizona, 85287, United States.
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6
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Fried JP, Swett JL, Nadappuram BP, Fedosyuk A, Sousa PM, Briggs DP, Ivanov AP, Edel JB, Mol JA, Yates JR. Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102543. [PMID: 34337856 DOI: 10.1002/smll.202102543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3 N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | | | | | - Pedro Miguel Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Dayrl P Briggs
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University London, London, E1 4NS, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
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7
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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8
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Tang Z, Dong M, He X, Guan W. On Stochastic Reduction in Laser-Assisted Dielectric Breakdown for Programmable Nanopore Fabrication. ACS APPLIED MATERIALS & INTERFACES 2021; 13:13383-13391. [PMID: 33705089 DOI: 10.1021/acsami.0c23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The controlled dielectric breakdown emerged as a promising alternative toward accessible solid-state nanopore fabrication. Several prior studies have shown that laser-assisted dielectric breakdown could help control the nanopore position and reduce the possibility of forming multiple pores. Here, we developed a physical model to estimate the probability of forming a single nanopore under different combinations of the laser power and the electric field. This model relies on the material- and experiment-specific parameters: the Weibull statistical parameters and the laser-induced photothermal etching rate. Both the model and our experimental data suggest that a combination of a high laser power and a low electric field is statistically favorable for forming a single nanopore at a programmed location. While this model relies on experiment-specific parameters, we anticipate it could provide the experimental insights for nanopore fabrication by the laser-assisted dielectric breakdown method, enabling broader access to solid-state nanopores and their sensing applications.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaodong He
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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9
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Tang L, Nadappuram BP, Cadinu P, Zhao Z, Xue L, Yi L, Ren R, Wang J, Ivanov AP, Edel JB. Combined quantum tunnelling and dielectrophoretic trapping for molecular analysis at ultra-low analyte concentrations. Nat Commun 2021; 12:913. [PMID: 33568635 PMCID: PMC7876030 DOI: 10.1038/s41467-021-21101-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/06/2021] [Indexed: 01/04/2023] Open
Abstract
Quantum tunnelling offers a unique opportunity to study nanoscale objects with atomic resolution using electrical readout. However, practical implementation is impeded by the lack of simple, stable probes, that are required for successful operation. Existing platforms offer low throughput and operate in a limited range of analyte concentrations, as there is no active control to transport molecules to the sensor. We report on a standalone tunnelling probe based on double-barrelled capillary nanoelectrodes that do not require a conductive substrate to operate unlike other techniques, such as scanning tunnelling microscopy. These probes can be used to efficiently operate in solution environments and detect single molecules, including mononucleotides, oligonucleotides, and proteins. The probes are simple to fabricate, exhibit remarkable stability, and can be combined with dielectrophoretic trapping, enabling active analyte transport to the tunnelling sensor. The latter allows for up to 5-orders of magnitude increase in event detection rates and sub-femtomolar sensitivity. Probes that effectively utilize quantum tunneling are sought after for high-resolution study of nanoscale objects. Here the authors present an easily fabricated probe of two nanoelectrodes that enables highly sensitive quantum-tunneling-based sensing of single molecules.
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Affiliation(s)
- Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering; International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China. .,Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK. .,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China.
| | | | - Paolo Cadinu
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Zhiyu Zhao
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Liang Xue
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Long Yi
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Ren Ren
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Jiangwei Wang
- Center of Electron Microscopy and State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - 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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Vladyka A, Albrecht T. Unsupervised classification of single-molecule data with autoencoders and transfer learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/aba6f2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Albrecht T. Single-Molecule Analysis with Solid-State Nanopores. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:371-387. [PMID: 30707594 DOI: 10.1146/annurev-anchem-061417-125903] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.
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Affiliation(s)
- Tim Albrecht
- School of Chemistry, University of Birmingham, Birmingham B15 2TT, United Kingdom;
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12
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Fu K, Han D, Ma C, Bohn PW. Electrochemistry at single molecule occupancy in nanopore-confined recessed ring-disk electrode arrays. Faraday Discuss 2018; 193:51-64. [PMID: 27711896 DOI: 10.1039/c6fd00062b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Electrochemical reactions at nanoscale structures possess unique characteristics, e.g. fast mass transport, high signal-to-noise ratio at low concentration, and insignificant ohmic losses even at low electrolyte concentrations. These properties motivate the fabrication of high density, laterally ordered arrays of nanopores, embedding vertically stacked metal-insulator-metal electrode structures and exhibiting precisely controlled pore size and interpore spacing for use in redox cycling. These nanoscale recessed ring-disk electrode (RRDE) arrays exhibit current amplification factors, AFRC, as large as 55-fold with Ru(NH3)62/3+, indicative of capture efficiencies at the top and bottom electrodes, Φt,b, exceeding 99%. Finite element simulations performed to investigate the concentration distribution of redox species and to assess operating characteristics are in excellent agreement with experiment. AFRC increases as the pore diameter, at constant pore spacing, increases in the range 200-500 nm and as the pore spacing, at constant pore diameter, decreases in the range 1000-460 nm. Optimized nanoscale RRDE arrays exhibit a linear current response with concentration ranging from 0.1 μM to 10 mM and a small capacitive current with scan rate up to 100 V s-1. At the lowest concentrations, the average pore occupancy is 〈n〉 ∼ 0.13 molecule establishing productive electrochemical signals at occupancies at and below the single molecule level in these nanoscale RRDE arrays.
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Affiliation(s)
- Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Chaoxiong Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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14
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Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution. SENSORS 2017; 17:s17040885. [PMID: 28420199 PMCID: PMC5424762 DOI: 10.3390/s17040885] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 01/22/2023]
Abstract
Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO2-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.
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15
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Carlsen AT, Briggs K, Hall AR, Tabard-Cossa V. Solid-state nanopore localization by controlled breakdown of selectively thinned membranes. NANOTECHNOLOGY 2017; 28:085304-85304. [PMID: 28045003 PMCID: PMC5408306 DOI: 10.1088/1361-6528/aa564d] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate precise positioning of nanopores fabricated by controlled breakdown (CBD) on solid-state membranes by spatially varying the electric field strength with localized membrane thinning. We show 100 × 100 nm2 precision in standard SiN x membranes (30-100 nm thick) after selective thinning by as little as 25% with a helium ion beam. Control over nanopore position is achieved through the strong dependence of the electric field-driven CBD mechanism on membrane thickness. Confinement of pore formation to the thinned region of the membrane is confirmed by TEM imaging and by analysis of DNA translocations. These results enhance the functionality of CBD as a fabrication approach and enable the production of advanced nanopore devices for single-molecule sensing applications.
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Affiliation(s)
- Autumn T. Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Adam R. Hall
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest University School of Medicine, Winston Salem, North Carolina 27101, United States
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Lemmer M, Inkpen MS, Kornysheva K, Long NJ, Albrecht T. Unsupervised vector-based classification of single-molecule charge transport data. Nat Commun 2016; 7:12922. [PMID: 27694904 PMCID: PMC5063956 DOI: 10.1038/ncomms12922] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/16/2016] [Indexed: 01/04/2023] Open
Abstract
The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. Data analysis is then guided by certain expectations, for example, a plateau feature in the tunnelling current distance trace, and the molecular conductance extracted from suitable histogram analysis. However, differences in molecular conformation or electrode contact geometry, the number of molecules in the junction or dynamic effects may lead to very different molecular signatures. Since their manifestation is a priori unknown, an unsupervised classification algorithm, making no prior assumptions regarding the data is clearly desirable. Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. We demonstrate how different event shapes are clearly separated using this algorithm and how statistics about different event classes can be extracted, when conventional methods of analysis fail.
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Affiliation(s)
- Mario Lemmer
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Michael S. Inkpen
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Katja Kornysheva
- Institute for Cognitive Neuroscience, University College London, Alexandra House, 17-19 Queen Square, London WC1N 3AR, UK
| | - Nicholas J. Long
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, Imperial College Road, London SW7 2AZ, UK
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17
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Nanopore-CMOS Interfaces for DNA Sequencing. BIOSENSORS-BASEL 2016; 6:bios6030042. [PMID: 27509529 PMCID: PMC5039661 DOI: 10.3390/bios6030042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/18/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022]
Abstract
DNA sequencers based on nanopore sensors present an opportunity for a significant break from the template-based incumbents of the last forty years. Key advantages ushered by nanopore technology include a simplified chemistry and the ability to interface to CMOS technology. The latter opportunity offers substantial promise for improvement in sequencing speed, size and cost. This paper reviews existing and emerging means of interfacing nanopores to CMOS technology with an emphasis on massively-arrayed structures. It presents this in the context of incumbent DNA sequencing techniques, reviews and quantifies nanopore characteristics and models and presents CMOS circuit methods for the amplification of low-current nanopore signals in such interfaces.
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18
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Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping. Nat Commun 2016; 7:10217. [PMID: 26732171 PMCID: PMC4729827 DOI: 10.1038/ncomms10217] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/11/2015] [Indexed: 12/16/2022] Open
Abstract
Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108–1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput. Nanopore sensors have shown tremendous potential for biomolecule sensing, though the diffusion-controlled capture can limit the speed of analysis. Here, the authors report a dielectrophoretic method to concentrate DNA near the tip of a nanopore, reducing the limit of detection by three orders of magnitude.
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19
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Cullen J, Lobo CJ, Ford MJ, Toth M. Electron-Beam-Induced Deposition as a Technique for Analysis of Precursor Molecule Diffusion Barriers and Prefactors. ACS APPLIED MATERIALS & INTERFACES 2015; 7:21408-21415. [PMID: 26340502 DOI: 10.1021/acsami.5b06341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Electron-beam-induced deposition (EBID) is a direct-write chemical vapor deposition technique in which an electron beam is used for precursor dissociation. Here we show that Arrhenius analysis of the deposition rates of nanostructures grown by EBID can be used to deduce the diffusion energies and corresponding preexponential factors of EBID precursor molecules. We explain the limitations of this approach, define growth conditions needed to minimize errors, and explain why the errors increase systematically as EBID parameters diverge from ideal growth conditions. Under suitable deposition conditions, EBID can be used as a localized technique for analysis of adsorption barriers and prefactors.
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Affiliation(s)
- Jared Cullen
- School of Mathematical and Physical Sciences, University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Charlene J Lobo
- School of Mathematical and Physical Sciences, University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Michael J Ford
- School of Mathematical and Physical Sciences, University of Technology Sydney , Ultimo, New South Wales 2007, Australia
| | - Milos Toth
- School of Mathematical and Physical Sciences, University of Technology Sydney , Ultimo, New South Wales 2007, Australia
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20
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Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, Kizek R. Fabrication of solid-state nanopores and its perspectives. Electrophoresis 2015; 36:2367-79. [DOI: 10.1002/elps.201400612] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Sylvie Skalickova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Branislav Ruttkay-Nedecky
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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Mathwig K, Albrecht T, Goluch ED, Rassaei L. Challenges of Biomolecular Detection at the Nanoscale: Nanopores and Microelectrodes. Anal Chem 2015; 87:5470-5. [DOI: 10.1021/acs.analchem.5b01167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Klaus Mathwig
- Pharmaceutical
Analysis, Groningen Research Institute of Pharmacy, University of Groningen, P.O. Box 196, 9700 AD Groningen, The Netherlands
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, Exhibition Road, South Kensington
Campus, London, SW7 2AZ, U.K
| | - Edgar D. Goluch
- Department
of Chemical Engineering, Northeastern University, 360 Huntington Avenue, 313SN, Boston, Massachusetts 02115, United States
| | - Liza Rassaei
- Department
of Chemical Engineering, Delft University of Technology, Julianalaan
136, 2628 BL Delft, The Netherlands
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22
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Rutkowska A, Freedman K, Skalkowska J, Kim MJ, Edel JB, Albrecht T. Electrodeposition and Bipolar Effects in Metallized Nanopores and Their Use in the Detection of Insulin. Anal Chem 2015; 87:2337-44. [DOI: 10.1021/ac504463r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Agnieszka Rutkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Kevin Freedman
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Justyna Skalkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Min Jun Kim
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
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23
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Crick CR, Albella P, Ng B, Ivanov AP, Roschuk T, Cecchini MP, Bresme F, Maier SA, Edel JB. Precise attoliter temperature control of nanopore sensors using a nanoplasmonic bullseye. NANO LETTERS 2015; 15:553-9. [PMID: 25467211 DOI: 10.1021/nl504536j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Targeted temperature control in nanopores is greatly important in further understanding biological molecules. Such control would extend the range of examinable molecules and facilitate advanced analysis, including the characterization of temperature-dependent molecule conformations. The work presented within details well-defined plasmonic gold bullseye and silicon nitride nanopore membranes. The bullseye nanoantennae are designed and optimized using simulations and theoretical calculations for interaction with 632.8 nm laser light. Laser heating was monitored experimentally through nanopore conductance measurements. The precise heating of nanopores is demonstrated while minimizing the accumulation of heat in the surrounding membrane material.
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Affiliation(s)
- Colin R Crick
- Department of Chemistry and ‡Department of Physics, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
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Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
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Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
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25
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Pang P, Ashcroft BA, Song W, Zhang P, Biswas S, Qing Q, Yang J, Nemanich RJ, Bai J, Smith JT, Reuter K, Balagurusamy VSK, Astier Y, Stolovitzky G, Lindsay S. Fixed-gap tunnel junction for reading DNA nucleotides. ACS NANO 2014; 8:11994-2003. [PMID: 25380505 PMCID: PMC4278685 DOI: 10.1021/nn505356g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/07/2014] [Indexed: 05/21/2023]
Abstract
Previous measurements of the electronic conductance of DNA nucleotides or amino acids have used tunnel junctions in which the gap is mechanically adjusted, such as scanning tunneling microscopes or mechanically controllable break junctions. Fixed-junction devices have, at best, detected the passage of whole DNA molecules without yielding chemical information. Here, we report on a layered tunnel junction in which the tunnel gap is defined by a dielectric layer, deposited by atomic layer deposition. Reactive ion etching is used to drill a hole through the layers so that the tunnel junction can be exposed to molecules in solution. When the metal electrodes are functionalized with recognition molecules that capture DNA nucleotides via hydrogen bonds, the identities of the individual nucleotides are revealed by characteristic features of the fluctuating tunnel current associated with single-molecule binding events.
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Affiliation(s)
- Pei Pang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Brian Alan Ashcroft
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Weisi Song
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Peiming Zhang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sovan Biswas
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Quan Qing
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Jialing Yang
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Robert J. Nemanich
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Jingwei Bai
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Joshua T. Smith
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Kathleen Reuter
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | | | - Yann Astier
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
- Address correspondence to ,
| | - Gustavo Stolovitzky
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Stuart Lindsay
- Biodesign Institute, Department of Physics, Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
- Address correspondence to ,
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26
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Affiliation(s)
- Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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27
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Larkin J, Foquet M, Turner SW, Korlach J, Wanunu M. Reversible positioning of single molecules inside zero-mode waveguides. NANO LETTERS 2014; 14:6023-9. [PMID: 25209321 PMCID: PMC4189617 DOI: 10.1021/nl503134x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/07/2014] [Indexed: 05/20/2023]
Abstract
We have developed a hybrid nanopore/zero-mode waveguide device for single-molecule fluorescence and DNA sequencing applications. The device is a freestanding solid-state membrane with sub-5 nm nanopores that reversibly delivers individual biomolecules to the base of 70 nm diameter waveguides for interrogation. Rapid and reversible molecular loading is achieved by controlling the voltage across the device. Using this device we demonstrate protein and DNA loading with efficiency that is orders of magnitude higher than diffusion-based molecular loading.
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Affiliation(s)
- Joseph Larkin
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Mathieu Foquet
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Stephen W. Turner
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Jonas Korlach
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
- E-mail: . Fax: (617) 373 2943
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28
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