1
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Shi X, Pumm AK, Maffeo C, Kohler F, Feigl E, Zhao W, Verschueren D, Golestanian R, Aksimentiev A, Dietz H, Dekker C. A DNA turbine powered by a transmembrane potential across a nanopore. NATURE NANOTECHNOLOGY 2024; 19:338-344. [PMID: 37884658 PMCID: PMC10950783 DOI: 10.1038/s41565-023-01527-8] [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: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023]
Abstract
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24-27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.
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Affiliation(s)
- Xin Shi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anna-Katharina Pumm
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching, Germany
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fabian Kohler
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Elija Feigl
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Wenxuan Zhao
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
- The SW7 Group, London, UK
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Hendrik Dietz
- Department of Bioscience, School of Natural Sciences, Technical University of Munich, Garching, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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2
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Li Y, Sandler SE, Keyser UF, Zhu J. DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals. NANO LETTERS 2023; 23:7054-7061. [PMID: 37487050 PMCID: PMC10416563 DOI: 10.1021/acs.nanolett.3c01823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Nanopores have developed into powerful single-molecule sensors capable of identifying and characterizing small polymers, such as DNA, by electrophoretically driving them through a nanoscale pore and monitoring temporary blockades in the ionic pore current. However, the relationship between nanopore signals and the physical properties of DNA remains only partly understood. Herein, we introduce a programmable DNA carrier platform to capture carefully designed DNA nanostructures. Controlled translocation experiments through our glass nanopores allowed us to disentangle this relationship. We vary DNA topology by changing the length, strand duplications, sequence, unpaired nucleotides, and rigidity of the analyte DNA and find that the ionic current drop is mainly determined by the volume and flexibility of the DNA nanostructure in the nanopore. Finally, we use our understanding of the role of DNA topology to discriminate circular single-stranded DNA molecules from linear ones with the same number of nucleotides using the nanopore signal.
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Affiliation(s)
- Yunxuan Li
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Sarah E. Sandler
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
- School
of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
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3
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Liu HL, Zhan K, Wang K, Xia XH. Nanopore-based surface-enhanced Raman scattering technologies. Sci Bull (Beijing) 2022; 67:1539-1541. [PMID: 36546279 DOI: 10.1016/j.scib.2022.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hai-Ling Liu
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kan Zhan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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4
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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5
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Fotouhi B, Faramarzi V, Ahmadi V. DNA sequencing by Förster resonant energy transfer. OPTICS EXPRESS 2022; 30:21854-21865. [PMID: 36224897 DOI: 10.1364/oe.454459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/19/2022] [Indexed: 06/16/2023]
Abstract
We propose a new DNA sequencing concept based on nonradiative Förster resonant energy transfer (FRET) from a donor quantum dot (QD) to an acceptor molecule. The FRET mechanism combined with the nanopore-based DNA translocation is suggested as a novel concept for sequencing DNA molecules. A recently-developed hybrid quantum/classical method is employed, which uses time-dependent density functional theory and quasistatic finite difference time domain calculations. Due to the significant absorbance of DNA bases for photon energies higher than 4 eV, biocompatibility, and stability, we use Zinc-Oxide (ZnO) QD as a donor in the FRET mechanism. The most sensitivity for the proposed method to DNA is achieved for the Hoechst fluorescent-dye acceptor and 1 nm ZnO-QD. Results show that the insertion of each type of DNA nucleobases between the donor and acceptor changes the frequency of the emitted light from the acceptor molecule between 0.25 to 1.6 eV. The noise analysis shows that the method can determine any unknown DNA nucleobases if the signal-to-noise ratio is larger than 5 dB. The proposed concept and excellent results shed light on a new promising class of DNA sequencers.
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6
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Fried JP, Wu Y, Tilley RD, Gooding JJ. Optical Nanopore Sensors for Quantitative Analysis. NANO LETTERS 2022; 22:869-880. [PMID: 35089719 DOI: 10.1021/acs.nanolett.1c03976] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.
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Affiliation(s)
- Jasper P Fried
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
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7
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Luo S, Hoff BH, Maier SA, de Mello JC. Scalable Fabrication of Metallic Nanogaps at the Sub-10 nm Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102756. [PMID: 34719889 PMCID: PMC8693066 DOI: 10.1002/advs.202102756] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/09/2021] [Indexed: 06/01/2023]
Abstract
Metallic nanogaps with metal-metal separations of less than 10 nm have many applications in nanoscale photonics and electronics. However, their fabrication remains a considerable challenge, especially for applications that require patterning of nanoscale features over macroscopic length-scales. Here, some of the most promising techniques for nanogap fabrication are evaluated, covering established technologies such as photolithography, electron-beam lithography (EBL), and focused ion beam (FIB) milling, plus a number of newer methods that use novel electrochemical and mechanical means to effect the patterning. The physical principles behind each method are reviewed and their strengths and limitations for nanogap patterning in terms of resolution, fidelity, speed, ease of implementation, versatility, and scalability to large substrate sizes are discussed.
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Affiliation(s)
- Sihai Luo
- Department of ChemistryNorwegian University of Science and Technology (NTNU)TrondheimNO‐7491Norway
| | - Bård H. Hoff
- Department of ChemistryNorwegian University of Science and Technology (NTNU)TrondheimNO‐7491Norway
| | - Stefan A. Maier
- Nano‐Institute MunichFaculty of PhysicsLudwig‐Maximilians‐Universität MünchenMünchen80539Germany
- Blackett LaboratoryDepartment of PhysicsImperial College LondonLondonSW7 2AZUK
| | - John C. de Mello
- Department of ChemistryNorwegian University of Science and Technology (NTNU)TrondheimNO‐7491Norway
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8
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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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9
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Shen Q, Zhou PL, Huang BT, Zhou J, Liu HL, Ahmed SA, Ding XL, Li J, Zhai YM, Wang K. Mass transport through a sub-10 nm single gold nanopore: SERS and ionic current measurement. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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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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11
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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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12
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Zhang Y, Min C, Dou X, Wang X, Urbach HP, Somekh MG, Yuan X. Plasmonic tweezers: for nanoscale optical trapping and beyond. LIGHT, SCIENCE & APPLICATIONS 2021; 10:59. [PMID: 33731693 PMCID: PMC7969631 DOI: 10.1038/s41377-021-00474-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/24/2020] [Accepted: 01/14/2021] [Indexed: 05/06/2023]
Abstract
Optical tweezers and associated manipulation tools in the far field have had a major impact on scientific and engineering research by offering precise manipulation of small objects. More recently, the possibility of performing manipulation with surface plasmons has opened opportunities not feasible with conventional far-field optical methods. The use of surface plasmon techniques enables excitation of hotspots much smaller than the free-space wavelength; with this confinement, the plasmonic field facilitates trapping of various nanostructures and materials with higher precision. The successful manipulation of small particles has fostered numerous and expanding applications. In this paper, we review the principles of and developments in plasmonic tweezers techniques, including both nanostructure-assisted platforms and structureless systems. Construction methods and evaluation criteria of the techniques are presented, aiming to provide a guide for the design and optimization of the systems. The most common novel applications of plasmonic tweezers, namely, sorting and transport, sensing and imaging, and especially those in a biological context, are critically discussed. Finally, we consider the future of the development and new potential applications of this technique and discuss prospects for its impact on science.
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Affiliation(s)
- Yuquan Zhang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Changjun Min
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
| | - Xiujie Dou
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Xianyou Wang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Hendrik Paul Urbach
- Optics Research Group, Delft University of Technology, Lorentzweg 1, 2628CJ, Delft, The Netherlands
| | - Michael G Somekh
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xiaocong Yuan
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology & Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.
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13
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Hu R, Tong X, Zhao Q. Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability. Adv Healthc Mater 2020; 9:e2000933. [PMID: 32734703 DOI: 10.1002/adhm.202000933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Xin Tong
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
- Peking University Yangtze Delta Institute of Optoelectronics Nantong Jiangsu 226010 China
- Collaborative Innovation Center of Quantum Matter Beijing 100084 China
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14
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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15
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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16
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Waugh M, Briggs K, Gunn D, Gibeault M, King S, Ingram Q, Jimenez AM, Berryman S, Lomovtsev D, Andrzejewski L, Tabard-Cossa V. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 2019; 15:122-143. [DOI: 10.1038/s41596-019-0255-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
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17
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St-Denis T, Yazda K, Capaldi X, Bustamante J, Safari M, Miyahara Y, Zhang Y, Grutter P, Reisner W. An apparatus based on an atomic force microscope for implementing tip-controlled local breakdown. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:123703. [PMID: 31893796 DOI: 10.1063/1.5129665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores are powerful tools for sensing of single biomolecules in solution. Fabrication of solid-state nanopores is still challenging, however; in particular, new methods are needed to facilitate the integration of pores with larger nanofluidic and electronic device architectures. We have developed the tip-controlled local breakdown (TCLB) approach, in which an atomic force microscope (AFM) tip is brought into contact with a silicon nitride membrane that is placed onto an electrolyte reservoir. The application of a voltage bias at the AFM tip induces a dielectric breakdown that leads to the formation of a nanopore at the tip position. In this work, we report on the details of the apparatus used to fabricate nanopores using the TCLB method, and we demonstrate the formation of nanopores with smaller, more controlled diameters using a current limiting circuit that zeroes the voltage upon pore formation. Additionally, we demonstrate the capability of TCLB to fabricate pores aligned to embedded topographical features on the membranes.
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Affiliation(s)
- T St-Denis
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - K Yazda
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - X Capaldi
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - J Bustamante
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - M Safari
- Norcada, 4548-99 Street NW, Edmonton, Alberta T6E 5H5, Canada
| | - Y Miyahara
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Y Zhang
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - P Grutter
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - W Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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18
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Garoli D, Yamazaki H, Maccaferri N, Wanunu M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. NANO LETTERS 2019; 19:7553-7562. [PMID: 31587559 DOI: 10.1021/acs.nanolett.9b02759] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia , via Morego 30 , I-16163 , Genova , Italy
| | - Hirohito Yamazaki
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Faïencerie , L-1511 Luxembourg , Luxembourg
| | - Meni Wanunu
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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19
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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20
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019; 65:69-77. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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21
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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de Vreede LJ, Ying C, Houghtaling J, Figueiredo Da Silva J, Hall AR, Lovera A, Mayer M. Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores. NANOTECHNOLOGY 2019; 30:265301. [PMID: 30849769 DOI: 10.1088/1361-6528/ab0e2a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This paper presents a maskless method to manufacture fused silica chips for low-noise resistive-pulse sensing. The fabrication includes wafer-scale density modification of fused silica with a femtosecond-pulsed laser, low-pressure chemical vapor deposition (LPVCD) of silicon nitride (SiN x ) and accelerated chemical wet etching of the laser-exposed regions. This procedure leads to a freestanding SiN x window, which is permanently attached to a fused silica support chip and the resulting chips are robust towards Piranha cleaning at ∼80 °C. After parallel chip manufacturing, we created a single nanopore in each chip by focused helium-ion beam or by controlled breakdown. Compared to silicon chips, the resulting fused silica nanopore chips resulted in a four-fold improvement of both the signal-to-noise ratio and the capture rate for signals from the translocation of IgG1 proteins at a recording bandwidth of 50 kHz. At a bandwidth of ∼1 MHz, the noise from the fused silica nanopore chips was three- to six-fold reduced compared to silicon chips. In contrast to silicon chips, fused silica chips showed no laser-induced current noise-a significant benefit for experiments that strive to combine nanopore-based electrical and optical measurements.
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Affiliation(s)
- Lennart J de Vreede
- Biophysics group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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23
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Spitzberg JD, Zrehen A, van Kooten XF, Meller A. Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1900422. [PMID: 30941823 DOI: 10.1002/adma.201900422] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/19/2019] [Indexed: 05/26/2023]
Abstract
Plasmonic and nanopore sensors have separately received much attention for achieving single-molecule precision. A plasmonic "hotspot" confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface-analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular-scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid-state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single-molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single-molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid-state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.
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Affiliation(s)
- Joshua D Spitzberg
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | - Adam Zrehen
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | | | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
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24
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Ravindranath AL, Shariatdoust MS, Mathew S, Gordon R. Colloidal lithography double-nanohole optical trapping of nanoparticles and proteins. OPTICS EXPRESS 2019; 27:16184-16194. [PMID: 31163802 DOI: 10.1364/oe.27.016184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Double-nanoholes fabricated by colloidal lithography were used for trapping single colloidal particles and single proteins. A gap separation of 60 nm between the cusps of the double-nanohole was achieved in a gold film of 70 nm thickness sputter coated onglass. The cusp separation was reduced steadily down to 10 nm by plasma etching the colloidal particles prior to sputter coating. Scanning electron microscopy was used to locate a particular double-nanohole and it was registered for later microscopy experiments. 30 nm polystyrene particles, the rubisco protein and bovine serum albumin were trapped using a laser focused through the aperture. Compared to other methods that require top-down nanofabrication, this approach is inexpensive and produces high-quality samples.
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25
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Faramarzi V, Ahmadi V, Fotouhi B, Abasifard M. A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS 2 Nanopores. Sci Rep 2019; 9:6230. [PMID: 30996229 PMCID: PMC6470134 DOI: 10.1038/s41598-019-41165-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 03/01/2019] [Indexed: 11/09/2022] Open
Abstract
We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or MoS2 nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.
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Affiliation(s)
- Vahid Faramarzi
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, P. O. Box 14115-194, Tehran, 1411713116, Iran
| | - Vahid Ahmadi
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, P. O. Box 14115-194, Tehran, 1411713116, Iran.
| | - Bashir Fotouhi
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, P. O. Box 14115-194, Tehran, 1411713116, Iran
| | - Mostafa Abasifard
- Faculty of Electrical and Computer Engineering, Tarbiat Modares University, P. O. Box 14115-194, Tehran, 1411713116, Iran
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26
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Roshan KA, Tang Z, Guan W. High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore. NANOTECHNOLOGY 2019; 30:095502. [PMID: 30523901 DOI: 10.1088/1361-6528/aaf48e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigate the current transport characteristics in the electrolyte-dielectric-electrolyte structure commonly used in the in situ controlled breakdown (CBD) fabrication of solid-state nanopores. It is found that the stochastic breakdown process could lead to fidelity issues of false positives (an incorrect indication of a true nanopore formation) and false negatives (inability to detect initial nanopore formation). Robust and deterministic detection of initial physical breakdown to alleviate false positives and false negatives is critical for precise nanopore size control. To this end, we report a high fidelity moving Z-score method based CBD fabrication of solid-state nanopore. We demonstrate 100% success rate of realizing the initial nanopore conductance of 3 ± 1 nS (corresponds to size of 1.7 ± 0.6 nm) regardless of the dielectric membrane characteristics. Our study also elucidates the Joule heating is the dominant mechanism for electric field-based nanopore enlargement. Single DNA molecule sensing using nanopores fabricated by this method was successfully demonstrated. We anticipate the moving Z-score based CBD method could enable broader access to the solid state nanopore-based single molecule analysis.
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Affiliation(s)
- Kamyar Akbari Roshan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, United States of America
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27
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Yamazaki H, Hu R, Zhao Q, Wanunu M. Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores. ACS NANO 2018; 12:12472-12481. [PMID: 30457833 DOI: 10.1021/acsnano.8b06805] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sculpting solid-state materials at the nanoscale is an important step in the manufacturing of numerous types of sensor devices, in particular solid-state nanopore sensors. Here we present mechanistic insight into laser-induced thinning of low-stress silicon nitride (SiN x) membranes and films. In a recent study, we observed that focusing a visible wavelength laser beam on a SiN x membrane results in efficient localized heating, and we used this effect to control temperature at a solid-state nanopore sensor. A side-effect of the observed heating was that the pores expand/degrade under prolonged high-power illumination, prompting us to study the mechanism of this etching process. We find that SiN x can be etched under exposure to light of ∼107 W/cm2 average intensity, with etch rates that are influenced by the supporting electrolyte. Combining this controlled etching with dielectric breakdown, an electrokinetic process for making pores, nanopores of arbitrary dimensions as small as 1-2 nm in diameter and thickness can easily be fabricated. Evidence gathered from biomolecule-pore interactions suggests that the pore geometries obtained using this method are more funnel-like, rather than hourglass-shaped. Refined control over pore dimensions can expand the range of applications of solid-state nanopores, for example, biopolymer sequencing and detection of specific biomarkers.
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Affiliation(s)
- Hirohito Yamazaki
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Meni Wanunu
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
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28
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He F, Liang L, Zhou S, Xie W, He S, Wang Y, Tlili C, Tong S, Wang D. Label-Free Sensitive Detection of Microcystin-LR via Aptamer-Conjugated Gold Nanoparticles Based on Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14825-14833. [PMID: 30021440 DOI: 10.1021/acs.langmuir.8b00945] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A versatile and highly sensitive strategy for nanopore detection of microcystin-LR (MC-LR) is proposed herein based on the aptamer and host-guest interactions by employing a gold nanoparticle (AuNP) probe. The aptamer of MC-LR and its complementary DNA (cDNA) are respectively immobilized on AuNPs with distinct sizes (5 nm AuNPs for the aptamer and 20 nm for the cDNA), and the constructed polymeric AuNP network via the hybridization of the aptamer and cDNA was disintegrated upon the addition of MC-LR. The specific interactions between the aptamer and MC-LR disrupt and release the cDNA-AuNPs that were then removed by centrifugation, leaving the MC-LR-aptamer-AuNP species in the supernatant for subsequent nanopore determination. By monitoring the current blockade of released MC-LR-aptamer-AuNPs using a specific tailored nanopore (10 and 20 nm in diameter, generated by current dielectric breakdown), we could deduce the presence of MC-LR, as the bulky NP network could not pass through a nanopore with a relatively smaller size. We realized the detection of MC-LR with a concentration as low as 0.1 nM; additionally, we have proved the specificity of the interaction between the aptamer and MC-LR by replacing MC-LR with other congener toxins (MC-RR and MC-YR), chlorophyll (a component abundantly coexists in water), and the mixture of the four.
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Affiliation(s)
- Feng He
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shuo Zhou
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Chaker Tlili
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shoufeng Tong
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
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29
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Ying C, Houghtaling J, Eggenberger OM, Guha A, Nirmalraj P, Awasthi S, Tian J, Mayer M. Formation of Single Nanopores with Diameters of 20-50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown. ACS NANO 2018; 12:11458-11470. [PMID: 30335956 DOI: 10.1021/acsnano.8b06489] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanopores with diameters from 20 to 50 nm in silicon nitride (SiN x) windows are useful for single-molecule studies of globular macromolecules. While controlled breakdown (CBD) is gaining popularity as a method for fabricating nanopores with reproducible size control and broad accessibility, attempts to fabricate large nanopores with diameters exceeding ∼20 nm via breakdown often result in undesirable formation of multiple nanopores in SiN x membranes. To reduce the probability of producing multiple pores, we combined two strategies: laser-assisted breakdown and controlled pore enlargement by limiting the applied voltage. Based on laser power-dependent increases in nanopore conductance upon illumination and on the absence of an effect of ionic strength on the ratio between the nanopore conductance before and after laser illumination, we suggest that the increased rate of controlled breakdown results from laser-induced heating. Moreover, we demonstrate that conductance values before and after coating the nanopores with a fluid lipid bilayer can indicate fabrication of a single nanopore versus multiple nanopores. Complementary flux measurements of Ca2+ through the nanopore typically confirmed assessments of single or multiple nanopores that we obtained using the coating method. Finally, we show that thermal annealing of CBD pores significantly increased the success rate of coating and reduced the current noise before and after lipid coating. We characterize the geometry of these nanopores by analyzing individual resistive pulses produced by translocations of spherical proteins and demonstrate the usefulness of these nanopores for estimating the approximate molecular shape of IgG proteins.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jared Houghtaling
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
- Department of Biomedical Engineering , University of Michigan , 2200 Bonisteel Boulevard , Ann Arbor , Michigan 48109 , United States
| | - Olivia M Eggenberger
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Anirvan Guha
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Peter Nirmalraj
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Saurabh Awasthi
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics , Nankai University , Tianjin 300071 , China
| | - Michael Mayer
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
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30
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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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Optically-Monitored Nanopore Fabrication Using a Focused Laser Beam. Sci Rep 2018; 8:9765. [PMID: 29950607 PMCID: PMC6021433 DOI: 10.1038/s41598-018-28136-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/18/2018] [Indexed: 12/25/2022] Open
Abstract
Solid-state nanopores (ssNPs) are extremely versatile single-molecule sensors and their potential have been established in numerous biomedical applications. However, the fabrication of ssNPs remains the main bottleneck to their widespread use. Herein, we introduce a rapid and localizable ssNPs fabrication method based on feedback-controlled optical etching. We show that a focused blue laser beam irreversibly etches silicon nitride (SiNx) membranes in solution. Furthermore, photoluminescence (PL) emitted from the SiNx is used to monitor the etching process in real-time, hence permitting rate adjustment. Transmission electron microscopy (TEM) images of the etched area reveal an inverted Gaussian thickness profile, corresponding to the intensity point spread function of the laser beam. Continued laser exposure leads to the opening of a nanopore, which can be controlled to reproducibly fabricate nanopores of different sizes. The optically-formed ssNPs exhibit electrical noise on par with TEM-drilled pores, and translocate DNA and proteins readily. Notably, due to the localized thinning, the laser-drilled ssNPs exhibit highly suppressed background PL and improved spatial resolution. Given the total control over the nanopore position, this easily implemented method is ideally suited for electro-optical sensing and opens up the possibility of fabricating large nanopore arrays in situ.
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Yun J, Cho YB, Jang W, Lee JG, Shin SJ, Han SH, Lee Y, Chung TD. Dielectric Breakdown and Post-Breakdown Dissolution of Si/SiO 2 Cathodes in Acidic Aqueous Electrochemical Environment. Sci Rep 2018; 8:1911. [PMID: 29382915 PMCID: PMC5789982 DOI: 10.1038/s41598-018-20247-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/10/2018] [Indexed: 11/17/2022] Open
Abstract
Understanding the conducting mechanisms of dielectric materials under various conditions is of increasing importance. Here, we report the dielectric breakdown (DB) and post-breakdown mechanism of Si/SiO2, a widely used semiconductor and dielectric, in an acidic aqueous electrochemical environment. Cathodic breakdown was found to generate conduction spots on the Si/SiO2 surface. Using scanning electrochemical microscopy (SECM), the size and number of conduction spots are confirmed to increase from nanometer to micrometer scale during the application of negative voltage. The morphologies of these conduction spots reveal locally recessed inverted-pyramidal structures with exposed Si{111} sidewalls. The pits generation preceded by DB is considered to occur via cathodic dissolution of Si and exfoliation of SiO2 that are induced by local pH increases due to the hydrogen evolution reaction (HER) at the conduction spots. The HER at the conduction spots is more sluggish due to strongly hydrogen-terminated Si{111} surfaces.
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Affiliation(s)
- Jeongse Yun
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yun-Bin Cho
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Woohyuk Jang
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Gyeong Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Samuel Jaeho Shin
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seok Hee Han
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Youngmi Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Republic of Korea.
| | - Taek Dong Chung
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea. .,Advanced Institutes of Convergence Technology, Suwon-si, Gyeonggi-do, 16229, Republic of Korea.
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Fabrication of multiple nanopores in a SiN x membrane via controlled breakdown. Sci Rep 2018; 8:1234. [PMID: 29352158 PMCID: PMC5775244 DOI: 10.1038/s41598-018-19450-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022] Open
Abstract
This paper reports a controlled breakdown (CBD) method to fabricate multiple nanopores in a silicon nitride (SiNx) membrane with control over both nanopore count and nanopore diameter. Despite the stochastic process of the breakdown, we found that the nanopores created via CBD, tend to be of the same diameter. We propose a membrane resistance model to explain and control the multiple nanopores forming in the membrane. We prove that the membrane resistance can reflect the number of nanopores in the membrane and that the diameter of the nanopores is controlled by the exposure time and strength of the electric field. This controllable multiple nanopore formation via CBD avoids the utilization of complicated instruments and time-intensive manufacturing. We anticipate CBD has the potential to become a nanopore fabrication technique which, integrated into an optical setup, could be used as a high-throughput and multichannel characterization technique.
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Roelen Z, Bustamante JA, Carlsen A, Baker-Murray A, Tabard-Cossa V. Instrumentation for low noise nanopore-based ionic current recording under laser illumination. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:015007. [PMID: 29390667 DOI: 10.1063/1.5006262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiNx membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ∼10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - José A Bustamante
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Aidan Baker-Murray
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Zrehen A, Gilboa T, Meller A. Real-time visualization and sub-diffraction limit localization of nanometer-scale pore formation by dielectric breakdown. NANOSCALE 2017; 9:16437-16445. [PMID: 29058736 DOI: 10.1039/c7nr02629c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Herein, we introduce synchronous, real-time, electro-optical monitoring of nanopore formation by DB. Using the same principle as sub-diffraction microscopy, our nanopore localization platform based on wide-field microscopy and calcium indicators provides nanoscale sensitivity. This enables us to establish critical limitations of the fabrication process and improve its reliability. In particular, we find that under certain conditions, multiple nanopores may form and that nanopores may preferentially localize at the membrane junction, either of which potentially render nanopore sensing ineffective. As the breakdown parameters of silicon materials are highly manufacturer-specific, we anticipate that our visualization platform will enable users to easily optimize DB fabrication according to specific needs. Furthermore, our technique furthers the applicability of DB to more complicated architectures, such as membranes with selectively thinned regions and plasmonic nanowells.
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Affiliation(s)
- Adam Zrehen
- Department of Biomedical Engineering, The Technion - Israel Institute of Technology, Haifa, 32000, Israel.
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Yin B, Xie W, Liang L, Deng Y, He S, He F, Zhou D, Tlili C, Wang D. Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection. ACS OMEGA 2017; 2:7127-7135. [PMID: 31457292 PMCID: PMC6645049 DOI: 10.1021/acsomega.7b01245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/06/2017] [Indexed: 05/11/2023]
Abstract
In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.
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Arcadia CE, Reyes CC, Rosenstein JK. In Situ Nanopore Fabrication and Single-Molecule Sensing with Microscale Liquid Contacts. ACS NANO 2017; 11:4907-4915. [PMID: 28485922 DOI: 10.1021/acsnano.7b01519] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In this article, we introduce a flexible technique for high-throughput solid-state nanopore analysis of single biomolecules. By confining the electrolyte to a micron-scale liquid meniscus at the tip of a glass micropipette, we enable automation and reuse of a single solid-state membrane chip for measurements with hundreds of distinct nanopores per day. In addition to overcoming important experimental bottlenecks, the microscale liquid contact dramatically reduces device capacitance, which is a key limiting factor to the speed and fidelity of solid-state nanopore sensor recordings.
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Affiliation(s)
- Christopher E Arcadia
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| | - Carlos C Reyes
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| | - Jacob K Rosenstein
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
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39
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Optical trapping-assisted SERS platform for chemical and biosensing applications: Design perspectives. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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42
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Li Y, Chen C, Willems K, Lagae L, Groeseneken G, Stakenborg T, Van Dorpe P. Asymmetric plasmonic induced ionic noise in metallic nanopores. NANOSCALE 2016; 8:12324-12329. [PMID: 27273622 DOI: 10.1039/c6nr01837h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present distinct asymmetric plasmon-induced noise properties of ionic transport observed through gold coated nanopores. We thoroughly investigated the effects of bias voltage and laser illumination. We show that the potential drop across top-coated silicon nanocavity pores can give rise to a large noise asymmetry (∼2-3 orders of magnitude). Varying the bias voltage has an appreciable effect on the noise density spectra, typically in the Lorentzian components. The laser power is found to strongly affect the ionic noise level as well as the voltage threshold for light-induced noise generation. The asymmetric noise phenomenon is attributed to plasmon-induced interfacial reactions which promote light-induced charge fluctuation in the ion flow and allow voltage modulation of photo-induced carriers surmounting over such Schottky junctions. We further compare the ionic noise performances of gold nanocavities containing different material stacks, among which thermal oxide passivation of the silicon successfully mitigates the light-induced noise and is also fully CMOS-compatible. The understanding of the described noise characteristics will help to foster multiple applications using related structures including plasmonic-based sensing or plasmon-induced catalysis such as water splitting or solar energy conversion devices.
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Affiliation(s)
- Yi Li
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Chang Chen
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Kherim Willems
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Liesbet Lagae
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Guido Groeseneken
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | | | - Pol Van Dorpe
- IMEC, Kapeldreef 75, Leuven, B3001, Belgium. and Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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Affiliation(s)
- Stephen M. Oja
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Yunshan Fan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Chadd M. Armstrong
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Peter Defnet
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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