1
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Wang Y, Yu Z, Smith CS, Caneva S. Site-Specific Integration of Hexagonal Boron Nitride Quantum Emitters on 2D DNA Origami Nanopores. NANO LETTERS 2024; 24:8510-8517. [PMID: 38856705 PMCID: PMC11261624 DOI: 10.1021/acs.nanolett.4c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Optical emitters in hexagonal boron nitride (hBN) are promising probes for single-molecule sensing platforms. When engineered in nanoparticle form, they can be integrated as detectors in nanodevices, yet positional control at the nanoscale is lacking. Here we demonstrate the functionalization of DNA origami nanopores with optically active hBN nanoparticles (NPs) with nanometer precision. The NPs are active under three wavelengths of visible illumination and display both stable and blinking emission, enabling their accurate localization by using wide-field optical nanoscopy. Correlative opto-structural characterization reveals deterministic binding of bright, multicolor hBN NPs at the pore rim due to π-π stacking interactions at site-specific locations on the DNA origami. Our work provides a scalable, bottom-up approach toward deterministic assembly of solid-state emitters on arbitrary structural elements based on DNA origami. Such a nanoscale arrangement of optically active components can advance the development of single-molecule platforms, including optical nanopores and nanochannel sensors.
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Affiliation(s)
- Yabin Wang
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
- Delft
Center for Systems and Control, Delft University
of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - Ze Yu
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
| | - Carlas S. Smith
- Delft
Center for Systems and Control, Delft University
of Technology, Mekelweg 2, 2628 CD Delft, Netherlands
| | - Sabina Caneva
- Department
of Precision and Microsystems Engineering, Delft University of Technology, Mekelweg 2, 2628
CD, Delft, The Netherlands
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2
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Morder CJ, Schorr HC, Balss KM, Schultz ZD. Bleach Cleaning of Commercially Available Gold Nanopillar Arrays for Surface-Enhanced Raman Spectroscopy (SERS). APPLIED SPECTROSCOPY 2024; 78:268-276. [PMID: 38112337 PMCID: PMC10921819 DOI: 10.1177/00037028231219721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is a highly sensitive technique that can assist in trace analysis for biomedical, diagnostic, and environmental applications. However, a major limitation of SERS is surface contamination of the substrates used, which can complicate the spectral reproducibility, limits of detection, and detection of unknown analytes. This is especially prevalent with commercially available substrates as shipping under a controlled and clean environment is difficult. Here we report a method using dilute bleach solutions to remove surface contamination from commercially available substrates consisting of gold-coated nanopillar arrays that maintains functionality. The results show that this method can be used to remove background signals associated with typical surface contamination in commercially available substrates as well as remove thiolated self-assembled monolayers (SAMs). Results indicate the bleach oxidizes the surface contaminants, which can then be easily washed away. Although the metallic surface also becomes oxidized in this process, the surface can be reduced without loss of SERS activity. The SERS intensity of SAMs improved following bleach treatment across all concentrations studied.
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Affiliation(s)
- Courtney J. Morder
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
| | - Hannah C. Schorr
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
| | - Karin M. Balss
- Emerging Technologies, Manufacturing Science and Technology, Janssen Supply Chain, Spring House, PA 19477, USA
| | - Zachary D. Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
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3
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Hagan JT, Gonzalez A, Shi Y, Han GGD, Dwyer JR. Photoswitchable Binary Nanopore Conductance and Selective Electronic Detection of Single Biomolecules under Wavelength and Voltage Polarity Control. ACS NANO 2022; 16:5537-5544. [PMID: 35286058 DOI: 10.1021/acsnano.1c10039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We fabricated photoregulated thin-film nanopores by covalently linking azobenzene photoswitches to silicon nitride pores with ∼10 nm diameters. The photoresponsive coatings could be repeatedly optically switched with deterministic ∼6 nm changes to the effective nanopore diameter and of ∼3× to the nanopore ionic conductance. The sensitivity to anionic DNA and a neutral complex carbohydrate biopolymer (maltodextrin) could be photoswitched "on" and "off" with an analyte selectivity set by applied voltage polarity. Photocontrol of nanopore state and mass transport characteristics is important for their use as ionic circuit elements (e.g., resistors and binary bits) and as chemically tuned filters. It expands single-molecule sensing capabilities in personalized medicine, genomics, glycomics, and, augmented by voltage polarity selectivity, especially in multiplexed biopolymer information storage schemes. We demonstrate repeatedly photocontrolled stable nanopore size, polarity, conductance, and sensing selectivity, by illumination wavelength and voltage polarity, with broad utility including single-molecule sensing of biologically and technologically important polymers.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Alejandra Gonzalez
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Yuran Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Grace G D Han
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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4
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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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5
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Zhang D, Zhang X. Bioinspired Solid-State Nanochannel Sensors: From Ionic Current Signals, Current, and Fluorescence Dual Signals to Faraday Current Signals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100495. [PMID: 34117705 DOI: 10.1002/smll.202100495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Inspired from bioprotein channels of living organisms, constructing "abiotic" analogues, solid-state nanochannels, to achieve "smart" sensing towards various targets, is highly seductive. When encountered with certain stimuli, dynamic switch of terminal modified probes in terms of surface charge, conformation, fluorescence property, electric potential as well as wettability can be monitored via transmembrane ionic current, fluorescence intensity, faraday current signals of nanochannels and so on. Herein, the modification methodologies of nanochannels and targets-detecting application are summarized in ions, small molecules, as well as biomolecules, and systematically reviewed are the nanochannel-based detection means including 1) by transmembrane current signals; 2) by the coordination of current- and fluorescence-dual signals; 3) by faraday current signals from nanochannel-based electrode. The coordination of current and fluorescence dual signals offers great benefits for synchronous temporal and spatial monitoring. Faraday signals enable the nanoelectrode to monitor both redox and non-redox components. Notably, by incorporation with confined effect of tip region of a needle-like nanopipette, glorious in-vivo monitoring is conferred on the nanopipette detector at high temporal-spatial resolution. In addition, some outlooks for future application in reliable practical samples analysis and leading research endeavors in the related fantastic fields are provided.
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Affiliation(s)
- Dan Zhang
- Cancer Centre and Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
| | - Xuanjun Zhang
- Cancer Centre and Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, SAR, 999078, China
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6
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Smolyanitsky A, Luant B. Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport. PHYSICAL REVIEW LETTERS 2021; 127:138103. [PMID: 34623840 PMCID: PMC10932591 DOI: 10.1103/physrevlett.127.138103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that ssDNA transport through a pore in monolayer hexagonal boron nitride (h-BN) is marked by a basic nanomechanical conflict. It arises from the notably inhomogeneous flexural rigidity of ssDNA and causes high friction via transient DNA desorption costs exacerbated by solvation effects. For a similarly sized pore in bilayer h-BN, its self-passivated atomically smooth edge enables continuous ssDNA transport. Our findings shed light on the fundamental physics of biopolymer transport through pores in 2D materials.
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Affiliation(s)
- Alex Smolyanitsky
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado 80305, USA
| | - Binquan Luant
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
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7
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Li S, Zeng S, Wen C, Barbe L, Tenje M, Zhang Z, Hjort K, Zhang SL. Dynamics of DNA Clogging in Hafnium Oxide Nanopores. J Phys Chem B 2020; 124:11573-11583. [PMID: 33315405 PMCID: PMC7770817 DOI: 10.1021/acs.jpcb.0c07756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Interfacing
solid-state nanopores with biological systems has been
exploited as a versatile analytical platform for analysis of individual
biomolecules. Although clogging of solid-state nanopores due to nonspecific
interactions between analytes and pore walls poses a persistent challenge
in attaining the anticipated sensing efficacy, insufficient studies
focus on elucidating the clogging dynamics. Herein, we investigate
the DNA clogging behavior by passing double-stranded (ds) DNA molecules
of different lengths through hafnium oxide(HfO2)-coated
silicon (Si) nanopore arrays, at different bias voltages and electrolyte
pH values. Employing stable and photoluminescent-free HfO2/Si nanopore arrays permits a parallelized visualization of DNA clogging
with confocal fluorescence microscopy. We find that the probability
of pore clogging increases with both DNA length and bias voltage.
Two types of clogging are discerned: persistent and temporary. In
the time-resolved analysis, temporary clogging events exhibit a shorter
lifetime at higher bias voltage. Furthermore, we show that the surface
charge density has a prominent effect on the clogging probability
because of electrostatic attraction between the dsDNA and the HfO2 pore walls. An analytical model based on examining the energy
landscape along the DNA translocation trajectory is developed to qualitatively
evaluate the DNA–pore interaction. Both experimental and theoretical
results indicate that the occurrence of clogging is strongly dependent
on the configuration of translocating DNA molecules and the electrostatic
interaction between DNA and charged pore surface. These findings provide
a detailed account of the DNA clogging phenomenon and are of practical
interest for DNA sensing based on solid-state nanopores.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Laurent Barbe
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Maria Tenje
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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8
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D Y Bandara YMN, Saharia J, Karawdeniya BI, Hagan JT, Dwyer JR, Kim MJ. Beyond nanopore sizing: improving solid-state single-molecule sensing performance, lifetime, and analyte scope for omics by targeting surface chemistry during fabrication. NANOTECHNOLOGY 2020; 31:335707. [PMID: 32357346 DOI: 10.1088/1361-6528/ab8f4d] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Solid-state nanopores (SSNs) are single-molecule resolution sensors with a growing footprint in real-time bio-polymer profiling-most prominently, but far from exclusively, DNA sequencing. SSNs accessibility has increased with the advent of controlled dielectric breakdown (CDB), but severe fundamental challenges remain: drifts in open-pore current and (irreversible) analyte sticking. These behaviors impede basic research and device development for commercial applications and can be dramatically exacerbated by the chemical complexity and physical property diversity of different analytes. We demonstrate a SSN fabrication approach attentive to nanopore surface chemistry during pore formation, and thus create nanopores in silicon nitride (SiNx) capable of sensing a wide analyte scope-nucleic acid (double-stranded DNA), protein (holo-human serum transferrin) and glycan (maltodextrin). In contrast to SiNx pores fabricated without this comprehensive approach, the pores are Ohmic in electrolyte, have extremely stable open-pore current during analyte translocation (>1 h) over a broad range of pore diameters ([Formula: see text]3- ∼30 nm) with spontaneous current correction (if current deviation occurs), and higher responsiveness (i.e. inter-event frequency) to negatively charged analytes (∼6.5 × in case of DNA). These pores were fabricated by modifying CDB with a chemical additive-sodium hypochlorite-that resulted in dramatically different nanopore surface chemistry including ∼3 orders of magnitude weaker Ka (acid dissociation constant of the surface chargeable head-groups) compared to CDB pores which is inextricably linked with significant improvements in nanopore performance with respect to CDB pores.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75275, United States of America
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9
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Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
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10
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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11
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Taniguchi M. Analysis Method of the Ion Current-Time Waveform Obtained from Low Aspect Ratio Solid-state Nanopores. ANAL SCI 2020; 36:161-165. [PMID: 31813895 DOI: 10.2116/analsci.19r009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Low aspect ratio nanopores are expected to be applied to the detection of viruses and bacteria because of their high spatial resolution. Multiphysics simulations have revealed that the ion current-time waveform obtained from low aspect ratio nanopores contains information on not only the volume of viruses and bacteria, but also the structure, surface charge, and flow dynamics. Analysis using machine learning extracts information about these analytes from the ion current-time waveform. The combination of low aspect ratio nanopores, multiphysics simulation, and machine learning has made it possible to distinguish different types of viruses and bacteria with high accuracy.
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12
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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13
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Charron M, Briggs K, King S, Waugh M, Tabard-Cossa V. Precise DNA Concentration Measurements with Nanopores by Controlled Counting. Anal Chem 2019; 91:12228-12237. [DOI: 10.1021/acs.analchem.9b01900] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Martin Charron
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Kyle Briggs
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Simon King
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew Waugh
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Vincent Tabard-Cossa
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
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14
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Nouri R, Tang Z, Guan W. Calibration-Free Nanopore Digital Counting of Single Molecules. Anal Chem 2019; 91:11178-11184. [DOI: 10.1021/acs.analchem.9b01924] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zifan Tang
- 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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15
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Kubota T, Lloyd K, Sakashita N, Minato S, Ishida K, Mitsui T. Clog and Release, and Reverse Motions of DNA in a Nanopore. Polymers (Basel) 2019; 11:polym11010084. [PMID: 30960068 PMCID: PMC6401990 DOI: 10.3390/polym11010084] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/28/2018] [Accepted: 01/03/2019] [Indexed: 01/29/2023] Open
Abstract
Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations.
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Affiliation(s)
- Tomoya Kubota
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
| | - Kento Lloyd
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
| | - Naoto Sakashita
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
| | - Seiya Minato
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
| | - Kentaro Ishida
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
| | - Toshiyuki Mitsui
- Department of Mathematics and Physics, Aoyama-Gakuin University, Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan.
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16
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Yamazaki H, Mizuguchi T, Esashika K, Saiki T. Electro-osmotic trapping and compression of single DNA molecules while passing through a nanopore. Analyst 2019; 144:5381-5388. [DOI: 10.1039/c9an01253b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complicated DNA molecular behaviors exist during translocation into a nanopore because their large and coiled structure needs to unwind.
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Affiliation(s)
- Hirohito Yamazaki
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Takaha Mizuguchi
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Keiko Esashika
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Toshiharu Saiki
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
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17
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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18
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Kato Y, Sakashita N, Ishida K, Mitsui T. Gate-Voltage-Controlled Threading DNA into Transistor Nanopores. J Phys Chem B 2018; 122:827-833. [PMID: 28893067 DOI: 10.1021/acs.jpcb.7b06932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a simple method for DNA translocation driven by applying AC voltages, such as square and sawtooth waves, on an embedded thin film as a gate electrode inside of a dielectric nanopore, without applying a conventional bias voltage externally across the pore membrane. Square waveforms on a gate can drive a single DNA molecule into a nanopore, which often returns from the pore, causing an oscillation across the membrane. An optimized sawtooth-like negative voltage pulse on the gate can thread a fraction of a DNA molecule into a pore after a single pulse. This trapped DNA molecule continues to finish its translocation slowly through the pore. The DNA's slow speed was comparable to previous findings of the escaping DNA speed from a nanopore estimated by the Smoluchowski equation with excluded-volume interactions of a long-chain molecule and electrophoresis by extremely low electric fields. This simple scheme, controlling DNA molecules only by gate potential modulation at a nanopore, will provide an additional method to thread, translocate, or oscillate a single biomolecule at a gated nanopore.
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Affiliation(s)
- Yuta Kato
- Aoyama-Gakuin University , Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan
| | - Naoto Sakashita
- Aoyama-Gakuin University , Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan
| | - Kentaro Ishida
- Aoyama-Gakuin University , Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan
| | - Toshiyuki Mitsui
- Aoyama-Gakuin University , Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5258, Japan
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19
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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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20
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Plesa C, Verschueren D, Pud S, van der Torre J, Ruitenberg JW, Witteveen MJ, Jonsson MP, Grosberg AY, Rabin Y, Dekker C. Direct observation of DNA knots using a solid-state nanopore. NATURE NANOTECHNOLOGY 2016; 11:1093-1097. [PMID: 27525473 DOI: 10.1038/nnano.2016.153] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 07/14/2016] [Indexed: 05/19/2023]
Abstract
Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).
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Affiliation(s)
- Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sergii Pud
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Justus W Ruitenberg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Menno J Witteveen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Magnus P Jonsson
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Alexander Y Grosberg
- Department of Physics and Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA
| | - Yitzhak Rabin
- Department of Physics and Institute for Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 52900, Israel
| | - 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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21
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Shi X, Gao R, Ying YL, Si W, Chen YF, Long YT. A Scattering Nanopore for Single Nanoentity Sensing. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00408] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shi
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Wei Si
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - Yun-Fei Chen
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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22
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Di Ventra M, Taniguchi M. Decoding DNA, RNA and peptides with quantum tunnelling. NATURE NANOTECHNOLOGY 2016; 11:117-26. [PMID: 26839257 DOI: 10.1038/nnano.2015.320] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 12/07/2015] [Indexed: 05/25/2023]
Abstract
Drugs and treatments could be precisely tailored to an individual patient by extracting their cellular- and molecular-level information. For this approach to be feasible on a global scale, however, information on complete genomes (DNA), transcriptomes (RNA) and proteomes (all proteins) needs to be obtained quickly and at low cost. Quantum mechanical phenomena could potentially be of value here, because the biological information needs to be decoded at an atomic level and quantum tunnelling has recently been shown to be able to differentiate single nucleobases and amino acids in short sequences. Here, we review the different approaches to using quantum tunnelling for sequencing, highlighting the theoretical background to the method and the experimental capabilities demonstrated to date. We also explore the potential advantages of the approach and the technical challenges that must be addressed to deliver practical quantum sequencing devices.
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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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23
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Xu X, Hou R, Gao P, Miao M, Lou X, Liu B, Xia F. Highly Robust Nanopore-Based Dual-Signal-Output Ion Detection System for Achieving Three Successive Calibration Curves. Anal Chem 2016; 88:2386-91. [DOI: 10.1021/acs.analchem.5b04388] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xuemei Xu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ruizuo Hou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengcheng Gao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mao Miao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoding Lou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bifeng Liu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fan Xia
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
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24
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Liang L, Shen JW, Zhang Z, Wang Q. DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments. Biosens Bioelectron 2015; 89:280-292. [PMID: 26711358 DOI: 10.1016/j.bios.2015.12.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, two-dimensional (2D) materials (mainly including graphene, boron nitride, MoS2 etc.) have stimulated exploding interests in sensor applications. 2D-material based nanoscale DNA sequencing is a single-molecule technique with revolutionary potential. In this paper, we review the methodology of DNA sequencing based on the measurements of ionic current, force peak, and transverse electrical currents etc. by 2D materials. The advantages and disadvantages of DNA sequencing by 2D materials are discussed. Besides the recent development of experiments, we will focus on the theoretical calculations of DNA sequencing, which have been played a critical role in the development of this field. Special emphasis will focus on the disagreements between experiments and theoretical calculations, and the explanations for the discrepancy will be highlighted. Finally, some new plausible sequencing methods from computational studies will be discussed, which may be applied in the realistic DNA sequencing experiments in future.
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Affiliation(s)
- Lijun Liang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Zhisen Zhang
- Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, Xiamen 361005, People' s Republic of China
| | - Qi Wang
- Department of Chemistry and §Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China
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25
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Pud S, Verschueren D, Vukovic N, Plesa C, Jonsson MP, Dekker C. Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown. NANO LETTERS 2015; 15:7112-7. [PMID: 26333767 PMCID: PMC4859154 DOI: 10.1021/acs.nanolett.5b03239] [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: 05/07/2023]
Abstract
We present a novel cost-efficient method for the fabrication of high-quality self-aligned plasmonic nanopores by means of an optically controlled dielectric breakdown. Excitation of a plasmonic bowtie nanoantenna on a dielectric membrane localizes the high-voltage-driven breakdown of the membrane to the hotspot of the enhanced optical field, creating a nanopore that is automatically self-aligned to the plasmonic hotspot of the bowtie. We show that the approach provides precise control over the nanopore size and that these plasmonic nanopores can be used as single molecule DNA sensors with a performance matching that of TEM-drilled nanopores. The principle of optically controlled breakdown can also be used to fabricate nonplasmonic nanopores at a controlled position. Our novel fabrication process guarantees alignment of the nanopore with the optical hotspot of the nanoantenna, thus ensuring that pore-translocating biomolecules interact with the concentrated optical field that can be used for detection and manipulation of analytes.
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Affiliation(s)
| | | | - Nikola Vukovic
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | | | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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26
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Waugh M, Carlsen A, Sean D, Slater GW, Briggs K, Kwok H, Tabard-Cossa V. Interfacing solid-state nanopores with gel media to slow DNA translocations. Electrophoresis 2015; 36:1759-67. [PMID: 25929480 DOI: 10.1002/elps.201400488] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/27/2015] [Accepted: 04/07/2015] [Indexed: 11/10/2022]
Abstract
We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the regime of DNA movement exiting a nanopore interfaced with a gel medium, it is possible to address the issue of rapid biomolecule translocations through nanopores-presently one of the largest hurdles facing nanopore-based analysis-without affecting the signal quality or capture efficiency.
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Affiliation(s)
- Matthew Waugh
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - David Sean
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Harold Kwok
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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28
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Sugimoto M, Kato Y, Ishida K, Hyun C, Li J, Mitsui T. DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate. NANOTECHNOLOGY 2015; 26:065502. [PMID: 25611963 PMCID: PMC4326562 DOI: 10.1088/0957-4484/26/6/065502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We used fluorescence microscopy to investigate the diffusion and drift motion of λ DNA molecules on an Au-coated membrane surface near nanopores, prior to their translocation through solid-state nanopores. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules, which are presumably generated by electrokinetic flow, vary dramatically near the nanopores in our observations. We carefully investigate these DNA motions with different values of Vgate in order to alter the densities and polarities of the counterions, which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or repelled-DNA's anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could qualitatively explain these unusual DNA motions near metal-collated gated nanopores. Finally, we demonstrate the possibility of controlling the speed and direction of DNA motion near or through a nanopore, as in the case of recapturing a single DNA molecule multiple times with alternating current voltages on the Vgate.
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Affiliation(s)
- Manabu Sugimoto
- Department of Mathematics and Physics, Aoyama-Gakuin University 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
| | - Yuta Kato
- Department of Mathematics and Physics, Aoyama-Gakuin University 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
| | - Kentaro Ishida
- Department of Mathematics and Physics, Aoyama-Gakuin University 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
| | - Changbae Hyun
- Physics Department, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jiali Li
- Physics Department, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Toshiyuki Mitsui
- Department of Mathematics and Physics, Aoyama-Gakuin University 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
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29
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Plesa C, van Loo N, Ketterer P, Dietz H, Dekker C. Velocity of DNA during translocation through a solid-state nanopore. NANO LETTERS 2015; 15:732-7. [PMID: 25496458 DOI: 10.1021/nl504375c] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
While understanding translocation of DNA through a solid-state nanopore is vital for exploiting its potential for sensing and sequencing at the single-molecule level, surprisingly little is known about the dynamics of the propagation of DNA through the nanopore. Here we use linear double-stranded DNA molecules, assembled by the DNA origami technique, with markers at known positions in order to determine for the first time the local velocity of different segments along the length of the molecule. We observe large intramolecular velocity fluctuations, likely related to changes in the drag force as the DNA blob unfolds. Furthermore, we observe an increase in the local translocation velocity toward the end of the translocation process, consistent with a speeding up due to unfolding of the last part of the DNA blob. We use the velocity profile to estimate the uncertainty in determining the position of a feature along the DNA given its temporal location and demonstrate the error introduced by assuming a constant translocation velocity.
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Affiliation(s)
- Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Lorentzweg 1, 2628 CJ Delft, The Netherlands
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30
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Anderson BN, Assad ON, Gilboa T, Squires AH, Bar D, Meller A. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS NANO 2014; 8:11836-45. [PMID: 25363680 PMCID: PMC4334260 DOI: 10.1021/nn505545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
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Affiliation(s)
- Brett N. Anderson
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Ossama N. Assad
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Tal Gilboa
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Allison H. Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Daniel Bar
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Amit Meller
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
- Address correspondence to
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31
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Ivankin A, Henley RY, Larkin J, Carson S, Toscano ML, Wanunu M. Label-free optical detection of biomolecular translocation through nanopore arrays. ACS NANO 2014; 8:10774-81. [PMID: 25232895 PMCID: PMC4212781 DOI: 10.1021/nn504551d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.
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Affiliation(s)
- Andrey Ivankin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael L. Toscano
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Address correspondence to
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Auger T, Mathé J, Viasnoff V, Charron G, Di Meglio JM, Auvray L, Montel F. Zero-mode waveguide detection of flow-driven DNA translocation through nanopores. PHYSICAL REVIEW LETTERS 2014; 113:028302. [PMID: 25062242 DOI: 10.1103/physrevlett.113.028302] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 06/03/2023]
Abstract
We directly measure the flow-driven injection of DNA through nanopores at the level of single molecule and single pore using a modified zero-mode waveguide method. We observe a flow threshold independent of the pore radius, the DNA concentration, and length. We demonstrate that the flow injection of DNA in nanopores is controlled by an energy barrier as proposed in the de Gennes-Brochard suction model. Finally, we show that the height of the energy barrier is modulated by functionalizing the nanopores.
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Affiliation(s)
- Thomas Auger
- Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris Cedex 13, France
| | - Jérôme Mathé
- Laboratoire d'Analyse et de Modélisation pour la Biologie et l'Environnement, Université Évry-Val d'Essonne & CNRS (UMR 8587), 91025 Évry Cedex, France
| | - Virgile Viasnoff
- Mechanobiology Institute, National University of Singapore & CNRS (UMI 3639), 5A Engineering Drive 1, Singapore 117411, Singapore
| | - Gaëlle Charron
- Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris Cedex 13, France
| | - Jean-Marc Di Meglio
- Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris Cedex 13, France
| | - Loïc Auvray
- Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris Cedex 13, France
| | - Fabien Montel
- Matiére et Systèmes Complexes, Université Paris Diderot & CNRS (UMR 7057), 75205 Paris Cedex 13, France
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Tracking single-particle dynamics via combined optical and electrical sensing. Sci Rep 2013; 3:1855. [PMID: 23685401 PMCID: PMC3657717 DOI: 10.1038/srep01855] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/02/2013] [Indexed: 02/07/2023] Open
Abstract
While fluorescent imaging has been extensively used for single-particle tracking, temporal and spatial resolution of the wide-field microscopy technology is not satisfactory for investigating fast-moving features. Here we report a method for probing nanometer-scale motion of an individual particle through a microstructured channel at sub-MHz by combining a resistive pulse technique to the optical sensing. We demonstrate unambiguous discriminations of translocation and non-translocation events inferred from spike-like electrical signals by fluorescence images captured synchronously to ionic current measurements. We also find a trajectory-dependent translocation dynamics of voltage-driven single-particles through a microchannel. This electrical/optical approach may find applications in sensor technologies based on micro- and nano-electromechanical systems.
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Hyun C, Kaur H, Rollings R, Xiao M, Li J. Threading immobilized DNA molecules through a solid-state nanopore at >100 μs per base rate. ACS NANO 2013; 7:5892-900. [PMID: 23758046 PMCID: PMC3782089 DOI: 10.1021/nn4012434] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In pursuit of developing solid-state nanopore-based DNA sequencing technology, we have designed and constructed an apparatus that can place a DNA-tethered probe tip near a solid-state nanopore, control the DNA moving speed, and measure the ionic current change when a DNA molecule is captured and released from a nanopore. The probe tip's position is sensed and controlled by a tuning fork based feedback force sensor and a nanopositioning system. Using this newly constructed apparatus, a DNA strand moving rate of >100 μs/base or <1 nm/ms in silicon nitride nanopores has been accomplished. This rate is 10 times slower than by manipulating DNA-tethered beads using optical tweezers and 1000 times slower than free DNA translocation through solid-state nanopores reported previously, which provides enough temporal resolution to read each base on a tethered DNA molecule using available single-channel recording electronics on the market today. This apparatus can measure three signals simultaneously: ionic current through a nanopore, tip position, and tip vibrational amplitude during the process of a DNA molecule's capture and release by a nanopore. We show results of this apparatus for measuring λ DNA's capture and release distances and for current blockage signals of λ DNA molecules biotinylated with one end and with both ends tethered to a tip.
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Affiliation(s)
- Changbae Hyun
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Harpreet Kaur
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Ryan Rollings
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Min Xiao
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville AR 72701
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Kurz V, Nelson EM, Shim J, Timp G. Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule. ACS NANO 2013; 7:4057-69. [PMID: 23607372 DOI: 10.1021/nn400182s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A nanopore is the ultimate analytical tool. It can be used to detect DNA, RNA, oligonucleotides, and proteins with submolecular sensitivity. This extreme sensitivity is derived from the electric signal associated with the occlusion that develops during the translocation of the analyte across a membrane through a pore immersed in electrolyte. A larger occluded volume results in an improvement in the signal-to-noise ratio, and so the pore geometry should be made comparable to the size of the target molecule. However, the pore geometry also affects the electric field, the charge density, the electro-osmotic flow, the capture volume, and the response time. Seeking an optimal pore geometry, we tracked the molecular motion in three dimensions with high resolution, visualizing with confocal microscopy the fluorescence associated with DNA translocating through nanopores with diameters comparable to the double helix, while simultaneously measuring the pore current. Measurements reveal single molecules translocating across the membrane through the pore commensurate with the observation of a current blockade. To explain the motion of the molecule near the pore, finite-element simulations were employed that account for diffusion, electrophoresis, and the electro-osmotic flow. According to this analysis, detection using a nanopore comparable in diameter to the double helix represents a compromise between sensitivity, capture volume, the minimum detectable concentration, and response time.
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Affiliation(s)
- Volker Kurz
- Departments of Electrical Engineering and Biological Science, University of Notre Dame, Notre Dame, Indiana 46556, United States
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