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Yanagi I, Akahori R, Aoki M, Harada K, Takeda KI. Multichannel detection of ionic currents through two nanopores fabricated on integrated Si3N4 membranes. LAB ON A CHIP 2016; 16:3340-3350. [PMID: 27440476 DOI: 10.1039/c6lc00639f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Integration of solid-state nanopores and multichannel detection of signals from each nanopore are effective measures for realizing high-throughput nanopore sensors. In the present study, we demonstrated fabrication of Si3N4 membrane arrays and the simultaneous measurement of ionic currents through two nanopores formed in two adjacent membranes. Membranes with thicknesses as low as 6.4 nm and small nanopores with diameters of less than 2 nm could be fabricated using the poly-Si sacrificial-layer process and multilevel pulse-voltage injection. Using the fabricated nanopore membranes, we successfully achieved simultaneous detection of clear ionic-current blockades when single-stranded short homopolymers (poly(dA)60) passed through two nanopores. In addition, we investigated the signal crosstalk and leakage current among separated chambers. When two nanopores were isolated on the front surface of the membrane, there was no signal crosstalk or leakage current between the chambers. However, when two nanopores were isolated on the backside of the Si substrate, signal crosstalk and leakage current were observed owing to high-capacitance coupling between the chambers and electrolysis of water on the surface of the Si substrate. The signal crosstalk and leakage current could be suppressed by oxidizing the exposed Si surface in the membrane chip. Finally, the observed ionic-current blockade when poly(dA)60 passed through the nanopore in the oxidized chip was approximately half of that observed in the non-oxidized chip.
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Affiliation(s)
- Itaru Yanagi
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Rena Akahori
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Mayu Aoki
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Kunio Harada
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
| | - Ken-Ichi Takeda
- Hitachi, Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8603, Japan.
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Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda KI. Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Sci Rep 2016; 6:31324. [PMID: 27499264 PMCID: PMC4976334 DOI: 10.1038/srep31324] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/18/2016] [Indexed: 02/06/2023] Open
Abstract
The practical use of solid-state nanopores for DNA sequencing requires easy fabrication of the nanopores, reduction of the DNA movement speed and reduction of the ionic current noise. Here, we report an integrated nanopore platform with a nanobead structure that decelerates DNA movement and an insulating polyimide layer that reduces noise. To enable rapid nanopore fabrication, we introduced a controlled dielectric breakdown (CDB) process into our system. DNA translocation experiments revealed that single nanopores were created by the CDB process without sacrificing performance in reducing DNA movement speed by up to 10 μs/base or reducing noise up to 600 pArms at 1 MHz. Our platform provides the essential components for proceeding to the next step in the process of DNA sequencing.
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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
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Kazuma Matsui
- Center for Technology Innovation - Healthcare, Research &Development Group, Hitachi Ltd.,1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan
| | - Takahide Yokoi
- 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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Kong J, Bell NAW, Keyser UF. Quantifying Nanomolar Protein Concentrations Using Designed DNA Carriers and Solid-State Nanopores. NANO LETTERS 2016; 16:3557-62. [PMID: 27121643 PMCID: PMC4901370 DOI: 10.1021/acs.nanolett.6b00627] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/26/2016] [Indexed: 05/19/2023]
Abstract
Designed "DNA carriers" have been proposed as a new method for nanopore based specific protein detection. In this system, target protein molecules bind to a long DNA strand at a defined position creating a second level transient current drop against the background DNA translocation. Here, we demonstrate the ability of this system to quantify protein concentrations in the nanomolar range. After incubation with target protein at different concentrations, the fraction of DNA translocations showing a secondary current spike allows for the quantification of the corresponding protein concentration. For our proof-of-principle experiments we use two standard binding systems, biotin-streptavidin and digoxigenin-antidigoxigenin, that allow for measurements of the concentration down to the low nanomolar range. The results demonstrate the potential for a novel quantitative and specific protein detection scheme using the DNA carrier method.
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Morin TJ, Shropshire T, Liu X, Briggs K, Huynh C, Tabard-Cossa V, Wang H, Dunbar WB. Nanopore-Based Target Sequence Detection. PLoS One 2016; 11:e0154426. [PMID: 27149679 PMCID: PMC4858282 DOI: 10.1371/journal.pone.0154426] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/13/2016] [Indexed: 01/10/2023] Open
Abstract
The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented.
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Affiliation(s)
- Trevor J. Morin
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | | | - Xu Liu
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ontario, Canada
| | - Cindy Huynh
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
| | | | - Hongyun Wang
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
- Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
| | - William B. Dunbar
- Two Pore Guys Inc., Santa Cruz, CA, United States of America
- Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA, United States of America
- * E-mail:
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Jones PD, Stelzle M. Can Nanofluidic Chemical Release Enable Fast, High Resolution Neurotransmitter-Based Neurostimulation? Front Neurosci 2016; 10:138. [PMID: 27065794 PMCID: PMC4815362 DOI: 10.3389/fnins.2016.00138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
Artificial chemical stimulation could provide improvements over electrical neurostimulation. Physiological neurotransmission between neurons relies on the nanoscale release and propagation of specific chemical signals to spatially-localized receptors. Current knowledge of nanoscale fluid dynamics and nanofluidic technology allows us to envision artificial mechanisms to achieve fast, high resolution neurotransmitter release. Substantial technological development is required to reach this goal. Nanofluidic technology—rather than microfluidic—will be necessary; this should come as no surprise given the nanofluidic nature of neurotransmission. This perspective reviews the state of the art of high resolution electrical neuroprostheses and their anticipated limitations. Chemical release rates from nanopores are compared to rates achieved at synapses and with iontophoresis. A review of microfluidic technology justifies the analysis that microfluidic control of chemical release would be insufficient. Novel nanofluidic mechanisms are discussed, and we propose that hydrophobic gating may allow control of chemical release suitable for mimicking neurotransmission. The limited understanding of hydrophobic gating in artificial nanopores and the challenges of fabrication and large-scale integration of nanofluidic components are emphasized. Development of suitable nanofluidic technology will require dedicated, long-term efforts over many years.
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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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Zhang Y, Reisner W. Fabrication and characterization of nanopore-interfaced nanochannel devices. NANOTECHNOLOGY 2015; 26:455301. [PMID: 26472174 DOI: 10.1088/0957-4484/26/45/455301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanofluidic devices combining nanochannels and nanopores may enable a range of novel applications in the field of single-molecule biosensing and manipulation. Here we combine classic lithographically based fabrication and electron beam milling to construct a device that integrates sealed transverse features, such as nanocavities and nanochannels, with embedded pores vertically intersecting the nanochannels. Using fluorescent microscopy, we demonstrate that DNA molecules can be introduced into the nanochannels and translated transversely across the embedded pore in an extended-conformation without undergoing cross-pore translocation. Upon application of a trans-pore voltage drop, the molecules will undergo cross-pore translocation into an adjoining macroscopic reservoir.
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Affiliation(s)
- Yuning Zhang
- Dept. of Physics, McGill University, 3600 Rue University, Montreal QC H3A 2T8, Canada
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