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Khatri S, Pandey P, Mejia G, Ghimire G, Leng F, He J. Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes. J Am Chem Soc 2023; 145:28075-28084. [PMID: 37996390 PMCID: PMC11036617 DOI: 10.1021/jacs.3c09311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Glass nanopipettes have gained widespread use as a versatile single-entity detector in chemical and biological sensing, analysis, and imaging. Its advantages include low cost, easy accessibility, simplicity of use, and high versatility. However, conventional nanopipettes based on the volume exclusion mechanism have limitations in detecting small biomolecules due to their small volume and high mobility in aqueous solution. To overcome this challenge, we have employed a novel approach by capitalizing on the strong nanoconfinement effect of nanopipettes. This is achieved by utilizing both the hard confinement provided by the long taper nanopipette tip at the cis side and the soft confinement offered by the hydrogel at the trans side. Through this approach, we have effectively slowed down the exit motion of small molecules, allowing us to enrich and jam them at the nanopipette tip. Consequently, we have achieved high throughput detection of small biomolecules with sizes as small as 1 nm, including nucleoside triphosphates, short peptides, and small proteins with excellent signal-to-noise ratios. Furthermore, molecular complex formation through specific intermolecular interactions, such as hydrogen bonding between closely spaced nucleotides in the jam-packed nanopipette tip, has been detected based on the unique ionic current changes.
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Affiliation(s)
- Santosh Khatri
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - German Mejia
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Govinda Ghimire
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Fenfei Leng
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
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Yanagi I, Akahori R, Takeda KI. Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution. ACS OMEGA 2023; 8:21285-21292. [PMID: 37332803 PMCID: PMC10268630 DOI: 10.1021/acsomega.3c02703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The ionic current blockades when poly(dT)60 or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)2SO4 were investigated. The dwell time of poly(dT)60 in the nanopores in an aqueous solution containing (NH4)2SO4 was significantly longer compared to that in an aqueous solution that did not contain (NH4)2SO4. This dwell time prolongation effect due to the aqueous solution containing (NH4)2SO4 was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)2SO4, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH4)2SO4. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.
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Affiliation(s)
- Itaru Yanagi
- Center
for Exploratory Research, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Rena Akahori
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Ken-ichi Takeda
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
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He T, Narumi A, Wang Y, Xu L, Sato SI, Shen X, Kakuchi T. Amphiphilic diblock copolymers of poly(glycidol) with biodegradable polyester/polycarbonate. organocatalytic one-pot ROP and self-assembling property. Polym Chem 2021. [DOI: 10.1039/d1py01026c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Poly(glycidol)-based block copolymers with excellent micelle formation properties were prepared via organocatalytic one-pot ROP.
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Affiliation(s)
- Tingyu He
- Research Center for Polymer Materials, School of Materials Science and Engineering, Changchun University of Science and Technology, Weixing Road 7989, Jilin 130022, China
| | - Atsushi Narumi
- Graduate School of Organic Materials Science, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Yanqiu Wang
- Research Center for Polymer Materials, School of Materials Science and Engineering, Changchun University of Science and Technology, Weixing Road 7989, Jilin 130022, China
| | - Liang Xu
- Research Center for Polymer Materials, School of Materials Science and Engineering, Changchun University of Science and Technology, Weixing Road 7989, Jilin 130022, China
| | - Shin-ichiro Sato
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Xiande Shen
- Research Center for Polymer Materials, School of Materials Science and Engineering, Changchun University of Science and Technology, Weixing Road 7989, Jilin 130022, China
- Chongqing Research Institute, Changchun University of Science and Technology, No. 618 Liangjiang Avenue, Longxing Town, Yubei District, Chongqing City 401135, China
| | - Toyoji Kakuchi
- Research Center for Polymer Materials, School of Materials Science and Engineering, Changchun University of Science and Technology, Weixing Road 7989, Jilin 130022, China
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
- Chongqing Research Institute, Changchun University of Science and Technology, No. 618 Liangjiang Avenue, Longxing Town, Yubei District, Chongqing City 401135, China
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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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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: 31] [Impact Index Per Article: 6.2] [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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Goto Y, Matsui K, Yanagi I, Takeda KI. Silicon nitride nanopore created by dielectric breakdown with a divalent cation: deceleration of translocation speed and identification of single nucleotides. NANOSCALE 2019; 11:14426-14433. [PMID: 31334729 DOI: 10.1039/c9nr03563j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanopore DNA sequencing with a solid-state nanopore requires deceleration of the ultrafast translocation speed of single-stranded DNA (ssDNA). We report an unexpected phenomenon: controlled dielectric breakdown (CBD) with a divalent metal cation, especially Ca2+, provides a silicon nitride nanopore with the ability to decelerate ssDNA speed to 100 μs per base even after solution replacement. This speed is two orders of magnitude slower than that for CBD with a conventional monovalent metal cation. Temperature dependence experiments revealed that the enthalpic barrier for a nanopore created via CBD with Ca2+ is 25-30kBT, comparable to that of a biological nanopore. The slowing effect originates from the strong interaction between ssDNA and divalent cations, which were coated on the sidewall of the nanopore during the CBD process. In addition, we found that the nanopore created via CBD with Ca2+ can decelerate the speed of even single-nucleotide monomers, dNMPs, to 0.1-10 ms per base. The four single nucleotides could be statistically identified according to their blockade currents. Our approach is simple and practical because it simultaneously allows nanopore fabrication, ssDNA deceleration and the identification of nucleotide monomers.
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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.
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Challenges of Single-Molecule DNA Sequencing with Solid-State Nanopores. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:131-142. [DOI: 10.1007/978-981-13-6037-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Akahori R, Yanagi I, Goto Y, Harada K, Yokoi T, Takeda KI. Discrimination of three types of homopolymers in single-stranded DNA with solid-state nanopores through external control of the DNA motion. Sci Rep 2017; 7:9073. [PMID: 28831056 PMCID: PMC5567245 DOI: 10.1038/s41598-017-08290-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
To achieve DNA sequencing with solid-state nanopores, the speed of the DNA in the nanopore must be controlled to obtain sequence-specific signals. In this study, we fabricated a nanopore-sensing system equipped with a DNA motion controller. DNA strands were immobilized on a Si probe, and approach of this probe to the nanopore vicinity could be controlled using a piezo actuator and stepper motor. The area of the Si probe was larger than the area of the membrane, which meant that the immobilized DNA could enter the nanopore without the need for the probe to scan to determine the location of the nanopore in the membrane. We demonstrated that a single-stranded DNA could be inserted into and removed from a nanopore in our experimental system. The number of different ionic-current levels observed while DNA remained in the nanopore corresponded to the number of different types of homopolymers in the DNA.
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Affiliation(s)
- Rena Akahori
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Itaru Yanagi
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Yusuke Goto
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Kunio Harada
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Takahide Yokoi
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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