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Ma T, Chang S, He J, Liang F. Emerging sensing platforms based on Cucurbit[ n]uril functionalized gold nanoparticles and electrodes. Chem Commun (Camb) 2023; 60:150-167. [PMID: 38054368 DOI: 10.1039/d3cc04851a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Cucurbit[n]urils (CB[n]s, n = 5-8, 10, and 14), synthetic macrocycles with unique host-guest properties, have triggered increasing research interest in recent years. Gold nanoparticles (Au NPs) and electrodes stand out as exceptional substrates for sensing due to their remarkable physicochemical characteristics. Coupling the CB[n]s with Au NPs and electrodes has enabled the development of emerging sensing platforms for various promising applications. However, monitoring the behavior of analytes at the single-molecule level is currently one of the most challenging topics in the field of CB[n]-based sensing. Constructing supramolecular junctions in a sensing platform provides an ideal structure for single-molecule analysis, which can provide insights for a fundamental understanding of supramolecular interactions and chemical reactions and guide the design of sensing applications. This feature article outlines the progress in the preparation of the CB[n] functionalized Au NPs and Au electrodes, as well as the construction and application of supramolecular junctions in sensing platforms, based on the methods of recognition tunneling (RT), surface-enhanced Raman spectroscopy (SERS), single-molecule force spectroscopy (SMFS), and electrochemical sensing (ECS). A brief perspective on the future development of and challenges in CB[n] mediated sensing platforms is also covered.
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Affiliation(s)
- Tao Ma
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Jin He
- Department of Physics, Florida International University, Miami, Florida 33199, USA.
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, Coal Conversion and New Carbon Materials Hubei Key Laboratory, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
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Huang C, Li Z, Zhu X, Ma X, Li N, Fan J. Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride. ACS NANO 2023; 17:3301-3312. [PMID: 36638059 DOI: 10.1021/acsnano.2c05002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Na Li
- School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education, Shanxi Normal University, Taiyuan030000, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
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Haji Abdolvahab R, Niknam Hamidabad M. Pore shapes effects on polymer translocation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:76. [PMID: 33306147 DOI: 10.1140/epje/i2020-12001-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers.
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Niknam Hamidabad M, Asgari S, Haji Abdolvahab R. Nanoparticle-assisted polymer translocation through a nanopore. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Abstract
We employ a three-dimensional molecular dynamics to simulate a driven polymer translocation through a nanopore by applying an external force, for four pore diameters and two external forces. To see the polymer and pore interaction effects on translocation time, we studied nine interaction energies. Moreover, to better understand the simulation results, we investigate polymer center of mass, shape factor and the monomer spatial distribution through the translocation process. Our results reveal that increasing the polymer-pore interaction energy is accompanied by an increase in the translocation time and decrease in the process rate. Furthermore, for pores with greater diameter, the translocation becomes faster. The shape analysis of the polymer indicates that the polymer shape is highly sensitive to the interaction energy. In great interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last. Overall, it can be concluded that the external force does not play a major role in the shape and distribution of translocated monomers. However, the interaction energy between monomer and nanopore has a major effect especially on the distribution of translocated monomers on the trans side.
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Gu Z, Wang H, Ying YL, Long YT. Ultra-low noise measurements of nanopore-based single molecular detection. Sci Bull (Beijing) 2017; 62:1245-1250. [PMID: 36659452 DOI: 10.1016/j.scib.2017.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/04/2017] [Indexed: 01/21/2023]
Abstract
Nanopore is an ultra-sensitive electrochemical technique for single molecular detection in confined space. To suppress the noise in detection of the weak current of nanopore, we investigated the influence of membrane capacitance and applied voltage on the noise of the current signal by model analysis, simulation and experiment. The obtained results demonstrated that membrane capacitance affects the noise by amplifying the noise of the applied voltage. Therefore, suppression of applied voltage noise is an efficient approach for reducing the noise in nanopore detection. Here, we developed an ultra-low noise instrument system for detecting the single molecule signal in nanopores. As demonstrated by nanopore experiments, the p-p noise of the developed system during the recording is reduced to 3.26pA using the filter of 5kHz. Therefore, the developed system could be applied in highly sensitive nanopore detection.
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Affiliation(s)
- Zhen Gu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huifeng Wang
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Abdolvahab RH. Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:41. [PMID: 28389823 DOI: 10.1140/epje/i2017-11528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Abstract
Chaperones are binding proteins working as a driving force in biopolymer translocation. They bind to the biopolymer near the pore and prevent its backsliding. Chaperones may have different spatial distributions. Recently, we showed the importance of their spatial distribution in translocation and its effects on the sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. Because of the exponential distribution of chaperones, the energy dependency of the translocation time will change. Here we find a minimum in translocation time versus binding effective energy (EBE) curve. The same trend can be seen in the scaling exponent of time versus polymer length, [Formula: see text] ([Formula: see text]), when plotted against EBE. Interestingly in some special cases, e.g. chaperones of size [Formula: see text] and with an exponential distribution rate of [Formula: see text], the minimum even reaches to an amount of less than 1 ([Formula: see text]). We explain the possibility of this rare result. Moreover, based on a theoretical discussion we show that, by taking into account the velocity dependency of the translocation on polymer length, one can truly predict the value of this minimum.
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Wang J, Quershi WA, Li Y, Xu J, Nie G. Analytical methods for nano-bio interface interactions. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0340-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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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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Yanagi I, Oura T, Haga T, Ando M, Yamamoto J, Mine T, Ishida T, Hatano T, Akahori R, Yokoi T, Anazawa T. Side-gated ultrathin-channel nanopore FET sensors. NANOTECHNOLOGY 2016; 27:115501. [PMID: 26876025 DOI: 10.1088/0957-4484/27/11/115501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A side-gated, ultrathin-channel nanopore FET (SGNAFET) is proposed for fast and label-free DNA sequencing. The concept of the SGNAFET comprises the detection of changes in the channel current during DNA translocation through a nanopore and identifying the four types of nucleotides as a result of these changes. To achieve this goal, both p- and n-type SGNAFETs with a channel thicknesses of 2 or 4 nm were fabricated, and the stable transistor operation of both SGNAFETs in air, water, and a KCl buffer solution were confirmed. In addition, synchronized current changes were observed between the ionic current through the nanopore and the SGNAFET's drain current during DNA translocation through the nanopore.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd, Research & Development Group, Center for Technology Innovation-Healthcare, 1-280, Higashi-Koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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Vierheilig J, Savio D, Ley RE, Mach RL, Farnleitner AH, Reischer GH. Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 72:1962-72. [PMID: 26606090 PMCID: PMC4884447 DOI: 10.2166/wst.2015.407] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.
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Affiliation(s)
- J Vierheilig
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Centre for Water Resource Systems (CWRS), Vienna University of Technology, Karlsplatz 13/222, A-1040 Vienna, Austria; Present address: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - D Savio
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Centre for Water Resource Systems (CWRS), Vienna University of Technology, Karlsplatz 13/222, A-1040 Vienna, Austria
| | - R E Ley
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - R L Mach
- Gene Technology Group, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
| | - A H Farnleitner
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Interuniversity Cooperation Centre Water & Health, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
| | - G H Reischer
- Research Group Environmental Microbiology and Molecular Ecology, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria E-mail: ; Interuniversity Cooperation Centre Water & Health, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
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