1
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Yang J, Pan T, Xie Z, Yuan W, Ho HP. In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules. Nat Commun 2024; 15:5132. [PMID: 38879544 PMCID: PMC11180207 DOI: 10.1038/s41467-024-48630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/06/2024] [Indexed: 06/19/2024] Open
Abstract
Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.
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Affiliation(s)
- Jianxin Yang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tianle Pan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
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2
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Zhou W, Guo Y, Guo W, Qiu H. High-Resolution and Low-Noise Single-Molecule Sensing with Bio-Inspired Solid-State Nanopores. J Phys Chem Lett 2024; 15:5556-5563. [PMID: 38752895 DOI: 10.1021/acs.jpclett.4c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Solid-state nanopores have been extensively explored as single-molecule sensors, bearing the potential for the sequencing of DNA. Although they offer advantages in terms of high mechanical robustness, tunable geometry, and compatibility with existing semiconductor fabrication techniques in comparison with their biological counterparts, efforts to sequence DNA with these nanopores have been hampered by insufficient spatial resolution and high noise in the measured ionic current signal. Here we show that these limitations can be overcome by the use of solid-state nanopores featuring a thin, narrow constriction as the sensing region, inspired by biological protein nanopores that have achieved notable success in DNA sequencing. Our extensive molecular dynamics simulations show that these bio-inspired nanopores can provide high spatial resolution equivalent to 2D material nanopores and, meanwhile, significantly inhibit noise levels. A theoretical model is also provided to assess the performance of the bio-inspired nanopore, which could guide its design and optimization.
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Affiliation(s)
- Wanqi Zhou
- State Key Laboratory of Mechanics and Control for Aerospace Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yufeng Guo
- State Key Laboratory of Mechanics and Control for Aerospace Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control for Aerospace Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control for Aerospace Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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3
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Lin X, Chen H, Wu G, Zhao J, Zhang Y, Sha J, Si W. Selective Capture and Manipulation of DNA through Double Charged Nanopores. J Phys Chem Lett 2024:5120-5129. [PMID: 38709198 DOI: 10.1021/acs.jpclett.4c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
In the past few decades, nanometer-scale pores have been employed as powerful tools for sensing biological molecules. Owing to its unique structure and properties, solid-state nanopores provide interesting opportunities for the development of DNA sequencing technology. Controlling DNA translocation in nanopores is an important means of improving the accuracy of sequencing. Here we present a proof of principle study of accelerating DNA captured across targeted graphene nanopores using surface charge density and find the intrinsic mechanism of the combination of electroosmotic flow induced by charges of nanopore and electrostatic attraction/repulsion between the nanopore and ssDNA. The theoretical study performed here provides a new means for controlling DNA transport dynamics and makes better and cheaper application of graphene in molecular sequencing.
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Affiliation(s)
- Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Haonan Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Jiajia Zhao
- Department of Pharmacology, Key Laboratory of Neuropsychiatric Diseases, China Pharmaceutical University, Nanjing 211198, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
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4
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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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5
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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6
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Sülzle J, Yang W, Shimoda Y, Ronceray N, Mayner E, Manley S, Radenovic A. Label-Free Imaging of DNA Interactions with 2D Materials. ACS PHOTONICS 2024; 11:737-744. [PMID: 38405387 PMCID: PMC10885193 DOI: 10.1021/acsphotonics.3c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/27/2024]
Abstract
Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.
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Affiliation(s)
- Jenny Sülzle
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Wayne Yang
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Yuta Shimoda
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Nathan Ronceray
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Eveline Mayner
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Suliana Manley
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Aleksandra Radenovic
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
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7
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H H, Mallajosyula SS. Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55095-55108. [PMID: 37965826 DOI: 10.1021/acsami.3c12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.
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Affiliation(s)
- Hemanth H
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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8
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Yu YS, Ren Q, Tan RR, Ding HM. Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore. Phys Chem Chem Phys 2023; 25:28034-28042. [PMID: 37846110 DOI: 10.1039/d3cp03767c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.
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Affiliation(s)
- You-Sheng Yu
- School of Science, East China University of Technology, Nanchang 330013, China
- National Lab of Solid State Microstructures, Nanjing University, Nanjing 210093, China
| | - Qiang Ren
- School of Science, East China University of Technology, Nanchang 330013, China
| | - Rong-Ri Tan
- Department of Physics, Jiangxi Science & Technology Normal University, Nanchang 330013, China.
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China.
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9
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Si W, Lin X, Wang L, Wu G, Zhang Y, Chen Y, Sha J. Nanopore actuation of a DNA-tracked nanovehicle. NANOSCALE 2023; 15:14659-14668. [PMID: 37622615 DOI: 10.1039/d3nr02633g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
As a kind of nanomachine that has great potential for applications in nanoscale sensing and manipulation, nanovehicles with unique shapes and functions have received extensive attention in recent years. Different from the existing common method of using synthetic chemistry to design and manufacture a nanovehicle, here we theoretically report a molecularly assembled DNA-tracked nanovehicle that can move on a solid-state surface using molecular dynamics simulations. A graphene membrane with four nanopores acts as the chassis of the nanoscale vehicle, and two circular ssDNAs across the nanopores serve as the wheels. The electroosmotic flows induced by independently charged nanopores with different surface charge densities under external electric fields were found to be the main power to actuate the controlled rotary motion of circular ssDNAs across every two nanopores. By tuning the rotary speed of each circular ssDNA, the linear and turning movements of the designed nanovehicle were realized. The designed nanovehicle makes it possible to have access to almost everywhere in the human body, which would lead to significant breakthroughs in the fields of nanoscale surgery, drug delivery and so on. The research not only enriches the family of nanorobots, but also opens another way for designing nanovehicles.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Liwei Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
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10
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Miao L, Huang B, Fang H, Chai J, Liu Z, Zhai Y. Single-Nanoparticle-Based Nanomachining for Fabrication of a Uniform Nanochannel Sensor. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305159. [PMID: 37486796 DOI: 10.1002/adma.202305159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Indexed: 07/26/2023]
Abstract
The structure of nanomaterials and nanodevices determines their functionality and applications. A single uniform nanochannel with a high aspect ratio is an attractive structure due to its unique rigid structures, easy preparation, and diverse pore structures and it holds significant promising importance in fields such as nanopore sensing and nanomanufacturing. Although the metal-nanoparticle-assistant silicon etching technique can produce uniform nanochannels, however, the fabrication of single through nanochannels remains a challenge thus far. A simple and versatile strategy is developed that allows for the retention of individual gold nanoparticle on a substrate, enabling single-nanoparticle nanomachining. This method involves three steps: the formation of a carbon protective layer on individual nanoparticles via electron-beam irradiation, selective removal of unprotected nanoparticles using a corrosive agent, and subsequent elimination of the carbon layer. This enables the fabrication of a single submillimeter-long uniform through nanochannel in the silicon wafer, which can be employed for nanopore sensing and shape-based nanoparticle distinguishing. The developed method can also facilitate single-nanoparticle studies and nanomachining for a broad application in materials science, electronics, micro/nano-optics, and catalysis.
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Affiliation(s)
- Longfei Miao
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Bintong Huang
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Hui Fang
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jia Chai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Ze Liu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Yueming Zhai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
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11
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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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12
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Meng L, Huang J, He Z, Zhou R. Single nucleobase identification for transversally-confined ssDNA using longitudinal ionic currents. NANOSCALE 2022; 14:6922-6929. [PMID: 35452063 DOI: 10.1039/d1nr07116e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
High-fidelity DNA sequencing using solid-state nanopores remains a big challenge, partly due to difficulties related to efficient molecular capture and subsequent control of the dwell time. To help address these issues, here we propose a sequencing platform consisting of stacked two-dimensional materials with tailored structures containing a funnel-shaped step defect and a nanopore drilled inside the nanochannel. Our all-atom molecular dynamics (MD) simulations showed that, assisted by the step defect, single-stranded DNA (ssDNA) can be transported to the nanopore in a deterministic way by pulsed transversal electric fields. Furthermore, different types of DNA bases can reside in the pore for a sufficiently long time which can be successfully differentiated by longitudinal ionic currents. By using the decoupled driving forces for ssDNA transport and ionic current measurements, this approach holds potential for high-fidelity DNA sequencing.
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Affiliation(s)
- Lijun Meng
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Jianxiang Huang
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Zhi He
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology, Shanghai Institute for Advanced Study, College of Life Sciences, and Department of Physics, Zhejiang University, Hangzhou 310027, China.
- Department of Chemistry, Colombia University, New York, NY 10027, USA
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13
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Si W, Yuan R, Wu G, Kan Y, Sha J, Chen Y, Zhang Y, Shen Y. Navigated Delivery of Peptide to the Nanopore Using In-Plane Heterostructures of MoS 2 and SnS 2 for Protein Sequencing. J Phys Chem Lett 2022; 13:3863-3872. [PMID: 35467868 DOI: 10.1021/acs.jpclett.2c00533] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The impressive success of DNA sequencing using nanopores makes it possible to realize nanopore based protein sequencing. Well-controlled capture and linear movement of the protein are essential for accurate nanopore protein sequencing. Here, by taking advantage of different binding affinities of protein to two isomorphic materials, we theoretically designed a heterostructual platform for delivering the unfolded peptide to the nanopore sensing region. Due to the stronger binding between the peptide and SnS2 compared to MoS2, the peptide would adsorb to the SnS2 nanostripe and keep its threadlike conformation in the MoS2/SnS2/MoS2 heterostructure. Through switching the direction of the applied electric field in real time, the peptide was strategically driven to move along the designed path to the target nanopore. The ionic current blockades were also found to be different as the compositions of the peptide were changed, indicating the possibility for differentiating different peptides using this platform.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Runyi Yuan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yajing Kan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yang Shen
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
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14
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Sun Y, Yi F, Li RH, Min X, Qin H, Cheng SQ, Liu Y. Inorganic-Organic Hybrid Membrane Based on Pillararene-Intercalated MXene Nanosheets for Efficient Water Purification. Angew Chem Int Ed Engl 2022; 61:e202200482. [PMID: 35099850 DOI: 10.1002/anie.202200482] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 01/14/2023]
Abstract
Discharge of antibiotic-containing wastewater causes environmental pollution and threatens biological and human health. An efficient treatment method for this wastewater is urgently required. We prepared inorganic-organic hybrid MXene-pillararene nanosheets with a large lateral size (5-8 μm). The hybrid nanosheets were stacked on supports via vacuum-assisted filtration to prepare membranes with regular parallel slits and an interlayer spacing of 1.36 nm, which were used to purify antibiotic-containing water. Permeance through the membrane increased 100-fold compared with most polymeric and other two-dimensional nanofiltration membranes with similar rejection. This high permeance and rejection was attributed to the large lateral size of the nanosheets, regular interlayer spacing, and electrostatic interaction between the membrane and antibiotics. These membranes will broaden the applications of lamellar materials for the separation of high-value-added drugs in academia and industry.
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Affiliation(s)
- Yue Sun
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, 300387, Tianjin, China.,Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Fan Yi
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Run-Hao Li
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Xuehong Min
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Huan Qin
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Shi-Qi Cheng
- Hubei Key Laboratory of Catalysis and Materials Science, College of Chemistry and Material Sciences, South-Central University for Nationalities, 430074, Wuhan, China
| | - Yi Liu
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, 300387, Tianjin, China
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15
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Sun Y, Yi F, Li R, Min X, Qin H, Cheng S, Liu Y. Inorganic–Organic Hybrid Membrane Based on Pillararene‐Intercalated MXene Nanosheets for Efficient Water Purification. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yue Sun
- State Key Laboratory of Separation Membrane and Membrane Process School of Chemistry Tiangong University 300387 Tianjin China
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Fan Yi
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Run‐Hao Li
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Xuehong Min
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Huan Qin
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Shi‐Qi Cheng
- Hubei Key Laboratory of Catalysis and Materials Science College of Chemistry and Material Sciences South-Central University for Nationalities 430074 Wuhan China
| | - Yi Liu
- State Key Laboratory of Separation Membrane and Membrane Process School of Chemistry Tiangong University 300387 Tianjin China
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16
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Revealing DNA Structure at Liquid/Solid Interfaces by AFM-Based High-Resolution Imaging and Molecular Spectroscopy. Molecules 2021; 26:molecules26216476. [PMID: 34770895 PMCID: PMC8587808 DOI: 10.3390/molecules26216476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
DNA covers the genetic information in all living organisms. Numerous intrinsic and extrinsic factors may influence the local structure of the DNA molecule or compromise its integrity. Detailed understanding of structural modifications of DNA resulting from interactions with other molecules and surrounding environment is of central importance for the future development of medicine and pharmacology. In this paper, we review the recent achievements in research on DNA structure at nanoscale. In particular, we focused on the molecular structure of DNA revealed by high-resolution AFM (Atomic Force Microscopy) imaging at liquid/solid interfaces. Such detailed structural studies were driven by the technical developments made in SPM (Scanning Probe Microscopy) techniques. Therefore, we describe here the working principles of AFM modes allowing high-resolution visualization of DNA structure under native (liquid) environment. While AFM provides well-resolved structure of molecules at nanoscale, it does not reveal the chemical structure and composition of studied samples. The simultaneous information combining the structural and chemical details of studied analyte allows achieve a comprehensive picture of investigated phenomenon. Therefore, we also summarize recent molecular spectroscopy studies, including Tip-Enhanced Raman Spectroscopy (TERS), on the DNA structure and its structural rearrangements.
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17
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Machado LD, Bizao RA, Pugno NM, Galvão DS. Controlling Movement at Nanoscale: Curvature Driven Mechanotaxis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100909. [PMID: 34302438 DOI: 10.1002/smll.202100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Locating and manipulating nano-sized objects to drive motion is a time and effort consuming task. Recent advances show that it is possible to generate motion without direct intervention, by embedding the source of motion in the system configuration. In this work, an alternative manner to controllably displace nano-objects without external manipulation is demonstrated, by employing spiral-shaped carbon nanotube (CNT) and graphene nanoribbon structures (GNR). The spiral shape contains smooth gradients of curvature, which lead to smooth gradients of bending energy. It is shown that these gradients as well as surface energy gradients can drive nano-oscillators. An energy analysis is also carried out by approximating the carbon nanotube to a thin rod and how torsional gradients can be used to drive motion is discussed. For the nanoribbons, the role of layer orientation is also analyzed. The results show that motion is not sustainable for commensurate orientations, in which AB stacking occurs. For incommensurate orientations, friction almost vanishes, and in this instance, the motion can continue even if the driving forces are not very high. This suggests that mild curvature gradients, which can already be found in existing nanostructures, could provide mechanical stimuli to direct motion.
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Affiliation(s)
- Leonardo D Machado
- Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, Natal-RN, 59072-970, Brazil
| | - Rafael A Bizao
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, São Paulo, 13566-590, Brazil
| | - Nicola M Pugno
- Laboratory of Bio-inspired, Bionic, Nano, Meta Materials & Mechanics, Department of Civil, Environmental and Mechanical Engineering, University of Trento, Trento, 38123, Italy
- School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK
| | - Douglas S Galvão
- Instituto de Física "Gleb Wataghin,", Universidade Estadual de Campinas, C. P. 6165, Campinas, SP, 13083-970, Brazil
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18
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He Z, Zhou R. Exploring an In-Plane Graphene and Hexagonal Boron Nitride Array for Separation of Single Nucleotides. ACS NANO 2021; 15:11704-11710. [PMID: 34258988 DOI: 10.1021/acsnano.1c02450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Regular nanofluidic sieving structures are emerging as rapid and compatible on-chip techniques for biomolecular separation. Although the current nanofluidic sieving devices, mostly based on three-dimensional nanostructures, have achieved a separation resolution of ∼20 nm, it is still far away from single-nucleotide resolution. Using all-atom molecular dynamics simulations, here we demonstrate a two-dimensional (2D) nanofluidic sieve consisting of an in-plane graphene (GRA)/hexagonal boron nitride (h-BN) nanoarray, which enables ultrahigh resolution in the successful separation of four types of single nucleotides. The alternating GRA and h-BN stripes can create size-dependent energy barriers for adsorbed nucleotides, which provide a strong modulation for their mobility, thus causing distinct band separations on the 2D surface. We further show that this 2D sieve is particularly sensitive when the sample dimensions are within the range from a half period to one period of the nanoarray. This 2D sieving structure may shed light on the development of lab-on-a-chip sequencing in the future.
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Affiliation(s)
- Zhi He
- Institute of Quantitative Biology, College of Optical Science and Engineering, and College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Optical Science and Engineering, and College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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19
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Niedzwiecki DJ, DiPaolo B, Lin CY, Castan A, Keneipp R, Drndić M. Devices for Nanoscale Guiding of DNA through a 2D Nanopore. ACS Sens 2021; 6:2534-2545. [PMID: 34228425 DOI: 10.1021/acssensors.1c00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We fabricate on-chip solid-state nanofluidic-2D nanopore systems that can limit the range of motion for DNA in the sensing region of a nanopore. We do so by creating devices containing one or more silicon nitride pores and silicon nitride pillars supporting a 2D pore that orient DNA within a nanopore device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We discuss two concepts with two and three independent electrical connections and corresponding nanopore chip device architectures to achieve this goal in practice. Here, we describe device fabrication and transmission electron microscope (TEM) images, and provide simulated translocations based on the finite element analysis in 3D to demonstrate its merit. In both methods, there is a main 2D nanopore which we refer to as a "sensing" nanopore (monolayer MoS2 in this paper). A secondary layer is either an array of guiding pores sharing the same electrode pair as the sensing pore (Method 1) or a single, independently contacted, guiding pore (Method 2). These pores are constructed parallel to the "sensing" pore and serve as "guiding" elements to stretch and feed DNA into the atomically thin sensing pore. We discuss the practical implementation of these concepts with nanofluidic and Si-based technology, including detailed fabrication steps and challenges involved for DNA applications in solution.
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Affiliation(s)
- David J. Niedzwiecki
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Brian DiPaolo
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Alice Castan
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Rachael Keneipp
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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20
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Yanagi I, Takeda KI. Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO 2sacrificial layer process. NANOTECHNOLOGY 2021; 32:415301. [PMID: 34214991 DOI: 10.1088/1361-6528/ac10e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO2. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO2sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)60passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.
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Affiliation(s)
- Itaru Yanagi
- 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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21
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Su S, Wang X, Xue J. Nanopores in two-dimensional materials: accurate fabrication. MATERIALS HORIZONS 2021; 8:1390-1408. [PMID: 34846448 DOI: 10.1039/d0mh01412e] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Two-dimensional (2D) materials such as graphene and molybdenum disulfide have been demonstrated with a wide range of applications in electronic devices, chemical catalysis, single-molecule detection, and energy conversion. In the 2D materials, nanopores can be created, and the 2D nanoporous membranes possess many unique properties such as ultrathin thickness, high surface area, and excellent particle sieving capability, showing extraordinary promise in plenty of applications, such as sea water desalination, gas separation, and DNA sequencing. The performances of these membranes are mainly determined by the nanopore size, structure, and density, which, in turn, rely on the fabrication techniques of the nanopores. This review covers the important progress of nanopore fabrication in 2D materials and comprehensively compares these methods for the features of the introduced nanopores and their formation processes. Future perspectives are discussed on the opportunities and challenges in fabricating high-grade 2D nanopores.
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Affiliation(s)
- Shihao Su
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, P. R. China.
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22
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Yang W, Radha B, Choudhary A, You Y, Mettela G, Geim A, Aksimentiev A, Keerthi A, Dekker C. Translocation of DNA through Ultrathin Nanoslits. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007682. [PMID: 33522015 PMCID: PMC8011289 DOI: 10.1002/adma.202007682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/03/2020] [Indexed: 05/29/2023]
Abstract
2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current-blockade traces-loading, translation, and exit. Coarse-grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near-uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D-nanoslit devices will provide unique ways to study polymer physics and enable lab-on-a-chip biotechnology.
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Affiliation(s)
- Wayne Yang
- Kavli Institute of Nanoscience Delft, Delft University of Technology, The Netherlands
| | - Boya Radha
- Department of Physics & Astronomy, School of Natural Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- National Graphene Institute, University of Manchester, Manchester M13 9PL, UK
| | - Adnan Choudhary
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yi You
- Department of Physics & Astronomy, School of Natural Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- National Graphene Institute, University of Manchester, Manchester M13 9PL, UK
| | - Gangaiah Mettela
- Department of Physics & Astronomy, School of Natural Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Andre Geim
- Department of Physics & Astronomy, School of Natural Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- National Graphene Institute, University of Manchester, Manchester M13 9PL, UK
| | - Aleksei Aksimentiev
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ashok Keerthi
- National Graphene Institute, University of Manchester, Manchester M13 9PL, UK
- Department of Chemistry, School of Natural Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Cees Dekker
- Kavli Institute of Nanoscience Delft, Delft University of Technology, The Netherlands
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23
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Winogradoff D, Li P, Joshi H, Quednau L, Maffeo C, Aksimentiev A. Chiral Systems Made from DNA. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003113. [PMID: 33717850 PMCID: PMC7927625 DOI: 10.1002/advs.202003113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Indexed: 05/05/2023]
Abstract
The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA's chirality, from plasmonics and spintronics to biosensing.
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Affiliation(s)
- David Winogradoff
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Pin‐Yi Li
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Himanshu Joshi
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Lauren Quednau
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Christopher Maffeo
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
| | - Aleksei Aksimentiev
- Center for the Physics of Living CellsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Department of PhysicsUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaILUSA
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24
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Graphene for Biosensing Applications in Point-of-Care Testing. Trends Biotechnol 2021; 39:1065-1077. [PMID: 33573848 DOI: 10.1016/j.tibtech.2021.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 02/06/2023]
Abstract
Graphene and graphene-related materials (GRMs) exhibit a unique combination of electronic, optical, and electrochemical properties, which make them ideally suitable for ultrasensitive and selective point-of-care testing (POCT) devices. POCT device-based applications in diagnostics require test results to be readily accessible anywhere to produce results within a short analysis timeframe. This review article provides a summary of methods and latest developments in the field of graphene and GRM-based biosensing in POCT and an overview of the main applications of the latter in nucleic acids and enzymatic biosensing, cell detection, and immunosensing. For each application, we discuss scientific and technological advances along with the remaining challenges, outlining future directions for widespread use of this technology in biomedical applications.
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25
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Huang C, Zhu X, Li N, Ma X, Li Z, Fan J. Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level. J Phys Chem Lett 2021; 12:793-799. [PMID: 33411544 DOI: 10.1021/acs.jpclett.0c02989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The identification ability of nanopore sequencing is severely hindered by the diversity of amino acids in a protein. To tackle this problem, a graphene nanoslit sensor is adopted to collect force and current signals to distinguish 20 residues. Extensive molecular dynamics simulations are performed on sequencing peptides under pulling force and applied electric field. Results show that the signals of force and current can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between tyrosine and alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well-grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents. Generally, the graphene nanoslit sensor can be employed to simultaneously sense two signals, thereby enhancing the identification ability and providing an effective mode of nanopore protein sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Na Li
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao, Shandong 266580, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077, Hong Kong, China
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26
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de Souza FAL, Sivaraman G, Fyta M, Scheicher RH, Scopel WL, Amorim RG. Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/h-BN nanopore. NANOSCALE 2020; 12:18289-18295. [PMID: 32857078 DOI: 10.1039/d0nr04363j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as promising candidates to pave the way for the next generation of label-free, fast, and low-cost DNA sequencing. In this work, we explore the sensitivity and selectivity of a graphene/h-BN based nanopore architecture towards detection and distinction of synthetic Hachimoji nucleobases. The study is based on a combination of density functional theory and the non-equilibrium Green's function formalism. Our findings show that the artificial nucleobases are weakly binding to the device, indicating a short residence time in the nanopore during translocation. Significant changes in the electron transmission properties of the device are noted depending on which artificial nucleobase resides in the nanopore, leading to a sensitivity in distinction of up to 80%. Our results thus indicate that the proposed nanopore device setup can qualitatively discriminate synthetic nucleobases, thereby opening up the feasibility of sequencing even unnatural DNA/RNA.
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Affiliation(s)
- Fábio A L de Souza
- Federal Institute of Education, Science and Technology of Espírito Santo, Ibatiba/ES, Brazil
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27
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Jiao S, Liu L, Wang J, Ma K, Lv J. A Novel Biosensor Based on Molybdenum Disulfide (MoS 2 ) Modified Porous Anodic Aluminum Oxide Nanochannels for Ultrasensitive microRNA-155 Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001223. [PMID: 32529739 DOI: 10.1002/smll.202001223] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/29/2020] [Indexed: 05/28/2023]
Abstract
Artificial photoresponsive nanochannels have attracted widespread attention because of their capacity to achieve ion transport through light modulation. Herein, a biosensor for ultrasensitive miRNA-155 detection is devised based on molybdenum disulfide (MoS2 ) modified porous anodic aluminum oxide (AAO) photoresponsive nanochannels by atomic layer deposition (ALD). According to the optimized experimental results, when the cycles of ALD, the wavelength, and the power of the excitation laser are 70 cycles, 450 nm, and 80 mW, respectively, the most supreme photocurrent performance of these photoresponsive nanochannels are obtained. AAO nanochannels modified with MoS2 can work as a photoelectrochemical (PEC) biosensor by generating photoexcitation current; what is more, the high channel density in AAO can magnify the ion current signal response effectively by aggrandizing the flux of electroactive species. By using AAO photoresponsive nanochannels with an average diameter of 150 nm as PEC biosensor, an ultrasensitive detection record ranging from 0.01 fM to 0.01 nM with a detection limit of 3 aM can be achieved. This work not only proposes a simple method for manufacturing semiconductor photoresponsive nanochannels, but also exhibits great potential in the ultrasensitive detection of biomolecules.
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Affiliation(s)
- Songlong Jiao
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Jianqiao Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Kejian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
| | - Jun Lv
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
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28
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Thiruraman JP, Masih Das P, Drndić M. Ions and Water Dancing through Atom-Scale Holes: A Perspective toward "Size Zero". ACS NANO 2020; 14:3736-3746. [PMID: 32195580 PMCID: PMC9463116 DOI: 10.1021/acsnano.0c01625] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We provide an overview of atom-scale apertures in solid-state membranes, from "pores" and "tubes" to "channels", with characteristic sizes comparable to the sizes of ions and water molecules. In this regime of ∼1 nm diameter pores, water molecules and ions are strongly geometrically confined: the size of water molecules (∼0.3 nm) and the size of "hydrated" ions in water (∼0.7-1 nm) are similar to the pore diameters, physically limiting the ion flow through the hole. The pore sizes are comparable to the classical Debye screening length governing the spatial range of electrostatic interaction, ∼0.3 to 1 nm for 1 to 0.1 M KCl. In such small structures, charges can be unscreened, leading to new effects. We discuss experiments on ∼1 nm diameter nanopores, with a focus on carbon nanotube pores and ion transport studies. Finally, we present an outlook for artificial "size zero" pores in the regime of small diameters and small thicknesses. Beyond mimicking protein channels in nature, solid-state pores may offer additional possibilities where sensing and control are performed at the pore, such as in electrically and optically addressable solid-state materials.
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29
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Cadinu P, Kang M, Nadappuram BP, Ivanov AP, Edel JB. Individually Addressable Multi-nanopores for Single-Molecule Targeted Operations. NANO LETTERS 2020; 20:2012-2019. [PMID: 32053383 DOI: 10.1021/acs.nanolett.9b05307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The fine-tuning of molecular transport is a ubiquitous problem of single-molecule methods. The latter is evident even in powerful single-molecule techniques such as nanopore sensing, where the quest for resolving more detailed biomolecular features is often limited by insufficient control of the dynamics of individual molecules within the detection volume of the nanopore. In this work, we introduce and characterize a reconfigurable multi-nanopore architecture that enables additional channels to manipulate the dynamics of DNA molecules in a nanopore. We show that the fabrication process of this device, consisting of four adjacent, individually addressable nanopores located at the tip of a quartz nanopipette, is fast and highly reproducible. By individually tuning the electric field across each nanopore, these devices can operate in several unique cooperative detection modes that allow moving, sensing, and trapping of DNA molecules with high efficiency and increased temporal resolution.
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Affiliation(s)
- Paolo Cadinu
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Minkyung Kang
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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30
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Liu Y, Song X, Yang Y, Li YQ, Zhao M, Mu Y, Li W. Anisotropic protein diffusion on nanosurface. NANOSCALE 2020; 12:5209-5216. [PMID: 32073019 DOI: 10.1039/c9nr08555f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The unique puckered structure of α-phase phosphorene carbide (α-PC) results in anisotropic electronic and thermal transporting properties. In the present work, the interactions between a model protein, villin headpiece sub-domain (HP35), and the surface of α-PC and monolayer black phosphorus (MBP, another puckered nanostructure) were explored by molecular dynamic (MD) simulations. It is found that HP35 diffuses quickly only along the zigzag direction of the α-PC surface. On the MBP surface, HP35 migrates mainly along the zigzag direction but can also easily stride over the ridges and grooves along the armchair direction. Moreover, the mild binding strength between α-PC and HP35 does not cause distortion in the protein structure. The intrinsic biocompatibility of α-PC, which is distinct from several other widely studied nanomaterials, such as carbon nanotubes, graphene and MoS2, makes it a promising candidate in functional biomedical applications.
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Affiliation(s)
- Yang Liu
- School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.
| | - Xiaohan Song
- School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science, Shandong Normal University, Jinan, 250014, China.
| | - Yong-Qiang Li
- School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.
| | - Mingwen Zhao
- School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Weifeng Li
- School of Physics and State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, China.
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31
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Tyagi A, Chu K, Hossain MD, Abidi IH, Lin W, Yan Y, Zhang K, Luo Z. Revealing the mechanism of DNA passing through graphene and boron nitride nanopores. NANOSCALE 2019; 11:23438-23448. [PMID: 31799536 DOI: 10.1039/c9nr07651d] [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
Nanopores on 2D materials have great potential for DNA sequencing, which is attributed to their high sequencing speed and reduced cost. However, identifying DNA bases at such a high speed with nanometer precision has remained a big challenge. Here, we implemented theoretical calculations to show the translocation of single-stranded DNA (ssDNA) through solid-state nanopores on a 2D hexagonal boron nitride (h-BN) and graphene sheet. A base-specific ssDNA sequencing technique was devised, based on the individual differences in the ion current responses for the (polyA)16, (polyG)16, (polyC)16, and (polyT)16 bases of ssDNA. Our sequential procedure for sequencing is built on a comparative approach between the current signals obtained from the nanopores to achieve base-specific detection. Our results indicate that at higher voltages (1.0, 1.2, 1.4, 1.6, 1.8 and 2.0 V nm-1), DNA translocation is tracked though the 1.5 and 2.0 nm nanopores, and at the 1.5 nm pore size, folded ssDNA close to the nanopore accounts for 93% and 81% of events for graphene and h-BN. Our calculations indicate charge transfer from the graphene to ssDNA, while the reverse happens in the case of the h-BN membrane. These results provide critical insights into our understanding of single molecule sequencing through solid-state nanopore research.
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Affiliation(s)
- Abhishek Tyagi
- State Key Laboratory of Precision Electronic Manufacturing Technology and Equipment, School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China. and Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Kelvin Chu
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Md Delowar Hossain
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Irfan Haider Abidi
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Weiyuan Lin
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Yuwei Yan
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Kai Zhang
- State Key Laboratory of Precision Electronic Manufacturing Technology and Equipment, School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Zhengtang Luo
- Department of Chemical and Biological Engineering, William Mong Institute of Nano Science and Technology and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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