1
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Yamazaki H, Mabuchi T, Kaito K, Matsuda K, Kato H, Uemura S. Photothermally Heated Asymmetric Thin Nanopores Suggest the Influence of Temperature on the Intermediate Conformational State of Cytochrome c in an Electric Field. NANO LETTERS 2024; 24:10219-10227. [PMID: 39133007 DOI: 10.1021/acs.nanolett.4c02547] [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: 08/13/2024]
Abstract
Nanopore sensing is a label-free single-molecule technique that enables the study of the dynamical structural properties of proteins. Here, we detect the translocation of cytochrome c (Cyt c) through an asymmetric thin nanopore with photothermal heating to evaluate the influence of temperature on Cyt c conformation during its translocation in an electric field. Before Cyt c translocates through an asymmetric thin SiNx nanopore, ∼1 ms trapping events occur due to electric field-induced denaturation. These trapping events were corroborated by a control analysis with a transmission electron microscopy-drilled pore and denaturant buffer. Cyt c translocation events exhibited markedly greater broad current blockade when the pores were photothermally heated. Collectively, our molecular dynamics simulation predicted that an increased temperature facilitates denaturation of the α-helical structure of Cyt c, resulting in greater blockade current during Cyt c trapping. Our photothermal heating method can be used to study the influence of temperature on protein conformation at the single-molecule level in a label-free manner.
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Affiliation(s)
- Hirohito Yamazaki
- Top Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takuya Mabuchi
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kouta Kaito
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Kyosuke Matsuda
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Hiromu Kato
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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2
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Wang S, Xie Z, Chen Z, Miao L, Li Y, Zhai Y, Ding T. Photothermophoretic Splitting of Gold Nanoparticles for Plasmonic Nanopores and Nanonets Sensing. J Phys Chem Lett 2024; 15:6568-6574. [PMID: 38885430 DOI: 10.1021/acs.jpclett.4c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Optical processing of single plasmonic nanoparticles reinvents the way of high-density information storage, high-performance sensing, and high-definition displays. However, such laser-fabricated nanoplasmonics with well-defined hot spots remain elusive due to the diffraction limit of light. Here we show Au nanoparticle (NP) decorated nanopores can be facilely generated with photothermal splitting of single Au NPs embedded in a silica matrix. The extremely high local temperature induced by plasmonic heating renders gradients of the temperature and surface tension around the Au NP, which drives the nanoscale thermophoretic and Marangoni flow of molten Au/silica. As a result, a nanopore decorated with fragmented Au NPs is formed in the silica film, which presents much stronger surface-enhanced Raman scattering as compared to a single Au NP due to the emergence of hot spots. This strategy can be used to generate plasmonic nanopores of various sizes in the silicon nitride (SiNx) films, which further transforms into nanonets at ambient conditions via light-induced reconstruction of silicon nitride membrane. These nanonets can serve as a robust platform for single particle trapping and analysis.
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Affiliation(s)
- Shuangshuang Wang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhipeng Xie
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Zihao Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Longfei Miao
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yong Li
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yueming Zhai
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Tao Ding
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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3
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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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4
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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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5
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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6
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Li Y, Sandler SE, Keyser UF, Zhu J. DNA Volume, Topology, and Flexibility Dictate Nanopore Current Signals. NANO LETTERS 2023; 23:7054-7061. [PMID: 37487050 PMCID: PMC10416563 DOI: 10.1021/acs.nanolett.3c01823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Nanopores have developed into powerful single-molecule sensors capable of identifying and characterizing small polymers, such as DNA, by electrophoretically driving them through a nanoscale pore and monitoring temporary blockades in the ionic pore current. However, the relationship between nanopore signals and the physical properties of DNA remains only partly understood. Herein, we introduce a programmable DNA carrier platform to capture carefully designed DNA nanostructures. Controlled translocation experiments through our glass nanopores allowed us to disentangle this relationship. We vary DNA topology by changing the length, strand duplications, sequence, unpaired nucleotides, and rigidity of the analyte DNA and find that the ionic current drop is mainly determined by the volume and flexibility of the DNA nanostructure in the nanopore. Finally, we use our understanding of the role of DNA topology to discriminate circular single-stranded DNA molecules from linear ones with the same number of nucleotides using the nanopore signal.
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Affiliation(s)
- Yunxuan Li
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Sarah E. Sandler
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, United Kingdom
- School
of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
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7
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Dong M, Nouri R, Tang Z, Guan W. Morphology around Nanopores Fabricated by Laser-Assisted Dielectric Breakdown and Its Impact on Ion and DNA Transport and Sensing. ACS APPLIED MATERIALS & INTERFACES 2023; 15:24747-24755. [PMID: 37163692 DOI: 10.1021/acsami.3c03123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Laser-assisted controlled dielectric breakdown (LaCBD) has emerged as an alternative to conventional CBD-based nanopore fabrication due to its localization capability, facilitated by the photothermal-induced thinning down in the hot spot. Here, we reported the potential impact of the laser on forming debris around the nanopore region in LaCBD. The debris was clearly observable by scanning electron microscopy (SEM) and photoluminescence (PL) spectroscopy. We found that debris formation is a unique phenomenon in LaCBD that is not observable in the conventional CBD approach. We also found that the LaCBD-induced debris is more evident when the laser power and voltage stress are higher. Moreover, the debris is asymmetrically distributed on the top and bottom sides of the membrane. We also found unexpected rectified ionic and molecular transport in those LaCBD nanopores with debris. Based on these observations, we developed and validated a model describing the debris formation kinetics in LaCBD by considering the generation, diffusion, drift, and gravity in viscous mediums. These findings indicate that while laser aids in nanopore localization, precautions should be taken due to the potential formation of debris and rectification of molecular transport. This study provides valuable insights into the kinetics of LaCBD and the characteristics of the LaCBD nanopore.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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8
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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9
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Lin CY, Fotis R, Xia Z, Kavetsky K, Chou YC, Niedzwiecki DJ, Biondi M, Thei F, Drndić M. Ultrafast Polymer Dynamics through a Nanopore. NANO LETTERS 2022; 22:8719-8727. [PMID: 36315497 DOI: 10.1021/acs.nanolett.2c03546] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrathin nanopore sensors allow single-molecule and polymer measurements at sub-microsecond time resolution enabled by high current signals (∼10-30 nA). We demonstrate for the first time the experimental probing of the ultrafast translocation and folded dynamics of double-stranded DNA (dsDNA) through a nanopore at 10 MHz bandwidth with acquisition of data points per 25 ns (150 MB/s). By introducing a rigorous algorithm, we are able to accurately identify each current level present within translocation events and elucidate the dynamic folded and unfolded behaviors. The remarkable sensitivity of this system reveals distortions of short-lived folded states at a lower bandwidth. This work revisits probing of dsDNA as a model polymer and develops broadly applicable methods. The combined improvements in sensor signals, instrumentation, and large data analysis methods uncover biomolecular dynamics at unprecedentedly small time scales.
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Affiliation(s)
- Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Riley Fotis
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania 19146, United States
| | - Kyril Kavetsky
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Material Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | | | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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11
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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12
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Muhammad Sajeer P, Simran, Nukala P, Manoj M. Varma. TEM based applications in solid state nanopores: From fabrication to liquid in-situ bio-imaging. Micron 2022; 162:103347. [DOI: 10.1016/j.micron.2022.103347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 10/31/2022]
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13
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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14
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Li S, Zeng S, Wen C, Zhang Z, Hjort K, Zhang SL. Docking and Activity of DNA Polymerase on Solid-State Nanopores. ACS Sens 2022; 7:1476-1483. [PMID: 35537188 PMCID: PMC9150166 DOI: 10.1021/acssensors.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integration of motor enzymes with biological nanopores has enabled commercial DNA sequencing technology; yet studies of the similar principle applying to solid-state nanopores are limited. Here, we demonstrate the real-life monitoring of phi29 DNA polymerase (DNAP) docking onto truncated-pyramidal nanopore (TPP) arrays through both electrical and optical readout. To achieve effective docking, atomic layer deposition of hafnium oxide is employed to reduce the narrowest pore opening size of original silicon (Si) TPPs to sub-10 nm. On a single TPP with pore opening size comparable to DNAP, ionic current measurements show that a polymerase-DNA complex can temporally dock onto the TPP with a certain docking orientation, while the majority become translocation events. On 5-by-5 TPP arrays, a label-free optical detection method using Ca2+ sensitive dye, are employed to detect the docking dynamics of DNAP. The results show that this label-free detection strategy is capable of accessing the docking events of DNAP on TPP arrays. Finally, we examine the activity of docked DNAP by performing on-site rolling circle amplification to synthesize single-stranded DNA (ssDNA), which serves as a proof-of-concept demonstration of utilizing this docking scheme for emerging nanopore sensing applications.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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15
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Lin K, Chen C, Wang C, Lian P, Wang Y, Xue S, Sha J, Chen Y. Fabrication of solid-state nanopores. NANOTECHNOLOGY 2022; 33:272003. [PMID: 35349996 DOI: 10.1088/1361-6528/ac622b] [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: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.
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Affiliation(s)
- Kabin Lin
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Congsi Wang
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Peiyuan Lian
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Yan Wang
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China
| | - Song Xue
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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16
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Fried JP, Wu Y, Tilley RD, Gooding JJ. Optical Nanopore Sensors for Quantitative Analysis. NANO LETTERS 2022; 22:869-880. [PMID: 35089719 DOI: 10.1021/acs.nanolett.1c03976] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.
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Affiliation(s)
- Jasper P Fried
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
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17
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Yang JM, Feng JD. Progress on optical measurements in single-molecule analysis with nanopores. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2021-1133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Zvuloni E, Zrehen A, Gilboa T, Meller A. Fast and Deterministic Fabrication of Sub-5 Nanometer Solid-State Pores by Feedback-Controlled Laser Processing. ACS NANO 2021; 15:12189-12200. [PMID: 34219449 PMCID: PMC8320231 DOI: 10.1021/acsnano.1c03773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/28/2021] [Indexed: 05/26/2023]
Abstract
Nanopores are single-molecule sensors capable of detecting and quantifying a broad range of unlabeled biomolecules including DNA and proteins. Nanopores' generic sensing principle has permitted the development of a vast range of biomolecular applications in genomics and proteomics, including single-molecule DNA sequencing and protein fingerprinting. Owing to their superior mechanical and electrical stability, many of the recent studies involved synthetic nanopores fabricated in thin solid-state membranes such as freestanding silicon nitride. However, to date, one of the bottlenecks in this field is the availability of a fast, reliable, and deterministic fabrication method capable of repeatedly forming small nanopores (i.e., sub 5 nm) in situ. Recently, it was demonstrated that a tightly focused laser beam can induce controlled etching of silicon nitride membranes suspended in buffered aqueous solutions. Herein, we demonstrate that nanopore laser drilling (LD) can produce nanopores deterministically to a prespecified size without user intervention. By optimizing the optical apparatus, and by designing a multistep control algorithm for the LD process, we demonstrate a fully automatic fabrication method for any user-defined nanopore size within minutes. The LD process results in a double bowl-shaped structure having a typical size of the laser point-spread function (PSF) at its openings. Numerical simulations of the characteristic LD nanopore shape provide conductance curves that fit the experimental result and support the idea that the pore is produced at the thinnest area formed by the back-to-back facings bowls. The presented LD fabrication method significantly enhances nanopore fabrication throughput and accuracy and hence can be adopted for a large range of biomolecular sensing applications.
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Affiliation(s)
- Eran Zvuloni
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
| | - Adam Zrehen
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
| | - Tal Gilboa
- Department
of Pathology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Amit Meller
- Department
of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel
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19
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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20
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Nanopores: a versatile tool to study protein dynamics. Essays Biochem 2021; 65:93-107. [PMID: 33296461 DOI: 10.1042/ebc20200020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.
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21
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Tang Z, Dong M, He X, Guan W. On Stochastic Reduction in Laser-Assisted Dielectric Breakdown for Programmable Nanopore Fabrication. ACS APPLIED MATERIALS & INTERFACES 2021; 13:13383-13391. [PMID: 33705089 DOI: 10.1021/acsami.0c23106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The controlled dielectric breakdown emerged as a promising alternative toward accessible solid-state nanopore fabrication. Several prior studies have shown that laser-assisted dielectric breakdown could help control the nanopore position and reduce the possibility of forming multiple pores. Here, we developed a physical model to estimate the probability of forming a single nanopore under different combinations of the laser power and the electric field. This model relies on the material- and experiment-specific parameters: the Weibull statistical parameters and the laser-induced photothermal etching rate. Both the model and our experimental data suggest that a combination of a high laser power and a low electric field is statistically favorable for forming a single nanopore at a programmed location. While this model relies on experiment-specific parameters, we anticipate it could provide the experimental insights for nanopore fabrication by the laser-assisted dielectric breakdown method, enabling broader access to solid-state nanopores and their sensing applications.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xiaodong He
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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22
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Alekseeva OK, Pushkareva IV, Pushkarev AS, Fateev VN. Graphene and Graphene-Like Materials for Hydrogen Energy. NANOTECHNOLOGIES IN RUSSIA 2020; 15:273-300. [PMID: 33391617 PMCID: PMC7768998 DOI: 10.1134/s1995078020030027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022]
Abstract
The review is devoted to current and promising areas of application of graphene and materials based on it for generating environmentally friendly hydrogen energy. Analysis of the results of theoretical and experimental studies of hydrogen accumulation in graphene materials confirms the possibility of creating on their basis systems for reversible hydrogen storage, which combine high capacity, stability, and the possibility of rapid hydrogen evolution under conditions acceptable for practical use. Recent advances in the development of chemically and heat-resistant graphene-based membrane materials make it possible to create new gas separation membranes that provide high permeability and selectivity and are promising for hydrogen purification in processes of its production from natural gas. The characteristics of polymer membranes that are currently used in industry for the most part can be significantly improved with small additions of graphene materials. The use of graphene-like materials as a support of nanoparticles or as functional additives in the composition of the electrocatalytic layer in polymer electrolyte membrane fuel cells makes it possible to improve their characteristics and to increase the activity and stability of the electrocatalyst in the reaction of oxygen evolution.
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Affiliation(s)
- O. K. Alekseeva
- National Research Center Kurchatov Institute, Moscow, Russia
| | | | - A. S. Pushkarev
- National Research Center Kurchatov Institute, Moscow, Russia
| | - V. N. Fateev
- National Research Center Kurchatov Institute, Moscow, Russia
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23
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He X, Tang Z, Liang S, Liu M, Guan W. Confocal scanning photoluminescence for mapping electron and photon beam-induced microscopic changes in SiN x during nanopore fabrication. NANOTECHNOLOGY 2020; 31:395202. [PMID: 32526718 DOI: 10.1088/1361-6528/ab9bd4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Focused electron and laser beams have shown the ability to form nanoscale pores in SiN x membranes. During the fabrication process, areas beyond the final nanopore location will inevitably be exposed to the electron beams or the laser beams due to the need for localization, alignment and focus. It remains unclear how these unintended exposures affect the integrity of the membrane. In this work, we demonstrate the use of confocal scanning photoluminescence (PL) for mapping the microscopic changes in SiN x nanopores when exposed to electron and laser beams. We developed and validated a model for the quantitative interpretation of the scanned PL result. The model shows that the scanning PL result is insensitive to the nanopore size. Instead, it is dominated by the product of two microscopic material factors: quantum yield profile (i.e. variations in electronic structure) and thickness profile (i.e. thinning of the membrane). We experimentally demonstrated that the electron and laser beams could alter the material electronic structures (i.e. quantum yield) even when no thinning of the membrane occurs. Our results suggest that minimizing the unintended e-beam or laser beam to the SiN x during the fabrication is crucial if one desires the microscopic integrity of the membrane.
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Affiliation(s)
- Xiaodong He
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America. School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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24
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Hu R, Tong X, Zhao Q. Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability. Adv Healthc Mater 2020; 9:e2000933. [PMID: 32734703 DOI: 10.1002/adhm.202000933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Xin Tong
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
- Peking University Yangtze Delta Institute of Optoelectronics Nantong Jiangsu 226010 China
- Collaborative Innovation Center of Quantum Matter Beijing 100084 China
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25
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Chou YC, Masih Das P, Monos DS, Drndić M. Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements. ACS NANO 2020; 14:6715-6728. [PMID: 32275381 PMCID: PMC9547353 DOI: 10.1021/acsnano.9b09964] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiNx) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl2) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO2 pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO2) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiNx pores (∼ 1.7 nm/day). EELS data reveal the atomic composition of bare and HfO2-coated pores.
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Affiliation(s)
- Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Paul Masih Das
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Dimitri S Monos
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania and The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
- Immunogenetics Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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26
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Fu J, Wu L, Qiao Y, Tu J, Lu Z. Microfluidic Systems Applied in Solid-State Nanopore Sensors. MICROMACHINES 2020; 11:mi11030332. [PMID: 32210148 PMCID: PMC7142662 DOI: 10.3390/mi11030332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/08/2020] [Accepted: 03/20/2020] [Indexed: 01/04/2023]
Abstract
Microfluidic system, as a kind of miniature integrated operating platform, has been applied to solid-state nanopore sensors after many years of experimental study. In the process of introducing microfluidic into solid-state nanopore sensors, many novel device structures are designed due to the abundance of analytes and the diversity of detection methods. Here we review the fundamental setup of nanopore-based microfluidic systems and the developments and advancements that have been taking place in the field. The microfluidic systems with a multichannel strategy to elevate the throughput and efficiency of nanopore sensors are then presented. Multifunctional detection represented by optical-electrical detection, which is realized by microfluidic integration, is also described. A high integration microfluidic system with nanopore is further discussed, which shows the prototype of commercialization.
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Affiliation(s)
| | | | | | - Jing Tu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
| | - Zuhong Lu
- Correspondence: (J.T.); (Z.L.); Tel.: +86-25-8379-2396 (J.T.); +86-25-8379-3779 (Z.L.)
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27
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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28
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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29
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Waugh M, Briggs K, Gunn D, Gibeault M, King S, Ingram Q, Jimenez AM, Berryman S, Lomovtsev D, Andrzejewski L, Tabard-Cossa V. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 2019; 15:122-143. [DOI: 10.1038/s41596-019-0255-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
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30
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St-Denis T, Yazda K, Capaldi X, Bustamante J, Safari M, Miyahara Y, Zhang Y, Grutter P, Reisner W. An apparatus based on an atomic force microscope for implementing tip-controlled local breakdown. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:123703. [PMID: 31893796 DOI: 10.1063/1.5129665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores are powerful tools for sensing of single biomolecules in solution. Fabrication of solid-state nanopores is still challenging, however; in particular, new methods are needed to facilitate the integration of pores with larger nanofluidic and electronic device architectures. We have developed the tip-controlled local breakdown (TCLB) approach, in which an atomic force microscope (AFM) tip is brought into contact with a silicon nitride membrane that is placed onto an electrolyte reservoir. The application of a voltage bias at the AFM tip induces a dielectric breakdown that leads to the formation of a nanopore at the tip position. In this work, we report on the details of the apparatus used to fabricate nanopores using the TCLB method, and we demonstrate the formation of nanopores with smaller, more controlled diameters using a current limiting circuit that zeroes the voltage upon pore formation. Additionally, we demonstrate the capability of TCLB to fabricate pores aligned to embedded topographical features on the membranes.
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Affiliation(s)
- T St-Denis
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - K Yazda
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - X Capaldi
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - J Bustamante
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - M Safari
- Norcada, 4548-99 Street NW, Edmonton, Alberta T6E 5H5, Canada
| | - Y Miyahara
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Y Zhang
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - P Grutter
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - W Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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Fürjes P. Controlled Focused Ion Beam Milling of Composite Solid State Nanopore Arrays for Molecule Sensing. MICROMACHINES 2019; 10:mi10110774. [PMID: 31766129 PMCID: PMC6915623 DOI: 10.3390/mi10110774] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022]
Abstract
Various nanoscale fabrication techniques are elaborated to form artificial nanoporous/nanochannel membranes to be applied for biosensing: one of the most prevalent is the micro-electromechanical systems (MEMS) compatible focused ion beam (FIB) milling. This technique can be easily adopted in micro- and nanomachining process sequences to develop composite multi-pore structures, although its precision and reproducibility are key points in the case of these thick multi-layered membranes. This work is to demonstrate a comprehensive characterisation of FIB milling to improve the reliability of the fabrication of solid state nanopore arrays with precisely predetermined pore geometries for a targeted molecule type to be recognised. The statistical geometric features of the fabricated nanopores were recorded as the function of the process parameters, and the resulting geometries were analysed in detail by high resolution scanning electron microscope (SEM), transmission electron microscope (TEM) and ion scanning microscopy. Continuous function of the pore diameter evolution rate was derived from the experimental results in the case of different material structures, and compared to former dissentient estimations. The additional metal layer was deposited onto the backside of the membrane and grounded during the ion milling to prevent the electrical charging of dielectric layers. The study proved that the conformity of the pore geometry and the reliability of their fabrication could be improved significantly. The applicability of the developed nanopore arrays for molecule detection was also considered by characterising the pore diameter dependent sensitivity of the membrane impedance modulation based measurement method.
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Affiliation(s)
- Péter Fürjes
- Microsystems Lab, Inst. of Technical Physics and Materials Science, Centre for Energy Research, Budapest H-1121, Hungary
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32
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Garoli D, Yamazaki H, Maccaferri N, Wanunu M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. NANO LETTERS 2019; 19:7553-7562. [PMID: 31587559 DOI: 10.1021/acs.nanolett.9b02759] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia , via Morego 30 , I-16163 , Genova , Italy
| | - Hirohito Yamazaki
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Faïencerie , L-1511 Luxembourg , Luxembourg
| | - Meni Wanunu
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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33
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Polarization Induced Electro-Functionalization of Pore Walls: A Contactless Technology. BIOSENSORS-BASEL 2019; 9:bios9040121. [PMID: 31614545 PMCID: PMC6956341 DOI: 10.3390/bios9040121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022]
Abstract
This review summarizes recent advances in micro- and nanopore technologies with a focus on the functionalization of pores using a promising method named contactless electro-functionalization (CLEF). CLEF enables the localized grafting of electroactive entities onto the inner wall of a micro- or nano-sized pore in a solid-state silicon/silicon oxide membrane. A voltage or electrical current applied across the pore induces the surface functionalization by electroactive entities exclusively on the inside pore wall, which is a significant improvement over existing methods. CLEF's mechanism is based on the polarization of a sandwich-like silicon/silicon oxide membrane, creating electronic pathways between the core silicon and the electrolyte. Correlation between numerical simulations and experiments have validated this hypothesis. CLEF-induced micro- and nanopores functionalized with antibodies or oligonucleotides were successfully used for the detection and identification of cells and are promising sensitive biosensors. This technology could soon be successfully applied to planar configurations of pores, such as restrictions in microfluidic channels.
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34
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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35
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019; 65:69-77. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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36
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Spitzberg JD, Zrehen A, van Kooten XF, Meller A. Plasmonic-Nanopore Biosensors for Superior Single-Molecule Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1900422. [PMID: 30941823 DOI: 10.1002/adma.201900422] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/19/2019] [Indexed: 05/26/2023]
Abstract
Plasmonic and nanopore sensors have separately received much attention for achieving single-molecule precision. A plasmonic "hotspot" confines and enhances optical excitation at the nanometer length scale sufficient to optically detect surface-analyte interactions. A nanopore biosensor actively funnels and threads analytes through a molecular-scale aperture, wherein they are interrogated by electrical or optical means. Recently, solid-state plasmonic and nanopore structures have been integrated within monolithic devices that address fundamental challenges in each of the individual sensing methods and offer complimentary improvements in overall single-molecule sensitivity, detection rates, dwell time and scalability. Here, the physical phenomena and sensing principles of plasmonic and nanopore sensing are summarized to highlight the novel complementarity in dovetailing these techniques for vastly improved single-molecule sensing. A literature review of recent plasmonic nanopore devices is then presented to delineate methods for solid-state fabrication of a range of hybrid device formats, evaluate the progress and challenges in the detection of unlabeled and labeled analyte, and assess the impact and utility of localized plasmonic heating. Finally, future directions and applications inspired by the present state of the art are discussed.
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Affiliation(s)
- Joshua D Spitzberg
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | - Adam Zrehen
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
| | | | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 32000, Israel
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
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37
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Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput Biol 2019; 15:e1007067. [PMID: 31145734 PMCID: PMC6559672 DOI: 10.1371/journal.pcbi.1007067] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 05/02/2019] [Indexed: 11/25/2022] Open
Abstract
Single-molecule techniques for protein sequencing are making headway towards single-cell proteomics and are projected to propel our understanding of cellular biology and disease. Yet, single cell proteomics presents a substantial unmet challenge due to the unavailability of protein amplification techniques, and the vast dynamic-range of protein expression in cells. Here, we describe and computationally investigate the feasibility of a novel approach for single-protein identification using tri-color fluorescence and plasmonic-nanopore devices. Comprehensive computer simulations of denatured protein translocation processes through the nanopores show that the tri-color fluorescence time-traces retain sufficient information to permit pattern-recognition algorithms to correctly identify the vast majority of proteins in the human proteome. Importantly, even when taking into account realistic experimental conditions, which restrict the spatial and temporal resolutions as well as the labeling efficiency, and add substantial noise, a deep-learning protein classifier achieves 97% whole-proteome accuracies. Applying our approach for protein datasets of clinical relevancy, such as the plasma proteome or cytokine panels, we obtain ~98% correct protein identification. This study suggests the feasibility of a method for accurate and high-throughput protein identification, which is highly versatile and applicable. Macromolecules identification methods are central for most biological and biomedical studies, and while the field of genomics advanced to single-molecule resolution, the proteomic field still relies on bulk and costly techniques. We describe a solution for single protein identification, based on the analysis of optical traces obtained from fluorescently-labeled proteins threaded through a nanopore and processed by a pattern recognition algorithm. To evaluate the feasibility of our method we constructed computer simulations of the system, producing and analyzing nearly 108 individual protein translocations from the human Swiss-Prot database. Our results suggest protein identification of >95% for the whole human proteome, even under non-ideal conditions. These results constitute the basis for a novel whole proteome identification method, with single molecule resolution.
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38
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Fabrication and practical applications of molybdenum disulfide nanopores. Nat Protoc 2019; 14:1130-1168. [PMID: 30903110 DOI: 10.1038/s41596-019-0131-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023]
Abstract
Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin membranes have the advantage of providing relatively high ionic currents at very small pore sizes. This increases the signal generated during translocation of biomolecules and improves the nanopores' efficiency when used for desalination or reverse electrodialysis applications. The atomic thickness of MoS2 nanopores approaches the inter-base distance of DNA, creating a potential candidate for DNA sequencing. In terms of geometry, MoS2 nanopores have a well-defined vertical profile due to their atomic thickness, which eliminates any unwanted effects associated with uneven pore profiles observed in other materials. This protocol details all the necessary procedures for the fabrication of solid-state devices. We discuss different methods for transfer of monolayer MoS2, different approaches for the creation of nanopores, their applicability in detecting DNA translocations and the analysis of translocation data through open-source programming packages. We present anticipated results through the application of our nanopores in DNA translocations and osmotic power generation. The procedure comprises four parts: fabrication of devices (2-3 d), transfer of MoS2 and cleaning procedure (24 h), the creation of nanopores within MoS2 (30 min) and performing DNA translocations (2-3 h). We anticipate that our protocol will enable large-scale manufacturing of single-molecule-analysis devices as well as next-generation DNA sequencing.
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39
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Danda G, Drndić M. Two-dimensional nanopores and nanoporous membranes for ion and molecule transport. Curr Opin Biotechnol 2019; 55:124-133. [DOI: 10.1016/j.copbio.2018.09.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/12/2018] [Accepted: 09/11/2018] [Indexed: 01/19/2023]
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40
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Zhao J, He G, Huang S, Villalobos LF, Dakhchoune M, Bassas H, Agrawal KV. Etching gas-sieving nanopores in single-layer graphene with an angstrom precision for high-performance gas mixture separation. SCIENCE ADVANCES 2019; 5:eaav1851. [PMID: 30746475 PMCID: PMC6357726 DOI: 10.1126/sciadv.aav1851] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/10/2018] [Indexed: 05/19/2023]
Abstract
One of the bottlenecks in realizing the potential of atom-thick graphene membrane for gas sieving is the difficulty in incorporating nanopores in an otherwise impermeable graphene lattice, with an angstrom precision at a high-enough pore density. We realize this design by developing a synergistic, partially decoupled defect nucleation and pore expansion strategy using O2 plasma and O3 treatment. A high density (ca. 2.1 × 1012 cm-2) of H2-sieving pores was achieved while limiting the percentage of CH4-permeating pores to 13 to 22 parts per million. As a result, a record-high gas mixture separation performance was achieved (H2 permeance, 1340 to 6045 gas permeation units; H2/CH4 separation factor, 15.6 to 25.1; H2/C3H8 separation factor, 38.0 to 57.8). This highly scalable pore etching strategy will accelerate the development of single-layer graphene-based energy-efficient membranes.
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Affiliation(s)
- J. Zhao
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
- State Key Laboratory of Materials-Oriented Chemical Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - G. He
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
| | - S. Huang
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
| | - L. F. Villalobos
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
| | - M. Dakhchoune
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
| | - H. Bassas
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
| | - K. V. Agrawal
- Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL), Sion CH-1951, Switzerland
- Corresponding author.
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41
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Yamazaki H, Hu R, Zhao Q, Wanunu M. Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores. ACS NANO 2018; 12:12472-12481. [PMID: 30457833 DOI: 10.1021/acsnano.8b06805] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sculpting solid-state materials at the nanoscale is an important step in the manufacturing of numerous types of sensor devices, in particular solid-state nanopore sensors. Here we present mechanistic insight into laser-induced thinning of low-stress silicon nitride (SiN x) membranes and films. In a recent study, we observed that focusing a visible wavelength laser beam on a SiN x membrane results in efficient localized heating, and we used this effect to control temperature at a solid-state nanopore sensor. A side-effect of the observed heating was that the pores expand/degrade under prolonged high-power illumination, prompting us to study the mechanism of this etching process. We find that SiN x can be etched under exposure to light of ∼107 W/cm2 average intensity, with etch rates that are influenced by the supporting electrolyte. Combining this controlled etching with dielectric breakdown, an electrokinetic process for making pores, nanopores of arbitrary dimensions as small as 1-2 nm in diameter and thickness can easily be fabricated. Evidence gathered from biomolecule-pore interactions suggests that the pore geometries obtained using this method are more funnel-like, rather than hourglass-shaped. Refined control over pore dimensions can expand the range of applications of solid-state nanopores, for example, biopolymer sequencing and detection of specific biomarkers.
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Affiliation(s)
- Hirohito Yamazaki
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Meni Wanunu
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
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42
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Varongchayakul N, Song J, Meller A, Grinstaff MW. Single-molecule protein sensing in a nanopore: a tutorial. Chem Soc Rev 2018; 47:8512-8524. [PMID: 30328860 DOI: 10.1039/c8cs00106e] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteins are the structural elements and machinery of cells responsible for a functioning biological architecture and homeostasis. Advances in nanotechnology are catalyzing key breakthroughs in many areas, including the analysis and study of proteins at the single-molecule level. Nanopore sensing is at the forefront of this revolution. This tutorial review provides readers a guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores. Specifically, the review describes the key materials, nanoscale features, and design requirements of nanopores. It also discusses general design requirements as well as details on the analysis of protein translocation. Finally, the article provides the background necessary to understand current research trends and to encourage the identification of new biomedical applications for protein sensing using nanopores.
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43
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Ying C, Houghtaling J, Eggenberger OM, Guha A, Nirmalraj P, Awasthi S, Tian J, Mayer M. Formation of Single Nanopores with Diameters of 20-50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown. ACS NANO 2018; 12:11458-11470. [PMID: 30335956 DOI: 10.1021/acsnano.8b06489] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanopores with diameters from 20 to 50 nm in silicon nitride (SiN x) windows are useful for single-molecule studies of globular macromolecules. While controlled breakdown (CBD) is gaining popularity as a method for fabricating nanopores with reproducible size control and broad accessibility, attempts to fabricate large nanopores with diameters exceeding ∼20 nm via breakdown often result in undesirable formation of multiple nanopores in SiN x membranes. To reduce the probability of producing multiple pores, we combined two strategies: laser-assisted breakdown and controlled pore enlargement by limiting the applied voltage. Based on laser power-dependent increases in nanopore conductance upon illumination and on the absence of an effect of ionic strength on the ratio between the nanopore conductance before and after laser illumination, we suggest that the increased rate of controlled breakdown results from laser-induced heating. Moreover, we demonstrate that conductance values before and after coating the nanopores with a fluid lipid bilayer can indicate fabrication of a single nanopore versus multiple nanopores. Complementary flux measurements of Ca2+ through the nanopore typically confirmed assessments of single or multiple nanopores that we obtained using the coating method. Finally, we show that thermal annealing of CBD pores significantly increased the success rate of coating and reduced the current noise before and after lipid coating. We characterize the geometry of these nanopores by analyzing individual resistive pulses produced by translocations of spherical proteins and demonstrate the usefulness of these nanopores for estimating the approximate molecular shape of IgG proteins.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jared Houghtaling
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
- Department of Biomedical Engineering , University of Michigan , 2200 Bonisteel Boulevard , Ann Arbor , Michigan 48109 , United States
| | - Olivia M Eggenberger
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Anirvan Guha
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Peter Nirmalraj
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Saurabh Awasthi
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics , Nankai University , Tianjin 300071 , China
| | - Michael Mayer
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
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