1
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Ahmed SA, Liu Y, Xiong T, Zhao Y, Xie B, Pan C, Ma W, Yu P. Iontronic Sensing Based on Confined Ion Transport. Anal Chem 2024; 96:8056-8077. [PMID: 38663001 DOI: 10.1021/acs.analchem.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Saud Asif Ahmed
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yueru Zhao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Boyang Xie
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Cong Pan
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
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2
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Li X, Fu YH, Wei N, Yu RJ, Bhatti H, Zhang L, Yan F, Xia F, Ewing AG, Long YT, Ying YL. Emerging Data Processing Methods for Single-Entity Electrochemistry. Angew Chem Int Ed Engl 2024; 63:e202316551. [PMID: 38411372 DOI: 10.1002/anie.202316551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ying-Huan Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nannan Wei
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
| | - Huma Bhatti
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Limin Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 430034, Wuhan, P. R. China
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296, Gothenburg, Sweden
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
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3
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Cheng P, Zhao C, Pan Q, Xiong Z, Chen Q, Miao X, He Y. Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2420. [PMID: 38676038 PMCID: PMC11053845 DOI: 10.3390/s24082420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.
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Affiliation(s)
| | | | | | | | - Qi Chen
- Hubei Yangtze Memory Laboratories, School of Integrated Circuit, Huazhong University of Science and Technology, Wuhan 430074, China
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4
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Hou J, Zhao C, Zhang H. Bio-Inspired Subnanofluidics: Advanced Fabrication and Functionalization. SMALL METHODS 2024; 8:e2300278. [PMID: 37203269 DOI: 10.1002/smtd.202300278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/02/2023] [Indexed: 05/20/2023]
Abstract
Biological ion channels can realize high-speed and high-selective ion transport through the protein filter with the sub-1-nanometer channel. Inspired by biological ion channels, various kinds of artificial subnanopores, subnanochannels, and subnanoslits with improved ion selectivity and permeability are recently developed for efficient separation, energy conversion, and biosensing. This review article discusses the advanced fabrication and functionalization methods for constructing subnanofluidic pores, channels, tubes, and slits, which have shown great potential for various applications. Novel fabrication methods for producing subnanofluidics, including top-down techniques such as electron beam etching, ion irradiation, and electrochemical etching, as well as bottom-up approaches starting from advanced microporous frameworks, microporous polymers, lipid bilayer embedded subnanochannels, and stacked 2D materials are well summarized. Meanwhile, the functionalization methods of subnanochannels are discussed based on the introduction of functional groups, which are classified into direct synthesis, covalent bond modifications, and functional molecule fillings. These methods have enabled the construction of subnanochannels with precise control of structure, size, and functionality. The current progress, challenges, and future directions in the field of subnanofluidic are also discussed.
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Affiliation(s)
- Jue Hou
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Chen Zhao
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Huacheng Zhang
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
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5
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Fang S, Zeng D, He S, Li Y, Pang Z, Wang Y, Liang L, Weng T, Xie W, Wang D. Fast Fabrication Nanopores on a PMMA Membrane by a Local High Electric Field Controlled Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2109. [PMID: 38610321 PMCID: PMC11013984 DOI: 10.3390/s24072109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
The sensitivity and accuracy of nanopore sensors are severely hindered by the high noise associated with solid-state nanopores. To mitigate this issue, the deposition of organic polymer materials onto silicon nitride (SiNx) membranes has been effective in obtaining low-noise measurements. Nonetheless, the fabrication of nanopores sub-10 nm on thin polymer membranes remains a significant challenge. This work proposes a method for fabricating nanopores on polymethyl methacrylate (PMMA) membrane by the local high electrical field controlled breakdown, exploring the impact of voltage and current on the breakdown of PMMA membranes and discussing the mechanism underlying the breakdown voltage and current during the formation of nanopores. By improving the electric field application method, transient high electric fields that are one-seven times higher than the breakdown electric field can be utilized to fabricate nanopores. A comparative analysis was performed on the current noise levels of nanopores in PMMA-SiNx composite membranes and SiNx nanopores with a 5 nm diameter. The results demonstrated that the fast fabrication of nanopores on PMMA-SiNx membranes exhibited reduced current noise compared to SiNx nanopores. This finding provides evidence supporting the feasibility of utilizing this technology for efficiently fabricating low-noise nanopores on polymer composite membranes.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Shixuan He
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yadong Li
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Zichen Pang
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
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6
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Bandara YMNDY, Karawdeniya BI, Dutt S, Kluth P, Tricoli A. Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown. Anal Chem 2024; 96:2124-2134. [PMID: 38277343 DOI: 10.1021/acs.analchem.3c04860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
With growing interest in solid-state nanopore sensing─a single-molecule technique capable of profiling a host of analyte classes─establishing facile and scalable approaches for fabricating molecular-size pores is becoming increasingly important. The introduction of nanopore fabrication by controlled breakdown (CBD) has transformed the economics and accessibility of nanopore fabrication. Here, we introduce the design of an Arduino-based, portable USB-powered CBD device, with an estimated cost of <150 USD, which is ≈10-100× cheaper than most commercial solutions, capable of fabricating single nanopores conducive for single molecule sensing experiments. We demonstrate the facile fabrication of 60 tailored nanopores (∼2.6-12.6 nm) with ∼80% of the pores within 1 nm of the target diameter. Selected pores were then tested with double-stranded DNA, the canonical molecular ruler, demonstrating their performance for single-molecule sensing applications. The device is constructed with off-the-shelf readily available components and controlled using a highly customizable MATLAB application, which has capabilities encompassing pore fabrication, pore enlargement, and current-voltage acquisition for pore size estimation. When combined with a portable amplifier, this device also provides a fully portable sensing platform, an important step toward portable solid-state nanopore sensing applications.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Nanotechnology Research Laboratory, Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Buddini I Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Shankar Dutt
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Antonio Tricoli
- Nanotechnology Research Laboratory, Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- Nanotechnology Research Laboratory, School of Biomedical Engineering, Faculty of Engineering, University of Sydney, NSW 2008, Australia
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7
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Hong H, Wei J, Lei X, Chen H, Sarro PM, Zhang G, Liu Z. Study on the controllability of the fabrication of single-crystal silicon nanopores/nanoslits with a fast-stop ionic current-monitored TSWE method. MICROSYSTEMS & NANOENGINEERING 2023; 9:63. [PMID: 37206700 PMCID: PMC10188523 DOI: 10.1038/s41378-023-00532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
The application of single-crystal silicon (SCS) nanopore structures in single-molecule-based analytical devices is an emerging approach for the separation and analysis of nanoparticles. The key challenge is to fabricate individual SCS nanopores with precise sizes in a controllable and reproducible way. This paper introduces a fast-stop ionic current-monitored three-step wet etching (TSWE) method for the controllable fabrication of SCS nanopores. Since the nanopore size has a quantitative relationship with the corresponding ionic current, it can be regulated by controlling the ionic current. Thanks to the precise current-monitored and self-stop system, an array of nanoslits with a feature size of only 3 nm was obtained, which is the smallest size ever reported using the TSWE method. Furthermore, by selecting different current jump ratios, individual nanopores of specific sizes were controllably prepared, and the smallest deviation from the theoretical value was 1.4 nm. DNA translocation measurement results revealed that the prepared SCS nanopores possessed the excellent potential to be applied in DNA sequencing.
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Affiliation(s)
- Hao Hong
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Jiangtao Wei
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Xin Lei
- School of Chemistry, Beihang University, 100084 Beijing, China
| | - Haiyun Chen
- School of Electronic and Information Engineering, Beijing Jiaotong University, 100084 Beijing, China
| | - Pasqualina M. Sarro
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Zewen Liu
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
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8
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Mao W, Cai X, Pan R, Tang S, Yang F, Cui Y, Sun J, Shen W. Light-enhanced transparent hydrogel for uric acid and glucose detection by four different analytical platforms. Anal Chim Acta 2023; 1239:340717. [PMID: 36628770 DOI: 10.1016/j.aca.2022.340717] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/13/2022] [Accepted: 12/08/2022] [Indexed: 12/13/2022]
Abstract
The lack of solid-phase media limits the portability of colorimetric sensing platforms. In this study, a series of transparent polyvinyl alcohol (PVA) hydrogels encapsulated antimony tin oxide nanoparticles (ATO NPs) and 3,3',5,5'-tetramethylbenzidine (TMB) were developed as the solid-phase sensing media for glucose and uric acid. Under the conditions of H2O2 and UV light, the hydrogel presented a multicatalytic ability (photo Fenton-like and peroxidase-like activities), which accelerated the oxidation of TMB, turning the hydrogel from colorless to blue and finally enhancing the detection signal. The plasticity of the hydrogel allowed it to be designed into various shapes (membrane, microsphere etc.) to adapt multiple detection platforms (a liquid/solid-phase UV spectrophotometer, a NanoPhotometer, and smartphone spectroscopy). The hydrogel sensing media exhibited excellent tunability and enhanced the photocatalytic ability. The proposed material was successfully applied to detect glucose and uric acids in real samples by four detection platforms to evaluate its practicability.
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Affiliation(s)
- Wei Mao
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China
| | - Xingwei Cai
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China
| | - Ruirong Pan
- Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu Province, PR China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China.
| | - Fu Yang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China
| | - Yanjuan Cui
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China
| | - Jun Sun
- School of Chemistry, The University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, PR China.
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9
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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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10
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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11
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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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12
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Liu G, Hao L, Li H, Zhang K, Yu X, Li D, Zhu X, Hao D, Ma Y, Ma L. Topography Mapping with Scanning Electrochemical Cell Microscopy. Anal Chem 2022; 94:5248-5254. [PMID: 35312291 DOI: 10.1021/acs.analchem.1c04692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-resolution scanning electrochemical cell microscopy (SECCM), synchronously visualizing the topography and electrochemical activity, could be used to directly correlate the structure and activity of materials nanoscopically. However, its topographical measurement is largely restricted by the size and stability of the meniscus droplet formed at the end of the nanopipette. In this paper, we report a scheme that could reliably gain several tens nanometer resolution (≥65 nm) of SECCM using homemade ∼50 nm inner diameter probes. Furthermore, the topography and hydrogen evolution reaction (HER) activity of ∼45 nm self-assembled Au nanoparticles monolayer were simultaneously recorded successfully. This scheme could make mapping of both topologic and chemical properties of samples in the nanometer regime with SECCM routinely, which potentially can largely expand the field of SECCM applications.
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Affiliation(s)
- Gen Liu
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Luzhen Hao
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Hao Li
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Kaimin Zhang
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Xue Yu
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Dong Li
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Xiaodong Zhu
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Danni Hao
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
| | - Yanqing Ma
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China.,State Laboratory of Precision Measuring Technology and Instruments, Tianjin University, Tianjin 300072, P. R. China
| | - Lei Ma
- Tianjin International Center for Nanoparticles and Nanosystems, Tianjin University, Tianjin 300072, P. R. China
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13
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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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14
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Yanagi I, Takeda KI. Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO 2sacrificial layer process. NANOTECHNOLOGY 2021; 32:415301. [PMID: 34214991 DOI: 10.1088/1361-6528/ac10e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO2. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO2sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)60passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.
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Affiliation(s)
- Itaru Yanagi
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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15
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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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16
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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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17
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Leung C, Briggs K, Laberge MP, Peng S, Waugh M, Tabard-Cossa V. Mechanisms of solid-state nanopore enlargement under electrical stress. NANOTECHNOLOGY 2020; 31:44LT01. [PMID: 32698174 DOI: 10.1088/1361-6528/aba86e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We present a thorough exploration of nanopore growth under electrical stress in electrolyte solution, and demonstrate that despite their superficial similarities, nanopore formation by controlled breakdown (CBD) and nanopore growth under moderate voltage stress are fundamentally different processes. In particular, we demonstrate that unlike the CBD process, nanopore growth is primarily driven by the level of ionic current passing through the nanopore, rather than the strength of the electric field generating the current, and that enlargement has a much weaker pH dependence than does CBD pore formation. In combination with other works in the field, our results suggest that despite clear current-dependence, Joule heating is unlikely to be the main driver of pore growth during electrical stress, pointing instead toward electrochemical dissolution of membrane material along the pore walls. While the chemistry underlying the growth process remains unclear, the dependence of growth rate on current allows decoupling of the pore enlargement mechanism from the possibility of forming additional nanopores during the growth process, providing a practical method by which to rapidly enlarge a nanopore without risking opening a second nanopore.
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Affiliation(s)
- Chelsea Leung
- Department of Physics, University of Ottawa, Ottawa, Canada
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18
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Brunet Cabré M, Djekic D, Romano T, Hanna N, Anders J, McKelvey K. Microscale Electrochemical Cell on a Custom CMOS Transimpedance Amplifier for High Temporal Resolution Single Entity Electrochemistry**. ChemElectroChem 2020. [DOI: 10.1002/celc.202001083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Denis Djekic
- Institute of Smart Sensors University of Stuttgart Keplerstraße 7 70174 Stuttgart Germany
| | | | - Nadim Hanna
- Institute of Smart Sensors University of Stuttgart Keplerstraße 7 70174 Stuttgart Germany
| | - Jens Anders
- Institute of Smart Sensors University of Stuttgart Keplerstraße 7 70174 Stuttgart Germany
| | - Kim McKelvey
- School of Chemistry Trinity College Dublin Dublin Ireland
- School of Chemical and Physical Sciences Victoria University of Wellington Kelburn, Wellington 6012 New Zealand
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19
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Fang S, Yin B, Xie W, Zhou D, Tang P, He S, Yuan J, Wang D. A novel dielectric breakdown apparatus for solid-state nanopore fabrication with transient high electric field. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:093203. [PMID: 33003785 DOI: 10.1063/5.0024079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The dielectric breakdown used to fabricate solid-state nanopores has separated the device from capital-intensive industries and has been widely adopted by various research teams, but there are still problems with low production efficiency and uncertain location. In this work, based on the transient breakdown phenomenon of nanofilms, a new type of dielectric breakdown apparatus for nanopore fabrication is reported. It integrates both nano-manipulation technology and dielectric breakdown nanopore fabrication technology. The nanometer distance detection method and circuit are introduced in detail. The generation principle and procedures of the transient high electric field are explained step by step. The characterization of the nanopores shows that this apparatus can fabricate sub-2 nm nanopores at a pre-located position. Besides, the nanopore diameter can be easily adjusted by setting the transient high electric field value.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Daming Zhou
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Peng Tang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
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20
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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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21
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Yin B, Fang S, Zhou D, Liang L, Wang L, Wang Z, Wang D, Yuan J. Nanopore Fabrication via Transient High Electric Field Controlled Breakdown and Detection of Single RNA Molecules. ACS APPLIED BIO MATERIALS 2020; 3:6368-6375. [DOI: 10.1021/acsabm.0c00812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bohua Yin
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Daming Zhou
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
| | - Deqiang Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
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22
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Polster JW, Acar ET, Aydin F, Zhan C, Pham TA, Siwy ZS. Gating of Hydrophobic Nanopores with Large Anions. ACS NANO 2020; 14:4306-4315. [PMID: 32181640 DOI: 10.1021/acsnano.9b09777] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding ion transport in nanoporous materials is critical to a wide variety of energy and environmental technologies, ranging from ion-selective membranes, drug delivery, and biosensing, to ion batteries and supercapacitors. While nanoscale transport is often described by continuum models that rely on a point charge description for ions and a homogeneous dielectric medium for the solvent, here, we show that transport of aqueous solutions at a hydrophobic interface can be highly dependent on the size and hydration strength of the solvated ions. Specifically, measurements of ion current through single silicon nitride nanopores that contain a hydrophobic-hydrophilic junction show that transport properties are dependent not only on applied voltage but also on the type of anion. We find that in Cl--containing solutions the nanopores only conducted ionic current above a negative voltage threshold. On the other hand, introduction of large polarizable anions, such as Br- and I-, facilitated the pore wetting, making the pore conductive at all examined voltages. Molecular dynamics simulations revealed that the large anions, Br- and I-, have a weaker solvation shell compared to that of Cl- and consequently were prone to migrate from the aqueous solution to the hydrophobic surface, leading to the anion accumulation responsible for pore wetting. The results are essential for designing nanoporous systems that are selective to ions of the same charge, for realization of ion-induced wetting in hydrophobic pores, as well as for a fundamental understanding on the role of ion hydration shell on the properties of solid/liquid interfaces.
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Affiliation(s)
- Jake W Polster
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Elif Turker Acar
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Chemistry, Faculty of Engineering, Istanbul University - Cerrahpasa, Avcılar, 34320 Istanbul, Turkey
| | - Fikret Aydin
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Cheng Zhan
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Tuan Anh Pham
- Quantum Simulations Group and Laboratory for Energy Applications for the Future, Lawrence Livermore National Laboratory, Livermore, California 94551, United States
| | - Zuzanna S Siwy
- Department of Chemistry, University of California, Irvine, California 92697, United States
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23
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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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24
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Lin CY, Turker Acar E, Polster JW, Lin K, Hsu JP, Siwy ZS. Modulation of Charge Density and Charge Polarity of Nanopore Wall by Salt Gradient and Voltage. ACS NANO 2019; 13:9868-9879. [PMID: 31348640 DOI: 10.1021/acsnano.9b01357] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Surface charge plays a very important role in biological processes including ionic and molecular transport across a cell membrane. Placement of charges and charge patterns on walls of polymer and solid-state nanopores allowed preparation of ion-selective systems as well as ionic diodes and transistors to be applied in building biological sensors and ionic circuits. In this article, we show that the surface charge of a 10 nm diameter silicon nitride nanopore placed in contact with a salt gradient is not a constant value, but rather it depends on applied voltage and magnitude of the salt gradient. We found that even when a nanopore was in contact with solutions of pH equivalent to the isoelectric point of the pore surface, the pore walls became charged with voltage-dependent charge density. Implications of the charge gating for detection of proteins passing through a nanopore were considered, as well. Experiments performed with single 30 nm long silicon nitride nanopores were described by continuum modeling, which took into account the surface reactions on the nanopore walls and local modulation of the solution pH in the pore and at the pore entrances. The results revealed that manipulation of surface charge can occur without changing pH of the background electrolyte, which is especially important for applications where maintaining pH at a constant and physiological level is necessary. The system presented also offers a possibility to modulate polarity and magnitude of surface charges in a two-electrode setup, which previously was accomplished in more complex multielectrode systems.
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Affiliation(s)
- Chih-Yuan Lin
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Elif Turker Acar
- Department of Chemistry, Faculty of Engineering , Istanbul University - Cerrahpasa , Avcılar, 34320 Istanbul , Turkey
| | | | - Kabin Lin
- School of Mechanical Engineering and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments , Southeast University , Nanjing 211189 , China
| | - Jyh-Ping Hsu
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
- Department of Chemical Engineering , National Taiwan University of Science and Technology , Taipei 10617 , Taiwan
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25
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Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules. Sci Rep 2019; 9:13143. [PMID: 31511597 PMCID: PMC6739384 DOI: 10.1038/s41598-019-49622-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/28/2019] [Indexed: 01/15/2023] Open
Abstract
For nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.
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26
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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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27
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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: 29] [Impact Index Per Article: 5.8] [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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28
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Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
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Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
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Kennedy E, Arcadia CE, Geiser J, Weber PM, Rose C, Rubenstein BM, Rosenstein JK. Encoding information in synthetic metabolomes. PLoS One 2019; 14:e0217364. [PMID: 31269053 PMCID: PMC6608926 DOI: 10.1371/journal.pone.0217364] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/10/2019] [Indexed: 12/17/2022] Open
Abstract
Biomolecular information systems offer exciting potential advantages and opportunities to complement conventional semiconductor technologies. Much attention has been paid to information-encoding polymers, but small molecules also play important roles in biochemical information systems. Downstream from DNA, the metabolome is an information-rich molecular system with diverse chemical dimensions which could be harnessed for information storage and processing. As a proof of principle of small-molecule postgenomic data storage, here we demonstrate a workflow for representing abstract data in synthetic mixtures of metabolites. Our approach leverages robotic liquid handling for writing digital information into chemical mixtures, and mass spectrometry for extracting the data. We present several kilobyte-scale image datasets stored in synthetic metabolomes, which can be decoded with accuracy exceeding 99% using multi-mass logistic regression. Cumulatively, >100,000 bits of digital image data was written into metabolomes. These early demonstrations provide insight into some of the benefits and limitations of small-molecule chemical information systems.
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Affiliation(s)
- Eamonn Kennedy
- School of Engineering, Brown University, Providence, RI, United States of America
| | | | - Joseph Geiser
- Department of Chemistry, Brown University, Providence, RI, United States of America
| | - Peter M. Weber
- Department of Chemistry, Brown University, Providence, RI, United States of America
| | - Christopher Rose
- School of Engineering, Brown University, Providence, RI, United States of America
| | - Brenda M. Rubenstein
- Department of Chemistry, Brown University, Providence, RI, United States of America
| | - Jacob K. Rosenstein
- School of Engineering, Brown University, Providence, RI, United States of America
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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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31
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Roshan KA, Tang Z, Guan W. High fidelity moving Z-score based controlled breakdown fabrication of solid-state nanopore. NANOTECHNOLOGY 2019; 30:095502. [PMID: 30523901 DOI: 10.1088/1361-6528/aaf48e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We investigate the current transport characteristics in the electrolyte-dielectric-electrolyte structure commonly used in the in situ controlled breakdown (CBD) fabrication of solid-state nanopores. It is found that the stochastic breakdown process could lead to fidelity issues of false positives (an incorrect indication of a true nanopore formation) and false negatives (inability to detect initial nanopore formation). Robust and deterministic detection of initial physical breakdown to alleviate false positives and false negatives is critical for precise nanopore size control. To this end, we report a high fidelity moving Z-score method based CBD fabrication of solid-state nanopore. We demonstrate 100% success rate of realizing the initial nanopore conductance of 3 ± 1 nS (corresponds to size of 1.7 ± 0.6 nm) regardless of the dielectric membrane characteristics. Our study also elucidates the Joule heating is the dominant mechanism for electric field-based nanopore enlargement. Single DNA molecule sensing using nanopores fabricated by this method was successfully demonstrated. We anticipate the moving Z-score based CBD method could enable broader access to the solid state nanopore-based single molecule analysis.
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Affiliation(s)
- Kamyar Akbari Roshan
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, United States of America
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32
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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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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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Park T, Lee SJ, Cha JH, Choi W. Scalable fabrication of nanopores in membranes via thermal annealing of Au nanoparticles. NANOSCALE 2018; 10:22623-22634. [PMID: 30484792 DOI: 10.1039/c8nr06441e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopores are promising candidates for versatile sensing of micro- and nanomaterials. However, the fabrication of isolated nanopores with optimal dimensions and distributions requires complex processes that involve the use of high-cost equipment. Herein, we report a scalable fabrication of isolated conical nanopores with adjustable dimensions and distribution densities on a Si3N4 membrane via thermal annealing of Au nanoparticles (AuNPs). The AuNP-dispersed solution was dropped and evaporated on the membrane, while the pH value and concentration of AuNPs controlled the zeta potential difference and the distribution density of the attached AuNPs. The optimized thermal annealing directly fabricated conical nanopores at the positions of the AuNPs because of the quasi-liquid state of the AuNPs and their interaction with the Si3N4 lattices. The 50, 100, and 200 nm AuNPs enabled one-step fabrication of 8-, 26-, and 63 nm nanopores, while the inter-distances and distribution densities were controllable over the membrane. The physicochemical analyses elucidated the underlying mechanisms of direct nanopore formation, and the precise adjustment of thermal annealing developed three unique nanopores that differently interacted with the AuNPs: (1) Au-residue-embedded nanopores, (2) isolated nanopores, and (3) nanopores with the remaining Au droplet. The AuNPs-driven fabrication of versatile nanopore membranes enables new applications for sensing and transporting small-scale materials.
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Affiliation(s)
- Taeyoung Park
- School of Mechanical Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 136-713, Republic of Korea.
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35
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Bentley CL, Edmondson J, Meloni GN, Perry D, Shkirskiy V, Unwin PR. Nanoscale Electrochemical Mapping. Anal Chem 2018; 91:84-108. [PMID: 30500157 DOI: 10.1021/acs.analchem.8b05235] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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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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37
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Wen C, Zeng S, Zhang Z, Zhang SL. Group Behavior of Nanoparticles Translocating Multiple Nanopores. Anal Chem 2018; 90:13483-13490. [PMID: 30372031 DOI: 10.1021/acs.analchem.8b03408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanopores have been implemented as nanosensors for DNA sequencing, biomolecule inspection, chemical analysis, nanoparticle detection, etc. For high-throughput and parallelized measurement using nanopore arrays, individual addressability has been a crucial technological solution in order to enable scrutiny of signals generated at each and every nanopore. Here, an alternative pathway of employing arrayed nanopores to perform sensor functions is investigated by examining the group behavior of nanoparticles translocating multiple nanopores. As no individual addressability is required, fabrication of nanopore devices along with microfluidic cells and readout circuits can be greatly simplified. Experimentally, arrays of less than 10 pores are shown to be capable of analyzing translocating nanoparticles with a good signal-to-noise margin. According to theoretical predictions, more pores (than 10) per array can perform high-fidelity analysis if the noise level of the measurement system can be better controlled. More pores per array would also allow for faster measurement at lower concentration because of larger capture cross sections for target nanoparticles. By experimentally varying the number of pores, the concentration of nanoparticles, or the applied bias voltage across the nanopores, we have identified the basic characteristics of this multievent process. By characterizing average pore current and associated standard deviation during translocation and by performing physical modeling and extensive numerical simulations, we have shown the possibility of determining the size and concentration of two kinds of translocating nanoparticles over 4 orders of magnitude in concentration. Hence, we have demonstrated the potential and versatility of the multiple-nanopore approach for high-throughput nanoparticle detection.
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Affiliation(s)
- Chenyu Wen
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Shuangshuang Zeng
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Zhen Zhang
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Shi-Li Zhang
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
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38
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Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
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Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
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Perera RT, Arcadia CE, Rosenstein JK. Probing the nucleation, growth, and evolution of hydrogen nanobubbles at single catalytic sites. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.07.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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40
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Yanagi I, Hamamura H, Akahori R, Takeda KI. Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration. Sci Rep 2018; 8:10129. [PMID: 29973672 PMCID: PMC6031669 DOI: 10.1038/s41598-018-28524-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
For the nanopore sensing of various large molecules, such as probe-labelled DNA and antigen-antibody complexes, the nanopore size has to be customized for each target molecule. The recently developed nanopore fabrication method utilizing dielectric breakdown of a membrane is simple and quite inexpensive, but it is somewhat unsuitable for the stable fabrication of a single large nanopore due to the risk of generating multiple nanopores. To overcome this bottleneck, we propose a new technique called “two-step breakdown” (TSB). In the first step of TSB, a local conductive thin portion (not a nanopore) is formed in the membrane by dielectric breakdown. In the second step, the created thin portion is penetrated by voltage pulses whose polarity is opposite to the polarity of the voltage used in the first step. By applying TSB to a 20-nm-thick SiN membrane, a single nanopore with a diameter of 21–26 nm could be fabricated with a high yield of 83%.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan.
| | - Hirotaka Hamamura
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Rena Akahori
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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Zhang M, Ngampeerapong C, Redin D, Ahmadian A, Sychugov I, Linnros J. Thermophoresis-Controlled Size-Dependent DNA Translocation through an Array of Nanopores. ACS NANO 2018; 12:4574-4582. [PMID: 29648793 DOI: 10.1021/acsnano.8b00961] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Large arrays of nanopores can be used for high-throughput biomolecule translocation with applications toward size discrimination and sorting at the single-molecule level. In this paper, we propose to discriminate DNA length by the capture rate of the molecules to an array of relatively large nanopores (50-130 nm) by introducing a thermal gradient by laser illumination in front of the pores balancing the force from an external electric field. Nanopore arrays defined by photolithography were batch processed using standard silicon technology in combination with electrochemical etching. Parallel translocation of single, fluorophore-labeled dsDNA strands is recorded by imaging the array with a fast CMOS camera. The experimental data show that the capture rates of DNA molecules decrease with increasing DNA length due to the thermophoretic effect of the molecules. It is shown that the translocation can be completely turned off for the longer molecule using an appropriate bias, thus allowing a size discrimination of the DNA translocation through the nanopores. A derived analytical model correctly predicts the observed capture rate. Our results demonstrate that by combining a thermal and a potential gradient at the nanopores, such large nanopore arrays can potentially be used as a low-cost, high-throughput platform for molecule sensing and sorting.
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Affiliation(s)
- Miao Zhang
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Chonmanart Ngampeerapong
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - David Redin
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Afshin Ahmadian
- School of Biotechnology, Division of Gene Technology, Science for Life Laboratory , KTH Royal Institute of Technology , SE-171 65 , Solna , Sweden
| | - Ilya Sychugov
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
| | - Jan Linnros
- Department of Applied Physics , KTH Royal Institute of Technology , Electrum 229 , 164 40 Kista , Sweden
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Abstract
Optimal voltages were found for particle detections, at which the current blockade ratio did not depend on surface charge density.
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Affiliation(s)
- Yinghua Qiu
- Department of Physics
- Northeastern University
- Boston
- USA
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43
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Jain T, Rasera BC, Guerrero RJS, Lim JM, Karnik R. Microfluidic multiplexing of solid-state nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:484001. [PMID: 29116942 DOI: 10.1088/1361-648x/aa9455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although solid-state nanopores enable electronic analysis of many clinically and biologically relevant molecular structures, there are few existing device architectures that enable high-throughput measurement of solid-state nanopores. Herein, we report a method for microfluidic integration of multiple solid-state nanopores at a high density of one nanopore per (35 µm2). By configuring microfluidic devices with microfluidic valves, the nanopores can be rinsed from a single fluid input while retaining compatibility for multichannel electrical measurements. The microfluidic valves serve the dual purpose of fluidic switching and electric switching, enabling serial multiplexing of the eight nanopores with a single pair of electrodes. Furthermore, the device architecture exhibits low noise and is compatible with electroporation-based in situ nanopore fabrication, providing a scalable platform for automated electronic measurement of a large number of integrated solid-state nanopores.
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Affiliation(s)
- Tarun Jain
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, United States of America
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Bentley CL, Kang M, Unwin PR. Nanoscale Structure Dynamics within Electrocatalytic Materials. J Am Chem Soc 2017; 139:16813-16821. [PMID: 29058886 DOI: 10.1021/jacs.7b09355] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Electrochemical interfaces used for sensing, (electro)catalysis, and energy storage are usually nanostructured to expose particular surface sites, but probing the intrinsic activity of these sites is often beyond current experimental capability. Herein, it is demonstrated how a simple meniscus imaging probe of just 30 nm in size can be deployed for direct electrochemical and topographical imaging of electrocatalytic materials at the nanoscale. Spatially resolved topographical and electrochemical data are collected synchronously to create topographical images in which step-height features as small as 2 nm are easily resolved and potential-resolved electrochemical activity movies composed of hundreds of images are obtained in a matter of minutes. The technique has been benchmarked by investigating the hydrogen evolution reaction on molybdenum disulfide, where it is shown that the basal plane possesses uniform activity, while surface defects (i.e., few to multilayer step edges) give rise to a morphology-dependent (i.e., height-dependent) enhancement in catalytic activity. The technique was then used to investigate the electro-oxidation of hydrazine at the surface of electrodeposited Au nanoparticles (AuNPs) supported on glassy carbon, where subnanoentity (i.e., sub-AuNP) reactivity mapping has been demonstrated. We show, for the first time, that electrochemical reaction rates vary significantly across an individual AuNP surface and that these single entities cannot be considered as uniformly active. The work herein provides a road map for future studies in electrochemical science, in which the activity of nanostructured materials can be viewed as quantitative movies, readily obtained, to reveal active sites directly and unambiguously.
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Affiliation(s)
- Cameron L Bentley
- Department of Chemistry, University of Warwick , Coventry CV4 7AL, U.K
| | - Minkyung Kang
- Department of Chemistry, University of Warwick , Coventry CV4 7AL, U.K
| | - Patrick R Unwin
- Department of Chemistry, University of Warwick , Coventry CV4 7AL, U.K
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Yin B, Xie W, Liang L, Deng Y, He S, He F, Zhou D, Tlili C, Wang D. Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection. ACS OMEGA 2017; 2:7127-7135. [PMID: 31457292 PMCID: PMC6645049 DOI: 10.1021/acsomega.7b01245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/06/2017] [Indexed: 05/11/2023]
Abstract
In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.
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