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You SM, Jeong KB, Kang DG, Kim SM, Kim YR. Label-free detection of glutathione and glutathione disulfide in biological fluid by using an alpha-hederin nanopore. Biosens Bioelectron 2024; 262:116559. [PMID: 38981320 DOI: 10.1016/j.bios.2024.116559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/08/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
Glutathione (GSH) is indispensable for maintaining redox homeostasis in biological fluids and serves as a key component in cellular defense mechanisms. Accurate assessment of GSH relative to its oxidized counterpart, glutathione disulfide (GSSG), is critical for the early diagnosis and understanding of conditions related to oxidative stress. Despite existing methods for their quantification, the label-free and simultaneous measurement of GSH and GSSG in biological fluid presents significant challenges. Herein, we report the use of an alpha-hederin (Ah) nanopore for the direct measurement of the GSH:GSSG ratio in simulated biological fluid, containing fetal bovine serum (FBS). This system hinges on detecting characteristic relative ion blockades (ΔI/Io) as GSH and GSSG molecules pass through the Ah nanopore under an applied electric field. The distinct current blockage signals derived from the translocation of GSH and GSSG enabled us to determine the molar ratio of GSH and its oxidized form. Notably, the interactions between the hydroxyl groups of the sugar moiety lining the nanopore's inner surface and the sulfhydryl group of GSH significantly influence the translocation dynamics, resulting in a longer translocation time for GSH compared to GSSG. The Ah nanopore technology proposed in this study offers a promising approach for real-time, single molecule-level monitoring of glutathione redox status in biological fluids, eliminating the need for labeling or extensive sample preparation.
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Affiliation(s)
- Sang-Mook You
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Baek Jeong
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Dong-Gook Kang
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sang-Min Kim
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Young-Rok Kim
- Institute of Life Sciences and Resources & Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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2
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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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Yin YD, Chen FF, Hu J, Yang L, Song XT, Wu GR, Xu M, Gu ZY. Solid-State Nanopore Distinguishes Ferritin and Apo-Ferritin with Identical Exteriors through Amplified Flexibility at Single-Molecule Level. Anal Chem 2023; 95:16496-16504. [PMID: 37916987 DOI: 10.1021/acs.analchem.3c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Protein identification and discrimination at the single-molecule level are big challenges. Solid-state nanopores as a sensitive biosensor have been used for protein analysis, although it is difficult to discriminate proteins with similar structures in the traditional discrimination method based on the current blockage fraction. Here, we select ferritin and apo-ferritin as the model proteins that exhibit identical exterior and different interior structures and verify the practicability of their discrimination with flexibility features by the strategy of gradually decreasing the nanopore size. We show that the larger nanopore (relative to the protein size) has no obvious effect on discriminating two proteins. Then, the comparable-sized nanopore plays a key role in discriminating two proteins based on the dwell time and fraction distribution, and the conformational changes of both proteins are also studied with this nanopore. Finally, in the smaller nanopore, the protein molecules are trapped rather than translocated, where two proteins are obviously discriminated through the current fluctuation caused by the vibration of proteins. This strategy has potential in the discrimination of other important similar proteins.
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Affiliation(s)
- Yun-Dong Yin
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Fang-Fang Chen
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jun Hu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Lei Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xi-Tong Song
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Guo-Rong Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Xu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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Kim D, Byun S, Pu Y, Huh H, Jung Y, Kim S, Lee KY. Design of a Current Sensing System with TIA Gain of 160 dBΩ and Input-Referred Noise of 1.8 pA rms for Biosensor. SENSORS (BASEL, SWITZERLAND) 2023; 23:3019. [PMID: 36991734 PMCID: PMC10051069 DOI: 10.3390/s23063019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
This paper proposes a high-gain low-noise current signal detection system for biosensors. When the biomaterial is attached to the biosensor, the current flowing through the bias voltage is changed so that the biomaterial can be sensed. A resistive feedback transimpedance amplifier (TIA) is used for the biosensor requiring a bias voltage. Current changes in the biosensor can be checked by plotting the current value of the biosensor in real time on the self-made graphical user interface (GUI). Even if the bias voltage changes, the input voltage of the analog to digital converter (ADC) does not change, so it is designed to plot the current of the biosensor accurately and stably. In particular, for multi-biosensors with an array structure, a method of automatically calibrating the current between biosensors by controlling the gate bias voltage of the biosensors is proposed. Input-referred noise is reduced using a high-gain TIA and chopper technique. The proposed circuit achieves 1.8 pArms input-referred noise with a gain of 160 dBΩ and is implemented in a TSMC 130 nm CMOS process. The chip area is 2.3 mm2, and the power consumption of the current sensing system is 12 mW.
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Affiliation(s)
- Donggyu Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungjun Byun
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Younggun Pu
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Hyungki Huh
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Yeonjae Jung
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Seokkee Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Kang-Yoon Lee
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
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Wang Z, Hu R, Zhu R, Lu W, Wei G, Zhao J, Gu ZY, Zhao Q. Metal-Organic Cage as Single-Molecule Carrier for Solid-State Nanopore Analysis. SMALL METHODS 2022; 6:e2200743. [PMID: 36216776 DOI: 10.1002/smtd.202200743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The ability to detect biomolecules at the single-molecule level is at the forefront of biological research, precision medicine, and early diagnosis. Recently, solid-state nanopore sensors have emerged as a promising technique for label-free and precise diagnosis assay. However, insufficient sensitivity and selectivity for small analytes are a great challenge for clinical diagnosis applications via solid-state nanopores. Here, for the first time, a metal-organic cage, PCC-57, is employed as a carrier to increase the sensitivity and selectivity of solid-state nanopores based on the intrinsic interaction of the nanocage with biomolecules. Firstly, it is found that the carrier itself is undetectable unless bound with the target analytes and used oligonucleotides as linkers to attach PCC-57 and target analytes. Secondly, two small analytes, oligonucleotide conjugated angiopep-2 and polyphosphoric acid, are successfully distinguished using the molecular carrier. Finally, selectivity of nanopore detection is achieved by attaching PCC-57 to oligonucleotide-tailed aptamers, and the human alpha-thrombin sample is successfully detected. It is believed that the highly designable metal-organic cage could serve as a rich carrier repository for a variety of biomolecules, facilitating single-molecule screening of clinically relevant biomolecules based on solid-state nanopores in the future.
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Affiliation(s)
- Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Rui Zhu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Zhi-Yuan Gu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, 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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Elaguech MA, Bahri M, Djebbi K, Zhou D, Shi B, Liang L, Komarova N, Kuznetsov A, Tlili C, Wang D. Nanopore-based aptasensor for label-free and sensitive vanillin determination in food samples. Food Chem 2022; 389:133051. [PMID: 35490517 DOI: 10.1016/j.foodchem.2022.133051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022]
Abstract
Dielectric breakdown technique was utlised to fabricate 5-6 nm nanopores for vanillin detection in various food samples. A highly selective aptamer (Van_74) with high binding affinity towards vanillin was used as capture probe. Under optimal conditions, aptamer/vanillin complex translocation induced deeper events than the bare aptamer. As a result, the proposed nanopore aptasensor exhibits a linear range from 0.5 to 5 nM (R2 = 0.972) and a low detection limit of 500 pM, which is significantly better than conventional platforms. Furthermore, our aptasensor showed excellent immunity against different interferons and was used to detect vanillin in different food samples. The food sample measurements were confirmed with an additional UV-Vis assay, the results of the two techniques were statistically evaluated and showed no statistically significant difference. Hence, this work represents a proof-of-concept involving the design and testing of aptamer/nanopore sensors for small molecules detection, which plays a critical role in food safety.
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Affiliation(s)
- Mohamed Amin Elaguech
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, PR China
| | - Mohamed Bahri
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, PR China
| | - Khouloud Djebbi
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, PR China
| | - Daming Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China
| | - Biao Shi
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China
| | | | - Alexander Kuznetsov
- SMC Technological Centre, Moscow 124498, Russia; Institute of Nanotechnology of Microelectronics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Chaker Tlili
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China.
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China; Chongqing School, University of Chinese Academy of Sciences (UCAS), Chongqing 400714, PR China; University of Chinese Academy of Sciences (UCAS), Beijing 100049, PR China.
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7
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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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8
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Engineering highly efficient Li+ responsive nanochannels via host–guest interaction and photochemistry regulation. J Colloid Interface Sci 2022; 615:674-684. [DOI: 10.1016/j.jcis.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 11/20/2022]
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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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Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
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Wang J, Ying YL, Zhong CB, Zhang LM, Yan F, Long YT. Instrumentational implementation for parallelized nanopore electrochemical measurements. Analyst 2021; 146:4111-4120. [PMID: 34116564 DOI: 10.1039/d1an00471a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China. and Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Li-Min Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
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12
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Yang H, Saqib M, Hao R. Single-Entity Detection With TEM-Fabricated Nanopores. Front Chem 2021; 9:664820. [PMID: 34026729 PMCID: PMC8138203 DOI: 10.3389/fchem.2021.664820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 12/04/2022] Open
Abstract
Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.
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Affiliation(s)
| | | | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
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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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14
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Lee K, Park J, Kang J, Lee TG, Kim HM, Kim KB. Surface modification of solid-state nanopore by plasma-polymerized chemical vapor deposition of poly(ethylene glycol) for stable device operation. NANOTECHNOLOGY 2020; 31:185503. [PMID: 31945750 DOI: 10.1088/1361-6528/ab6cdb] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biopolymer adsorption onto a membrane is a significant issue in the reliability of solid-state nanopore devices, since it degrades the device performance or promotes device failure. In this work, a poly(ethylene glycol) (PEG) layer was coated on a silicon nitride (SiNx) membrane by plasma-polymerized vapor deposition to inhibit biopolymer adsorption. From optical observations, the deposited PEG layer demonstrated increased hydrophilicity and anti-adsorption property compared to the SiNx surface. Electrical properties of the PEG/SiNx nanopore were characterized, showing Ohmic behavior and a 6.3 times higher flicker noise power due to the flexible conformation of PEG in water. Antifouling performance of each surface was analyzed by measuring the average time from voltage bias to the first adsorption during DNA translocation experiments, where the modified surface enabled two times prolonged device operation. The time to adsorption was dependent on the applied voltage, implying adsorption probability was dominated by the electrophoretic DNA approach to the nanopore. DNA translocation behaviors on each surface were identified from translocation signals, as the PEG layer promoted unfolded and fast movement of DNA through the nanopore. This work successfully analyzed the effect of the PEG layer on DNA adsorption and translocation in solid-state nanopore experiments.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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15
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Timp W, Timp G. Beyond mass spectrometry, the next step in proteomics. SCIENCE ADVANCES 2020; 6:eaax8978. [PMID: 31950079 PMCID: PMC6954058 DOI: 10.1126/sciadv.aax8978] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/19/2019] [Indexed: 05/08/2023]
Abstract
Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.
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Affiliation(s)
- Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory Timp
- Departments of Electrical Engineering and Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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Callahan N, Tullman J, Kelman Z, Marino J. Strategies for Development of a Next-Generation Protein Sequencing Platform. Trends Biochem Sci 2019; 45:76-89. [PMID: 31676211 DOI: 10.1016/j.tibs.2019.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/11/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
Proteomic analysis can be a critical bottleneck in cellular characterization. The current paradigm relies primarily on mass spectrometry of peptides and affinity reagents (i.e., antibodies), both of which require a priori knowledge of the sample. An unbiased protein sequencing method, with a dynamic range that covers the full range of protein concentrations in proteomes, would revolutionize the field of proteomics, allowing a more facile characterization of novel gene products and subcellular complexes. To this end, several new platforms based on single-molecule protein-sequencing approaches have been proposed. This review summarizes four of these approaches, highlighting advantages, limitations, and challenges for each method towards advancing as a core technology for next-generation protein sequencing.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA.
| | - Jennifer Tullman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, and University of Maryland, Rockville, MD 20850, USA
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