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Hu G, Yan H, Xi G, Gao Z, Wu Z, Lu Z, Tu J. Nanopore sensors for single molecular protein detection: Research progress based on computer simulations. IET Nanobiotechnol 2023; 17:257-268. [PMID: 36924083 DOI: 10.1049/nbt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 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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Pezzuoli D, Angeli E, Repetto D, Ferrera F, Guida P, Firpo G, Repetto L. Nanofluidic-Based Accumulation of Antigens for Miniaturized Immunoassay. SENSORS 2020; 20:s20061615. [PMID: 32183234 PMCID: PMC7146560 DOI: 10.3390/s20061615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/29/2023]
Abstract
The continuous advances of Nanofluidics have been stimulating the development of novel nanostructures and strategies to accumulate very diluted analytes, for implementing a new class of high sensitivity miniaturized polymeric sensors. We take advantage of the electrokinetic properties of these structures, which allow accumulating analytes inside asymmetric microfluidic structures to implement miniaturized sensors able to detect diluted solutions down to nearly 1.2 pg/mL. In particular, exploiting polydimethylsiloxane devices, fabricated by using the junction gap breakdown technique, we concentrate antigens inside a thin microfunnel functionalized with specific antibodies to favor the interaction and, if it is the case, the recognition between antigens in solution and antibodies anchored to the surface. The transduction mechanism consists in detecting the fluorescence signal of labeled avidin when it binds to biotinylated antigens. Here, we demonstrate that exploiting these electrokinetic phenomena, typical of nanofluidic structures, we succeeded in concentrating biomolecules in correspondence of a 1 pL sensing region, a strategy that grants to the device performance comparable to standard immunoassays.
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Affiliation(s)
- Denise Pezzuoli
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Elena Angeli
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
- Correspondence:
| | - Diego Repetto
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Francesca Ferrera
- Centre of Excellence for Biomedical Research, University of Genoa, viale Benedetto XV 9, 16132 Genoa, Italy
| | - Patrizia Guida
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Giuseppe Firpo
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
| | - Luca Repetto
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy
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Sun H, Yao F, Kang XF. Nanopore biphasic-pulse biosensor. Biosens Bioelectron 2019; 146:111740. [PMID: 31586766 DOI: 10.1016/j.bios.2019.111740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022]
Abstract
Nanopores as artificial biomimetic nanodevices are of great importance for their applications in biosensing, nanomedicine and bioelectronics. However, it remains a challenge to detect small biomolecules especially small-sized proteins with high sensitivity and selectivity. In the article, we report a simple and efficient method for small-sized protein detection by constructing biphasic-pulse nanopore biosensor. Unlike the traditional resistive pulse sensing, the biphasic-pulse event can provide unique and abundant fingerprint information. Although the nanopore biphasic-pulse electrical signal is originated from both the molecular exclusion electrical resistance and the surface-charged effect of confined molecule, its frequency and amplitude of the waveform can be adjusted by pH, applied potential and salt concentration. Based on the frequency of the biphasic pulse, nanomolar concentration of proteins could be specifically detected and the limit of detection is 1.2 nM. In addition, the biphasic-pulse nanopore shows well discrimination in similar-sized protein detection and its signal generation is highly reproducible. The nanopore biphasic-pulse biosensor should have broad applications as a new generation of powerful single-molecule device.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710069, PR China.
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Pezzuoli D, Angeli E, Repetto D, Guida P, Firpo G, Repetto L. Increased Flexibility in Lab-on-Chip Design with a Polymer Patchwork Approach. NANOMATERIALS 2019; 9:nano9121678. [PMID: 31775220 PMCID: PMC6955689 DOI: 10.3390/nano9121678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022]
Abstract
Nanofluidic structures are often the key element of many lab-on-chips for biomedical and environmental applications. The demand for these devices to be able to perform increasingly complex tasks triggers a request for increasing the performance of the fabrication methods. Soft lithography and poly(dimethylsiloxane) (PDMS) have since long been the basic ingredients for producing low-cost, biocompatible and flexible devices, replicating nanostructured masters. However, when the desired functionalities require the fabrication of shallow channels, the “roof collapse” phenomenon, that can occur when sealing the replica, can impair the device functionalities. In this study, we demonstrate that a “focused drop-casting” of h-PDMS (hard PDMS) on nanostructured regions, provides the necessary stiffness to avoid roof collapse, without increasing the probability of deep cracks formation, a drawback that shows up in the peel-off step, when h-PDMS is used all over the device area. With this new approach, we efficiently fabricate working devices with reproducible sub-100 nm structures. We verify the absence of roof collapse and deep cracks by optical microscopy and, in order to assess the advantages that are introduced by the proposed technique, the acquired images are compared with those of cracked devices, whose top layer, of h-PDMS, and with those of collapsed devices, made of standard PDMS. The geometry of the critical regions is studied by atomic force microscopy of their resin casts. The electrical resistance of the nanochannels is measured and shown to be compatible with the estimates that can be obtained from the geometry. The simplicity of the method and its reliability make it suitable for increasing the fabrication yield and reducing the costs of nanofluidic polymeric lab-on-chips.
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Zhu L, Miao M, Shao X, Du Z, Huang K, Luo Y, Xu W. A Universal Electrochemical Biosensor Using Nick-HCR Nanostructure as Molecular Gate of Nanochannel for Detecting Chromium(III) Ions and MicroRNA. Anal Chem 2019; 91:14992-14999. [DOI: 10.1021/acs.analchem.9b03489] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Longjiao Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Miao Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Zaihui Du
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
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Wang W, Yang C, Lin S, Vellaisamy K, Li G, Tan W, Leung CH, Ma DL. First Synthesis of an Oridonin-Conjugated Iridium(III) Complex for the Intracellular Tracking of NF-κB in Living Cells. Chemistry 2017; 23:4929-4935. [DOI: 10.1002/chem.201700770] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Wanhe Wang
- Department of Chemistry; Hong Kong Baptist University, Kowloon Tong; Hong Kong P. R. China
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao P. R. China
| | - Sheng Lin
- Department of Chemistry; Hong Kong Baptist University, Kowloon Tong; Hong Kong P. R. China
| | - Kasipandi Vellaisamy
- Department of Chemistry; Hong Kong Baptist University, Kowloon Tong; Hong Kong P. R. China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao P. R. China
| | - Weihong Tan
- Department of Chemistry, and Department of Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; Shands Cancer Center; UF Genetics Institute; McKnight Brain Institute; University of Florida; Gainesville USA
- Molecular Sciences and Biomedicine Laboratory; State Key Laboratory for Chemo/Biosensing and Chemometrics, Department of Chemistry; College of Chemistry and Chemical Engineering, College of Biology; Collaborative Innovation Center for Molecular Engineering and Theranostics; Hunan University; Changsha P. R. China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao P. R. China
| | - Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University, Kowloon Tong; Hong Kong P. R. China
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Wang H, Liu Q, Li W, Wen L, Zheng D, Bo Z, Jiang L. Colloidal Synthesis of Lettuce-like Copper Sulfide for Light-Gating Heterogeneous Nanochannels. ACS NANO 2016; 10:3606-3613. [PMID: 26876738 DOI: 10.1021/acsnano.5b08079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lettuce-like CuxS micron particles were successfully prepared by a colloidal hot-injection method, and the preliminary evaluation of the light-gating artificial ionic nanochannels designed using these particles was also demonstrated. A likely underlying mechanism behind the formation of the lettuce architecture was tentatively proposed via monitoring the evolution process. These particles are hydrophobic and possess a high surface area that can readily absorb the light-responsive 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran (Spiro) molecules. Finally, the heterogeneous nanochannels were constructed by spin-coating the preprepared CuxS particles loaded with Spiro onto the commercially available anodic alumina (AAO) substrate. The AAO-CuxS/Spiro heterogeneous nanochannels "close" under illumination of ultraviolet light (365 nm) and then "open" by visible light irradiation, which exhibits a regulated ionic transport property with good responsive switchability and stability.
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Affiliation(s)
| | | | | | - Liping Wen
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
| | | | | | - Lei Jiang
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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Crick CR, Sze JYY, Rosillo-Lopez M, Salzmann CG, Edel JB. Selectively Sized Graphene-Based Nanopores for in Situ Single Molecule Sensing. ACS APPLIED MATERIALS & INTERFACES 2015. [PMID: 26204996 PMCID: PMC4543996 DOI: 10.1021/acsami.5b06212] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The use of nanopore biosensors is set to be extremely important in developing precise single molecule detectors and providing highly sensitive advanced analysis of biological molecules. The precise tailoring of nanopore size is a significant step toward achieving this, as it would allow for a nanopore to be tuned to a corresponding analyte. The work presented here details a methodology for selectively opening nanopores in real-time. The tunable nanopores on a quartz nanopipette platform are fabricated using the electroetching of a graphene-based membrane constructed from individual graphene nanoflakes (ø ∼30 nm). The device design allows for in situ opening of the graphene membrane, from fully closed to fully opened (ø ∼25 nm), a feature that has yet to be reported in the literature. The translocation of DNA is studied as the pore size is varied, allowing for subfeatures of DNA to be detected with slower DNA translocations at smaller pore sizes, and the ability to observe trends as the pore is opened. This approach opens the door to creating a device that can be target to detect specific analytes.
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Affiliation(s)
- Colin R. Crick
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Jasmine Y. Y. Sze
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Martin Rosillo-Lopez
- Department of Chemistry, University College
London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Christoph G. Salzmann
- Department of Chemistry, University College
London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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