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Wang J, Zhou H, Liang R, Qin W. Chronopotentiometric Nanopore Sensor Based on a Stimulus-Responsive Molecularly Imprinted Polymer for Label-Free Dual-Biomarker Detection. Anal Chem 2024. [PMID: 38683892 DOI: 10.1021/acs.analchem.3c05817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The development of sensors for detection of biomarkers exhibits an exciting potential in diagnosis of diseases. Herein, we propose a novel electrochemical sensing strategy for label-free dual-biomarker detection, which is based on the combination of stimulus-responsive molecularly imprinted polymer (MIP)-modified nanopores and a polymeric membrane chronopotentiometric sensor. The ion fluxes galvanostatically imposed on the sensing membrane surface can be blocked by the recognition reaction between the target biomarker in the sample solution and the stimulus-responsive MIP receptor in the nanopores, thus causing a potential change. By using two external stimuli (i.e., pH and temperature), the recognition abilities of the stimulus-responsive MIP receptor can be effectively modulated so that dual-biomarker label-free chronopotentiometric detection can be achieved. Using alpha fetoprotein (AFP) and prostate-specific antigen (PSA) as model biomarkers, the proposed sensor offers detection limits of 0.17 and 0.42 ng/mL for AFP and PSA, respectively.
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Affiliation(s)
- Junhao Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huihui Zhou
- The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264099, China
| | - Rongning Liang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
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2
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Kumar A, Bakli C, Chakraborty S. Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores. Langmuir 2024; 40:7300-7309. [PMID: 38536237 DOI: 10.1021/acs.langmuir.3c02816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.
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Affiliation(s)
- Avinash Kumar
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Chirodeep Bakli
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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3
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Wang H, Tang H, Qiu X, Li Y. Solid-State Glass Nanopipettes: Functionalization and Applications. Chemistry 2024:e202400281. [PMID: 38507278 DOI: 10.1002/chem.202400281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
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4
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Punia B, Chaudhury S. Macromolecular Crowding Facilitates ssDNA Capture within Biological Nanopores: Role of Size Variation and Solution Heterogeneity. J Phys Chem B 2024; 128:1876-1883. [PMID: 38355410 DOI: 10.1021/acs.jpcb.3c08350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Genetic sequencing is a vital process that requires the transport of charged nucleic acids through transmembrane nanopores. Single-molecule studies show that macromolecular bulk crowding facilitates the capture of these polymers, leading to a high throughput of nanopore sensors. Motivated by these observations, a minimal discrete-state stochastic framework was developed to describe the role of poly(ethylene glycol) (PEG) crowders in varying concentrations in the transport of ssDNA through α-hemolysin nanopores. This theory suggested that the cooperative partitioning of polycationic PEGs controls the capture of ssDNA due to underlying electrostatic interactions. Herein, we investigate the impact of the size variation of PEGs on the capture event. Even though larger crowders attract ssDNA strongly to enhance its capture, our results show that considerable cooperative partitioning of PEGs is also required to achieve high interevent frequency. The exact analytical results are supported by existing single-molecule studies. Since real cellular conditions are heterogeneous, its influence on the ssDNA capture rate is studied by introducing a binary mixture of crowders. Our results indicate that the "polymer-pushing-polymer" concept possibly affects the capture rate depending on the mixture composition. These new findings provide valuable insights into the microscopic mechanism of the capture process, which eventually allows for accurate genome sequencing in crowded solutions.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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5
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Patiño-Guillén G, Pešović J, Panić M, Savić-Pavićević D, Bošković F, Keyser UF. Single-molecule RNA sizing enables quantitative analysis of alternative transcription termination. Nat Commun 2024; 15:1699. [PMID: 38402271 PMCID: PMC10894232 DOI: 10.1038/s41467-024-45968-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024] Open
Abstract
Transcription, a critical process in molecular biology, has found many applications in RNA synthesis, including mRNA vaccines and RNA therapeutics. However, current RNA characterization technologies suffer from amplification and enzymatic biases that lead to loss of native information. Here, we introduce a strategy to quantitatively study both transcription and RNA polymerase behaviour by sizing RNA with RNA nanotechnology and nanopores. To begin, we utilize T7 RNA polymerase to transcribe linear DNA lacking termination sequences. Surprisingly, we discover alternative transcription termination in the origin of replication sequence. Next, we employ circular DNA without transcription terminators to perform rolling circle transcription. This allows us to gain valuable insights into the processivity and transcription behaviour of RNA polymerase at the single-molecule level. Our work demonstrates how RNA nanotechnology and nanopores may be used in tandem for the direct and quantitative analysis of RNA transcripts. This methodology provides a promising pathway for accurate RNA structural mapping by enabling the study of full-length RNA transcripts at the single-molecule level.
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Affiliation(s)
| | - Jovan Pešović
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Marko Panić
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- University of Belgrade - Faculty of Biology, Centre for Human Molecular Genetics, Belgrade, Serbia
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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6
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Rockett T, Almahyawi M, Ghimire ML, Jonnalagadda A, Tagliaferro V, Seashols-Williams SJ, Bertino MF, Caputo GA, Reiner JE. Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine. ACS Sens 2024; 9:860-869. [PMID: 38286995 PMCID: PMC10897939 DOI: 10.1021/acssensors.3c02207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/31/2024]
Abstract
The development of novel methodologies that can detect biomarkers from cancer or other diseases is both a challenge and a need for clinical applications. This partly motivates efforts related to nanopore-based peptide sensing. Recent work has focused on the use of gold nanoparticles for selective detection of cysteine-containing peptides. Specifically, tiopronin-capped gold nanoparticles, trapped in the cis-side of a wild-type α-hemolysin nanopore, provide a suitable anchor for the attachment of cysteine-containing peptides. It was recently shown that the attachment of these peptides onto a nanoparticle yields unique current signatures that can be used to identify the peptide. In this article, we apply this technique to the detection of ovarian cancer marker peptides ranging in length from 8 to 23 amino acid residues. It is found that sequence variability complicates the detection of low-molecular-weight peptides (<10 amino acid residues), but higher-molecular-weight peptides yield complex, high-frequency current fluctuations. These fluctuations are characterized with chi-squared and autocorrelation analyses that yield significantly improved selectivity when compared to traditional open-pore analysis. We demonstrate that the technique is capable of detecting the only two cysteine-containing peptides from LRG-1, an emerging protein biomarker, that are uniquely present in the urine of ovarian cancer patients. We further demonstrate the detection of one of these LRG-1 peptides spiked into a sample of human female urine.
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Affiliation(s)
- Thomas
W. Rockett
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mohammed Almahyawi
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- King
Fahd Medical Research Center, King Abdulaziz
University, Jeddah 21589, Saudi Arabia
| | - Madhav L. Ghimire
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Aashna Jonnalagadda
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Tagliaferro
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Sarah J. Seashols-Williams
- Department
of Forensic Sciences, Virginia Commonwealth
University, Richmond, Virginia 23284, United States
| | - Massimo F. Bertino
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A. Caputo
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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7
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Zhang X, Dai Y, Sun J, Shen J, Lin M, Xia F. Solid-State Nanopore/Nanochannel Sensors with Enhanced Selectivity through Pore-in Modification. Anal Chem 2024; 96:2277-2285. [PMID: 38285919 DOI: 10.1021/acs.analchem.3c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Nanopore sensing technology, as an emerging analytical method, has the advantages of simple operation, fast output, and label-free and has been widely used in fields such as protein analysis, gene sequencing, and biomarker detection. Inspired by biological ion channels, scientists have prepared various artificial solid-state nanopores/nanochannels. Biological ion channels have extremely high ion transport selectivity, while solid-state nanopores/nanochannels have poor selectivity. The selectivity of solid-state nanopores and nanochannels can be enhanced by modifying channel charge, varying pore size, incorporating specific chemical functionality, and adjusting operating (or solution) conditions. This Perspective highlights pore-in modification strategies for enhancing the selectivity of solid-state nanopore/nanochannel sensors by summarizing the articles published in the last 10 years. The future development prospects and challenges of pore-in modification in solid-state nanopore and nanochannel sensors are discussed. This Perspective helps readers better understand nanopore sensing technology, especially the importance of detection selectivity. We believe that solid-state nanopore/nanochannel sensors will soon enter our homes after various challenges.
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Affiliation(s)
- Xiaojin Zhang
- 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, Wuhan 430074, China
| | - Yu Dai
- 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, Wuhan 430074, China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Meihua Lin
- 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, Wuhan 430074, 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, Wuhan 430074, China
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8
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Khatri S, Pandey P, Mejia G, Ghimire G, Leng F, He J. Nanoconfinement and Crowding Enhanced Single-Molecule Detection of Small Molecules with Nanopipettes. J Am Chem Soc 2023; 145:28075-28084. [PMID: 37996390 PMCID: PMC11036617 DOI: 10.1021/jacs.3c09311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Glass nanopipettes have gained widespread use as a versatile single-entity detector in chemical and biological sensing, analysis, and imaging. Its advantages include low cost, easy accessibility, simplicity of use, and high versatility. However, conventional nanopipettes based on the volume exclusion mechanism have limitations in detecting small biomolecules due to their small volume and high mobility in aqueous solution. To overcome this challenge, we have employed a novel approach by capitalizing on the strong nanoconfinement effect of nanopipettes. This is achieved by utilizing both the hard confinement provided by the long taper nanopipette tip at the cis side and the soft confinement offered by the hydrogel at the trans side. Through this approach, we have effectively slowed down the exit motion of small molecules, allowing us to enrich and jam them at the nanopipette tip. Consequently, we have achieved high throughput detection of small biomolecules with sizes as small as 1 nm, including nucleoside triphosphates, short peptides, and small proteins with excellent signal-to-noise ratios. Furthermore, molecular complex formation through specific intermolecular interactions, such as hydrogen bonding between closely spaced nucleotides in the jam-packed nanopipette tip, has been detected based on the unique ionic current changes.
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Affiliation(s)
- Santosh Khatri
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Popular Pandey
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - German Mejia
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Govinda Ghimire
- Physics Department, Florida International University, Miami, Florida, 33199, USA
| | - Fenfei Leng
- Chemistry and Biochemistry Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
| | - Jin He
- Physics Department, Florida International University, Miami, Florida, 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, Florida, 33199, USA
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9
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Yin B, Tang P, Wang L, Xie W, Chen X, Wang Y, Weng T, Tian R, Zhou S, Wang Z, Wang D. An aptamer-assisted nanopore strategy with a salt gradient for direct protein sensing. J Mater Chem B 2023; 11:11064-11072. [PMID: 37966856 DOI: 10.1039/d3tb01875j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Nanopore sensing is at the forefront of the technological revolution of the protein research field and has been widely used in molecular diagnosis and molecular dynamics, as well as for various sequencing applications. However, direct protein sensing with biological nanopores is still challenging owing to the large molecular size. Here, we propose an aptamer-assisted nanopore strategy for direct protein sensing and demonstrate its proof-of-concept utilities by experiments with SARS-Cov-2 nucleocapsid protein (NP), the most abundantly expressed viral protein, that is widely used in clinical diagnosis for COVID-19. NP binds with an oligonucleotide-tailed aptamer to form a protein-DNA complex which induces a discriminative two-level pattern of current blockades. We reveal the potential molecular interaction mechanism for the characteristic blockades and identify the salt gradient condition as the dominant factor of the phenomenon. Furthermore, we achieve a high sensitivity of 10 pM for NP detection within one hour and make a preliminary exploration on clinical diagnosis. This work promises a new platform for rapid and label-free protein detection.
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Affiliation(s)
- Bohua Yin
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Peng Tang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Xiaohan Chen
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Rong Tian
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Shuo Zhou
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
| | - Deqiang Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, Jilin, China.
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Fangzheng Avenue, Beibei District, Chongqing, 400714, Chongqing, China.
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10
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Murakami K, Kubota SI, Tanaka K, Tanaka H, Akabane K, Suzuki R, Shinohara Y, Takei H, Hashimoto S, Tanaka Y, Hojyo S, Sakamoto O, Naono N, Takaai T, Sato K, Kojima Y, Harada T, Hattori T, Fuke S, Yokota I, Konno S, Washio T, Fukuhara T, Teshima T, Taniguchi M, Murakami M. High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore. Lab Chip 2023; 23:4909-4918. [PMID: 37877206 DOI: 10.1039/d3lc00572k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
A digital platform that can rapidly and accurately diagnose pathogenic viral variants, including SARS-CoV-2, will minimize pandemics, public anxiety, and economic losses. We recently reported an artificial intelligence (AI)-nanopore platform that enables testing for Wuhan SARS-CoV-2 with high sensitivity and specificity within five minutes. However, which parts of the virus are recognized by the platform are unknown. Similarly, whether the platform can detect SARS-CoV-2 variants or the presence of the virus in clinical samples needs further study. Here, we demonstrated the platform can distinguish SARS-CoV-2 variants. Further, it identified mutated Wuhan SARS-CoV-2 expressing spike proteins of the delta and omicron variants, indicating it discriminates spike proteins. Finally, we used the platform to identify omicron variants with a sensitivity and specificity of 100% and 94%, respectively, in saliva specimens from COVID-19 patients. Thus, our results demonstrate the AI-nanopore platform is an effective diagnostic tool for SARS-CoV-2 variants.
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Affiliation(s)
- Kaoru Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shimpei I Kubota
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Kumiko Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroki Tanaka
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Keiichiroh Akabane
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Yuta Shinohara
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Hiroyasu Takei
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Shigeru Hashimoto
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Yuki Tanaka
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Shintaro Hojyo
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
| | - Osamu Sakamoto
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Norihiko Naono
- Aipore Inc., 26-1 Sakuragaokacho, Shibuya, Tokyo 150-8512, Japan
| | - Takayui Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Kazuki Sato
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Yuichi Kojima
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Toshiyuki Harada
- Department of Respiratory Medicine, Japan Community Healthcare Organization Hokkaido Hospital, Sapporo, 062-8618, Japan
| | - Takeshi Hattori
- Department of Respiratory Medicine, Hokkaido Medical Center, National Hospital Organization, Sapporo, 063-0005, Japan
| | - Satoshi Fuke
- Department of Respiratory Medicine, KKR Sapporo Medical Center, Sapporo, 062-0931, Japan
| | - Isao Yokota
- Department of Biostatistics, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Sapporo, 060-0815, Japan
| | - Takanori Teshima
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, 060-8638, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047, Osaka, Japan
| | - Masaaki Murakami
- Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo 060-0815, Japan
- Group of Quantum immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba 263-8555, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0020, Japan
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11
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Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA. Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. Nat Commun 2023; 14:6820. [PMID: 37884513 PMCID: PMC10603101 DOI: 10.1038/s41467-023-42406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.
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Affiliation(s)
- Hinako Kawabe
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Logan Miessner
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas Kaplan
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Jorge A Marchand
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA.
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12
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Trojanowicz M. Impact of nanotechnology on progress of flow methods in chemical analysis: A review. Anal Chim Acta 2023; 1276:341643. [PMID: 37573121 DOI: 10.1016/j.aca.2023.341643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
In evolution of instrumentation for analytical chemistry as crucial technological breakthroughs should be considered a common introduction of electronics with all its progress in integration, and then microprocessors which was followed by a widespread computerization. It is seems that a similar role can be attributed to the introduction of various elements of modern nanotechnology, observed with a fast progress since beginning of this century. It concerns all areas of the applications of analytical chemistry, including also progress in flow analysis, which are being developed since the middle of 20th century. Obviously, it should not be omitted the developed earlier and analytically applied planar structures like lipid membranes or self-assembled monolayers They had essential impact prior to discoveries of numerous extraordinary nanoparticles such as fullerenes, carbon nanotubes and graphene, or nanocrystalline semiconductors (quantum dots). Mostly, due to catalytic effects, significantly developed surface and the possibility of easy functionalization, their application in various stages of flow analytical procedures can significantly improve them. The application of new nanomaterials may be used for the development of new detection methods for flow analytical systems in macro-flow setups as well as in microfluidics and lateral flow immunoassay tests. It is also advantageous that quick flow conditions of measurements may be helpful in preventing unfavorable agglomeration of nanoparticles. A vast literature published already on this subject (e.g. almost 1000 papers about carbon nanotubes and flow-injection analytical systems) implies that for this reviews it was necessary to make an arbitrary selection of reported examples of this trend, focused mainly on achievements reported in the recent decade.
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Affiliation(s)
- Marek Trojanowicz
- Laboratory of Nuclear Analytical Techniques, Institute of Nuclear Chemistry and Technology, Warsaw, Poland; Department of Chemistry, University of Warsaw, Poland.
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13
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Abstract
Controlling and understanding the chemistry of molecular junctions is one of the major themes in various fields ranging from chemistry and nanotechnology to biotechnology and biology. Stochastic single-entity collision electrochemistry (SECE) provides powerful tools to study a single entity, such as single cells, single particles, and even single molecules, in a nanoconfined space. Molecular junctions formed by SECE collision show various potential applications in monitoring molecular dynamics with high spatial resolution and high temporal resolution and in feasible combination with hybrid techniques. This Perspective highlights the new breakthroughs, seminal studies, and trends in the area that have been most recently reported. In addition, future challenges for the study of molecular junction dynamics with SECE are discussed.
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Affiliation(s)
- Na Kong
- School of Life and Environmental Science, Centre for Sustainable Bioproducts, Deakin University, Geelong, Victoria 3216, Australia
| | - Jin He
- Physics Department, Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Wenrong Yang
- School of Life and Environmental Science, Centre for Sustainable Bioproducts, Deakin University, Geelong, Victoria 3216, Australia
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14
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Wang H, Wang T, Yuan X, Wang Y, Yue X, Wang L, Zhang J, Wang J. Plasmonic Nanostructure Biosensors: A Review. Sensors (Basel) 2023; 23:8156. [PMID: 37836985 PMCID: PMC10575025 DOI: 10.3390/s23198156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Plasmonic nanostructure biosensors based on metal are a powerful tool in the biosensing field. Surface plasmon resonance (SPR) can be classified into localized surface plasmon resonance (LSPR) and propagating surface plasmon polariton (PSPP), based on the transmission mode. Initially, the physical principles of LSPR and PSPP are elaborated. In what follows, the recent development of the biosensors related to SPR principle is summarized. For clarity, they are categorized into three groups according to the sensing principle: (i) inherent resonance-based biosensors, which are sensitive to the refractive index changes of the surroundings; (ii) plasmon nanoruler biosensors in which the distances of the nanostructure can be changed by biomolecules at the nanoscale; and (iii) surface-enhanced Raman scattering biosensors in which the nanostructure serves as an amplifier for Raman scattering signals. Moreover, the advanced application of single-molecule detection is discussed in terms of metal nanoparticle and nanopore structures. The review concludes by providing perspectives on the future development of plasmonic nanostructure biosensors.
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Affiliation(s)
- Huimin Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Tao Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Xuyang Yuan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Yuandong Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Xinzhao Yue
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Lu Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Jinyan Zhang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
| | - Jian Wang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China; (H.W.); (X.Y.); (Y.W.); (X.Y.); (L.W.); (J.Z.)
- Optics Valley Laboratory, Wuhan 430074, China
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15
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Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
- School of Chemistry and Materials Science, East China University of Technology, Nanchang, Jiangxi 330013, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
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16
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. Small 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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17
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De Silva ARI, Page RC. Ubiquitination detection techniques. Exp Biol Med (Maywood) 2023; 248:1333-1346. [PMID: 37787047 PMCID: PMC10625345 DOI: 10.1177/15353702231191186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Ubiquitination is an intricately regulated post-translational modification that involves the covalent attachment of ubiquitin to a substrate protein. The complex dynamic nature of the ubiquitination process regulates diverse cellular functions including targeting proteins for degradation, cell cycle, deoxyribonucleic acid (DNA) damage repair, and numerous cell signaling pathways. Ubiquitination also serves as a crucial mechanism in protein quality control. Dysregulation in ubiquitination could result in lethal disease conditions such as cancers and neurodegenerative diseases. Therefore, the ubiquitination cascade has become an attractive target for therapeutic interventions. Enormous efforts have been made to detect ubiquitination involving different detection techniques to better grasp the underlying molecular mechanisms of ubiquitination. This review discusses a wide range of techniques stretching from the simplest assays to real-time assays. This includes western blotting/immunoblotting, fluorescence assays, chemiluminescence assays, spectrophotometric assays, and nanopore sensing assays. This review compares these applications, and the inherent advantages and limitations.
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Affiliation(s)
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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18
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Abstract
Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.
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Affiliation(s)
- Xiaojin Zhang
- 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, Wuhan 430074, China
| | - Meihua Lin
- 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, Wuhan 430074, China
| | - Yu Dai
- 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, Wuhan 430074, 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, Wuhan 430074, China
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19
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Kamsma TM, Boon WQ, Ter Rele T, Spitoni C, van Roij R. Iontronic Neuromorphic Signaling with Conical Microfluidic Memristors. Phys Rev Lett 2023; 130:268401. [PMID: 37450821 DOI: 10.1103/physrevlett.130.268401] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/25/2023] [Indexed: 07/18/2023]
Abstract
Experiments have shown that the conductance of conical channels, filled with an aqueous electrolyte, can strongly depend on the history of the applied voltage. These channels hence have a memory and are promising elements in brain-inspired (iontronic) circuits. We show here that the memory of such channels stems from transient concentration polarization over the ionic diffusion time. We derive an analytic approximation for these dynamics which shows good agreement with full finite-element calculations. Using our analytic approximation, we propose an experimentally realizable Hodgkin-Huxley iontronic circuit where micrometer cones take on the role of sodium and potassium channels. Our proposed circuit exhibits key features of neuronal communication such as all-or-none action potentials upon a pulse stimulus and a spike train upon a sustained stimulus.
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Affiliation(s)
- T M Kamsma
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
- Mathematical Institute, Utrecht University, Budapestlaan 6, 3584 CD Utrecht, Netherlands
| | - W Q Boon
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
| | - T Ter Rele
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - C Spitoni
- Mathematical Institute, Utrecht University, Budapestlaan 6, 3584 CD Utrecht, Netherlands
| | - R van Roij
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, Netherlands
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20
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Bergkamp MH, Cajigas S, van IJzendoorn LJ, Prins MW. High-Throughput Single-Molecule Sensors: How Can the Signals Be Analyzed in Real Time for Achieving Real-Time Continuous Biosensing? ACS Sens 2023; 8:2271-2281. [PMID: 37216442 PMCID: PMC10294250 DOI: 10.1021/acssensors.3c00245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
Single-molecule sensors collect statistics of single-molecule interactions, and the resulting data can be used to determine concentrations of analyte molecules. The assays are generally end-point assays and are not designed for continuous biosensing. For continuous biosensing, a single-molecule sensor needs to be reversible, and the signals should be analyzed in real time in order to continuously report output signals, with a well-controlled time delay and measurement precision. Here, we describe a signal processing architecture for real-time continuous biosensing based on high-throughput single-molecule sensors. The key aspect of the architecture is the parallel computation of multiple measurement blocks that enables continuous measurements over an endless time span. Continuous biosensing is demonstrated for a single-molecule sensor with 10,000 individual particles that are tracked as a function of time. The continuous analysis includes particle identification, particle tracking, drift correction, and detection of the discrete timepoints where individual particles switch between bound and unbound states, yielding state transition statistics that relate to the analyte concentration in solution. The continuous real-time sensing and computation were studied for a reversible cortisol competitive immunosensor, showing how the precision and time delay of cortisol monitoring are controlled by the number of analyzed particles and the size of the measurement blocks. Finally, we discuss how the presented signal processing architecture can be applied to various single-molecule measurement methods, allowing these to be developed into continuous biosensors.
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Affiliation(s)
- Max H. Bergkamp
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | | | - Leo J. van IJzendoorn
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
| | - Menno W.J. Prins
- Department
of Biomedical Engineering, Eindhoven University
of Technology, Eindhoven 5612 AE, The Netherlands
- Department
of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven 5612 AE, The Netherlands
- Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, Eindhoven 5612 AE, The Netherlands
- Helia
Biomonitoring, Eindhoven 5612 AR, The Netherlands
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21
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Abstract
Label-free electrochemical biosensing leverages the advantages of label-free techniques, low cost, and fewer user steps, with the sensitivity and portability of electrochemical analysis. In this review, we identify four label-free electrochemical biosensing mechanisms: (a) blocking the electrode surface, (b) allowing greater access to the electrode surface, (c) changing the intercalation or electrostatic affinity of a redox probe to a biorecognition unit, and (d) modulating ion or electron transport properties due to conformational and surface charge changes. Each mechanism is described, recent advancements are summarized, and relative advantages and disadvantages of the techniques are discussed. Furthermore, two avenues for gaining further diagnostic information from label-free electrochemical biosensors, through multiplex analysis and incorporating machine learning, are examined.
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Affiliation(s)
- Kira L Rahn
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Umesha Peramune
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Tianyi Zhang
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
| | - Robbyn K Anand
- Department of Chemistry, Iowa State University, Ames, Iowa, USA;
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22
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Punia B, Chaudhury S. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores. J Phys Chem B 2023. [PMID: 37294938 DOI: 10.1021/acs.jpcb.3c02792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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23
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Șoldănescu I, Lobiuc A, Covașă M, Dimian M. Detection of Biological Molecules Using Nanopore Sensing Techniques. Biomedicines 2023; 11:1625. [PMID: 37371721 PMCID: PMC10295350 DOI: 10.3390/biomedicines11061625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.
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Affiliation(s)
- Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covașă
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
- Department of Computer, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
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24
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Zhu J, Tivony R, Bošković F, Pereira-Dias J, Sandler SE, Baker S, Keyser UF. Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches. J Am Chem Soc 2023. [PMID: 37220424 DOI: 10.1021/jacs.3c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
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25
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Vaneev AN, Timoshenko RV, Gorelkin PV, Klyachko NL, Erofeev AS. Recent Advances in Nanopore Technology for Copper Detection and Their Potential Applications. Nanomaterials (Basel) 2023; 13:nano13091573. [PMID: 37177118 PMCID: PMC10181076 DOI: 10.3390/nano13091573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
Recently, nanopore technology has emerged as a promising technique for the rapid, sensitive, and selective detection of various analytes. In particular, the use of nanopores for the detection of copper ions has attracted considerable attention due to their high sensitivity and selectivity. This review discusses the principles of nanopore technology and its advantages over conventional techniques for copper detection. It covers the different types of nanopores used for copper detection, including biological and synthetic nanopores, and the various mechanisms used to detect copper ions. Furthermore, this review provides an overview of the recent advancements in nanopore technology for copper detection, including the development of new nanopore materials, improvements in signal amplification, and the integration of nanopore technology with other analytical methods for enhanced detection sensitivity and accuracy. Finally, we summarize the extensive applications, current challenges, and future perspectives of using nanopore technology for copper detection, highlighting the need for further research in the field to optimize the performance and applicability of the technique.
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Affiliation(s)
- Alexander N Vaneev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Roman V Timoshenko
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Petr V Gorelkin
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Natalia L Klyachko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexander S Erofeev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
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26
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Yu C, Wang Y, Wu R, Li B. Single Molecular Nanopores as a Label-Free Method for Homogeneous Conformation Investigation and Anti-Interference Molecular Analysis. ACS Appl Mater Interfaces 2023; 15:23602-23612. [PMID: 37141628 DOI: 10.1021/acsami.3c01884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this paper, we propose a "reciprocal strategy" that, on the one hand, explores the ability of solid-state nanopores in a homogeneous high-fidelity characterization of nucleic acid assembly and, on the other hand, the formed nucleic acid assembly with a large size serves as an amplifier to provide a highly distinguished and anti-interference signal for molecular sensing. Four-hairpin hybridization chain reaction (HCR) with G-rich tail tags is taken as the proof-of-concept demonstration. G-rich tail tags are commonly used to form G-quadruplex signal probes on the side chain of HCR duplex concatemers. When such G-tailed HCR concatemers translocate the nanopore, abnormal, much higher nanopore signals over normal duplexes can be observed. Combined with atomic force microscopy, we reveal the G-rich tail may easily induce the "intermolecular interaction" between HCR concatemers to form "branched assembly structure (BAS)". To the best of our knowledge, this is the first evidence for the formation BAS of the G tailed HCR concatemers in a homogeneous solution. Systematic nanopore measurements further suggest the formation of these BASs is closely related to the types of salt ions, the amount of G, the concentration of substrate hairpins, the reaction time, and so forth. Under optimized conditions, these BASs can be grown to just the right size without being too large to block the pores, while producing a current 14 times that of conventional double-stranded chains. Here, these very abnormal large current blockages have, in turn, been taken as an anti-interference signal indicator for small targets in order to defend the high noises resulting from co-existing big species (e.g., enzymes or other long double-stranded DNA).
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Affiliation(s)
- Chunmiao Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yesheng Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Ruiping Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P. R. China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
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27
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Yu RJ, Li Q, Liu SC, Ma H, Ying YL, Long YT. Simultaneous observation of the spatial and temporal dynamics of single enzymatic catalysis using a solid-state nanopore. Nanoscale 2023; 15:7261-7266. [PMID: 37038732 DOI: 10.1039/d2nr06361a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We developed a bipolar SiNx nanopore for the observation of single-molecule heterogeneous enzymatic dynamics. Single glucose oxidase was immobilized inside the nanopore and its electrocatalytic behaviour was real-time monitored via continuous recording of ionic flux amplification. The temporal heterogeneity in enzymatic properties and its spatial dynamic orientations were observed simultaneously, and these two properties were found to be closely correlated. We anticipate that this method offers new perspectives on the correlation of protein structure and function at the single-molecule level.
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Affiliation(s)
- Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Qiao Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Hui Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
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28
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Xie W, He S, Fang S, Tian R, Liang L, Wang D. Phenylboronic acid-modified polyethyleneimine assisted neutral polysaccharide detection and weight-resolution analysis with a nanopipette. Nanoscale 2023; 15:7147-7153. [PMID: 37009671 DOI: 10.1039/d2nr07280g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In this work, an innovative method based on a nanopipette assisted with o-phenylboronic acid-modified polyethyleneimine (PEI-oBA) is proposed to detect neutral polysaccharides with different degrees of polymerization. Herein, dextran is used as the research target. Dextran, with its low molecular weight (104 < MW < 105 Da), has important applications in medicine and is one of the best plasma substitutes at present. Through the interaction between the boric acid group and a hydroxyl group, the synthesized high-charge polymer molecule PEI-oBA combines with dextran, increasing the electrophoretic force and exclusion volume of the target molecule to obtain a high signal-to-noise ratio for nanopore detection. These results show that the current amplitude increased significantly with the increase of dextran molecular weight. Furthermore, an aggregation-induced emission (AIE) molecule was introduced to adsorb onto PEI-oBA to verify that PEI-oBA combined with a polysaccharide entered the nanopipette together and was driven by electrophoresis. With the introduction of the modifiability of polymer molecules, the proposed method is conducive to improving the nanopore detection sensitivity of other important molecules with low charges and low molecular weights.
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Affiliation(s)
- Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
| | - Shixuan He
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
| | - Shaoxi Fang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
| | - Rong Tian
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, China
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29
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Xie W, He S, Fang S, Yin B, Tian R, Wang Y, Wang D. Analysis of starch dissolved in ionic liquid by glass nanopore at single molecular level. Int J Biol Macromol 2023; 239:124271. [PMID: 37019197 DOI: 10.1016/j.ijbiomac.2023.124271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023]
Abstract
In this paper, the glass nanopore technology was proposed to detect a single molecule of starch dissolved in ionic liquid [1-butyl-3-methylimidazolium chloride (BmimCl)]. Firstly, the influence of BmimCl on nanopore detection is discussed. It is found that a certain amount of strong polar ionic liquids will disturb the charge distribution in nanopores and increase the detection noise. Then, by analysis of the characteristic current signal of the conical nanopore, the motion behaviour of starch near the entrance of the nanopore was studied and analysis the dominant ion of starch in the BmimCl dissolution process. Finally, based on nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy simply discussed the mechanism of amylose and amylopectin dissolved in BmimCl. These results confirm that branched chain structure would affect the dissolution of polysaccharides in ionic liquids and the contribution of anions to the dissolution of polysaccharides are dominant. It is further proved that the current signal can be used to judge the charge and structure information of the analyte, and the dissolution mechanism can be assist analyzed at the single molecule level.
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30
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Jiang J, Li MY, Wu XY, Ying YL, Han HX, Long YT. Protein nanopore reveals the renin-angiotensin system crosstalk with single-amino-acid resolution. Nat Chem 2023; 15:578-586. [PMID: 36805037 DOI: 10.1038/s41557-023-01139-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
Abstract
The discovery of crosstalk effects on the renin-angiotensin system (RAS) is limited by the lack of approaches to quantitatively monitor, in real time, multiple components with subtle differences and short half-lives. Here we report a nanopore framework to quantitatively determine the effect of the hidden crosstalk between angiotensin-converting enzyme (ACE) and angiotensin-converting enzyme 2 (ACE2) on RAS. By developing an engineered aerolysin nanopore capable of single-amino-acid resolution, we show that the ACE can be selectively inhibited by ACE2 to prevent cleavage of angiotensin I, even when the concentration of ACE is more than 30-fold higher than that of ACE2. We also show that the activity of ACE2 for cleaving angiotensin peptides is clearly suppressed by the spike protein of SARS-CoV-2. This leads to the relaxation of ACE and the increased probability of accumulation of the principal effector angiotensin II. The spike protein of the SARS-CoV-2 Delta variant is demonstrated to have a much greater impact on the crosstalk than the wild type.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Huan-Xing Han
- Department of Pharmacy, Shanghai Changzheng Hospital, Shanghai, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
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31
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Li M, Xiong Y, Cao Y, Zhang C, Li Y, Ning H, Liu F, Zhou H, Li X, Ye X, Pang Y, Zhang J, Liang X, Qing G. Identification of tagged glycans with a protein nanopore. Nat Commun 2023; 14:1737. [PMID: 36977665 PMCID: PMC10050315 DOI: 10.1038/s41467-023-37348-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Structural complexity of glycans derived from the diversities in composition, linage, configuration, and branching considerably complicates structural analysis. Nanopore-based single-molecule sensing offers the potential to elucidate glycan structure and even sequence glycan. However, the small molecular size and low charge density of glycans have restricted direct nanopore detection of glycan. Here we show that glycan sensing can be achieved using a wild-type aerolysin nanopore by introducing a facile glycan derivatization strategy. The glycan molecule can induce impressive current blockages when moving through the nanopore after being connected with an aromatic group-containing tag (plus a carrier group for the neutral glycan). The obtained nanopore data permit the identification of glycan regio- and stereoisomers, glycans with variable monosaccharide numbers, and distinct branched glycans, either independently or with the use of machine learning methods. The presented nanopore sensing strategy for glycans paves the way towards nanopore glycan profiling and potentially sequencing.
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Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Hanwen Ning
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Fan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Han Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Jiaming Zhang
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China.
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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32
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Aluru NR, Aydin F, Bazant MZ, Blankschtein D, Brozena AH, de Souza JP, Elimelech M, Faucher S, Fourkas JT, Koman VB, Kuehne M, Kulik HJ, Li HK, Li Y, Li Z, Majumdar A, Martis J, Misra RP, Noy A, Pham TA, Qu H, Rayabharam A, Reed MA, Ritt CL, Schwegler E, Siwy Z, Strano MS, Wang Y, Yao YC, Zhan C, Zhang Z. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem Rev 2023; 123:2737-2831. [PMID: 36898130 PMCID: PMC10037271 DOI: 10.1021/acs.chemrev.2c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.
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Affiliation(s)
- Narayana R Aluru
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Fikret Aydin
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alexandra H Brozena
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Samuel Faucher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Kun Li
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zhongwu Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Arun Majumdar
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Joel Martis
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Tuan Anh Pham
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - Archith Rayabharam
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, 15 Prospect Street, New Haven, Connecticut06520, United States
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Eric Schwegler
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zuzanna Siwy
- Department of Physics and Astronomy, Department of Chemistry, Department of Biomedical Engineering, University of California, Irvine, Irvine92697, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Cheng Zhan
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Ze Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
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33
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Chen K, Choudhary A, Sandler SE, Maffeo C, Ducati C, Aksimentiev A, Keyser UF. Super-Resolution Detection of DNA Nanostructures Using a Nanopore. Adv Mater 2023; 35:e2207434. [PMID: 36630969 DOI: 10.1002/adma.202207434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabeled single molecules in their native states. Here, label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometers is demonstrated. Using a narrow solid-state nanopore, the passage of a series of nanostructures attached to a freely translocating DNA molecule is detected, resolving individual nanostructures placed as close as 6 nm apart and with a surface-to-surface gap distance of only 2 nm. Such super-resolution ability is attributed to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. This work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping, and digital information storage independent of molecular motors.
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Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Caterina Ducati
- Department of Materials Science & Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL 61801, USA
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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34
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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35
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Guan X, Li H, Chen L, Qi G, Jin Y. Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection. ACS Sens 2023; 8:427-442. [PMID: 36670058 DOI: 10.1021/acssensors.2c02102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.
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Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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36
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Qiao L, Szuttor K, Holm C, Slater GW. Ratcheting Charged Polymers through Symmetric Nanopores Using Pulsed Fields: Designing a Low Pass Filter for Concentrating Polyelectrolytes. Nano Lett 2023; 23:1343-1349. [PMID: 36705546 DOI: 10.1021/acs.nanolett.2c04588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation, and pulsed fields. Using Langevin dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it should be possible to integrate it directly into nanopore sequencing devices, increasing its potential utility.
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Affiliation(s)
- Le Qiao
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
| | - Kai Szuttor
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
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37
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Abstract
The unique combination of physical and chemical properties of MXenes has propelled a growing number of applications in biomedicine and healthcare. The expanding library of MXenes with tunable properties is paving the way for high-performance, application-specific MXene-based sensing and therapeutic platforms. In this article, we highlight the emerging biomedical applications of MXenes with specific emphasis on bioelectronics, biosensors, tissue engineering, and therapeutics. We present examples of MXenes and their composites enabling novel technological platforms and therapeutic strategies, and elucidate potential avenues for further developments. Finally, we discuss the materials, manufacturing, and regulatory challenges that need to be synergistically addressed for the clinical translation of MXene-based biomedical technologies. Graphical abstract
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Affiliation(s)
- Raghav Garg
- Department of Neurology, University of Pennsylvania, Philadelphia, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, USA
- Center for Neurotrauma, Neurodegeneration, and Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, USA
| | - Flavia Vitale
- Department of Neurology, University of Pennsylvania, Philadelphia, USA
- Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, USA
- Center for Neurotrauma, Neurodegeneration, and Restoration, Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, USA
- Department of Physical Medicine and Rehabilitation, University of Pennsylvania, Philadelphia, USA
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38
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. Micromachines (Basel) 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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39
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Xu X, Valavanis D, Ciocci P, Confederat S, Marcuccio F, Lemineur JF, Actis P, Kanoufi F, Unwin PR. The New Era of High-Throughput Nanoelectrochemistry. Anal Chem 2023; 95:319-356. [PMID: 36625121 PMCID: PMC9835065 DOI: 10.1021/acs.analchem.2c05105] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Xiangdong Xu
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Paolo Ciocci
- Université
Paris Cité, ITODYS, CNRS, F-75013 Paris, France
| | - Samuel Confederat
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,Faculty
of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.,Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.,
| | | | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.,
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40
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Bahri M, Gebre SH, Elaguech MA, Dajan FT, Sendeku MG, Tlili C, Wang D. Recent advances in chemical vapour deposition techniques for graphene-based nanoarchitectures: From synthesis to contemporary applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Liu HL, Zhan K, Wang K, Xia XH. Recent advances in nanotechnologies combining surface-enhanced Raman scattering and nanopore. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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42
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Wang Y, Zhu Z, Yu C, Wu R, Zhu J, Li B. Lego-Like Catalytic Hairpin Assembly Enables Controllable DNA-Oligomer Formation and Spatiotemporal Amplification in Single Molecular Signaling. Small 2023; 19:e2206283. [PMID: 36436946 DOI: 10.1002/smll.202206283] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
Abstract
While the solid-state nanopore shows increasing potential during sensitive and label-free single molecular analysis, target concentration and signal amplification method is in urgent need. In this article, a solution via designing a model nucleic acid circuit reaction that can produce "Y" shape-structure three-way DNA oligomers with controllable size and polymerization degree is proposed. Such a so-called lego-like three-way catalytic hairpin assembly (LK-3W-CHA) can provide both concentration amplification (via CHA circuit) and programmable size control (via lego-like building mode) to enhance spatiotemporal resolution in single molecular sensing of solid-state nanopore. Oligomers containing 1-4 DNA three-way junctions (Y monomers, Y1-Y4) are designed in proof-of-concept experiments and applications. When the oligomers are applied to direct translocation measurements, Y2-Y4 can significantly increase the signal resolution and stability than that of Y1. Meanwhile, Y1 to Y4 can be used as the tags on the long DNA carrier to provide very legible secondary signals for specific identification, multiple assays, and information storage. Compared with other possible tags, Y1-Y4 provides higher signal density and amplitude, and quasi-linear "inner reference" for each other, which may provide more systematic, reliable, and controllable experimental results.
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Affiliation(s)
- Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhentong Zhu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinbo Zhu
- Cavendish Lab, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
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43
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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44
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Dai Y, Zhang Y, Ma Q, Lin M, Zhang X, Xia F. Inner Wall and Outer Surface Distinguished Solid-State Nanopores for Sensing. Anal Chem 2022; 94:17343-17348. [PMID: 36473027 DOI: 10.1021/acs.analchem.2c04216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solid-state nanopores, inspired by biological nanopores, have the advantages of good mechanical properties, stability, and easy modification. They have attracted wide attention in the fields of sequencing, sensing, molecular sieving, nanofluidic devices, nanoelectrochemistry, and energy conversion. Because of the ion/molecule transport characteristic of the pore, the research on solid-state nanopores mainly focuses on the functional modification of its inner wall. In recent years, the outer surface of nanopores has also attracted the attention of researchers, and the functional elements on the outer surface have the functions of anti-interference and ionic signal enhancement. In this perspective, we review research progress of inner wall and outer surface distinguished solid-state nanopores, highlight their processing and advantages, summarize their functions and applications in sensing, and give insight into further research.
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Affiliation(s)
- Yu Dai
- 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, Wuhan 430074, P. R. China
| | - Yiwei Zhang
- 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, Wuhan 430074, P. R. China
| | - Qun Ma
- 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, Wuhan 430074, P. R. China
| | - Meihua Lin
- 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, Wuhan 430074, P. R. China
| | - Xiaojin Zhang
- 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, Wuhan 430074, 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, Wuhan 430074, P. R. China
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45
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Wang Y, Liu R, Ma Y, Shen X, Wang D. Electrodeposition of Metal Nanoparticles inside Carbon Nanopipettes for Sensing Applications. Anal Chem 2022; 94:16987-16991. [PMID: 36449549 DOI: 10.1021/acs.analchem.2c04449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Conductive nanopipettes offer promising confined spaces to enable advanced electrochemical sensing applications in small spaces. Herein, a series of metal-decorated carbon nanopipettes (CNPs) were developed, in which Au, Ag, and Pt are modified at the inner walls of CNPs by a simple electrodeposition method. The fabricated tips show good sensing performances for a variety of important analytes, such as glucose, hydrogen peroxide, and chloride and hydrogen ions in biological and catalytic systems. This simple and effective approach can be further extended to prepare other functionalized nanopipette electrodes toward more versatile and powerful measurements in electrochemical sensing and imaging applications.
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Affiliation(s)
- Yuhuan Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Rujia Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Yingfei Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Xiaoyue Shen
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
| | - Dengchao Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing100049, P. R. China
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46
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Hussein EA, White RJ. Maintaining Single-Channel Recordings on a Silver Nanoneedle through Probe Design and Feedback Tip Positioning Control. J Phys Chem B 2022; 126:10111-10119. [PMID: 36395597 DOI: 10.1021/acs.jpcb.2c06275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ion channel proteins showed great promise in the field of nanopore sensing and molecular flux imaging applications due to the atomic-level precision of the pore size and a high signal-to-noise ratio. More specifically, ion channel probes, where the protein channels are integrated at the end of a solid probe, can achieve highly localized detection. Metal probe materials such as gold and silver have been developed to support lipid bilayers and enable the use of smaller probes, or nanoneedles, compared to more traditional glass micropipette ion channel probes. Silver probes are preferable because they support sustained DC stable channel current due to the AgCl layer formed around the tip during the fabrication process. However, one of the current challenges in ion channel measurements is maintaining a single-channel recording. Multiple protein insertions complicate data analysis and destabilize the bilayer. Herein, we combine the promising probe material (Ag/AgCl) with an approach based on current feedback-controlled tip positioning to maintain long-term single-channel recordings for up to 3 h. We develop a hybrid positioning control system, where the channel current is used as feedback to control the vertical movement of the silver tip and, subsequently, control the number of protein channels inserted in the lipid membrane. Our findings reveal that the area of the lipid bilayer decreases with moving the silver tip up (i.e., decreasing the displacement in the z-direction). By reducing the bilayer area around the fine silver tip, we minimize the probability of multiple insertions and remove unwanted proteins. In addition, we characterize the effect of lipid properties such as fluidity on the lipid membrane area. We believe that the use of silver nanoneedles, which enables DC stable channel current, coupled with the developed tip displacement mechanism will offer more opportunities to employ these probes for chemical imaging and mapping different surfaces.
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Affiliation(s)
- Essraa A Hussein
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Ryan J White
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio45221, United States.,Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio45221, United States
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47
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Song Z, Liang Y, Yang J. Nanopore Detection Assisted DNA Information Processing. Nanomaterials (Basel) 2022; 12:nano12183135. [PMID: 36144924 PMCID: PMC9504103 DOI: 10.3390/nano12183135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 05/27/2023]
Abstract
The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.
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Affiliation(s)
- Zichen Song
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yuan Liang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
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48
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Li Y, Maffeo C, Joshi H, Aksimentiev A, Ménard B, Schulman R. Leakless end-to-end transport of small molecules through micron-length DNA nanochannels. Sci Adv 2022; 8:eabq4834. [PMID: 36070388 PMCID: PMC9451144 DOI: 10.1126/sciadv.abq4834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. Here, we design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.
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Affiliation(s)
- Yi Li
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christopher Maffeo
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Himanshu Joshi
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Brice Ménard
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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Yang L, Hu J, Li MC, Xu M, Gu ZY. Solid-state nanopore: chemical modifications, interactions, and functionalities. Chem Asian J 2022; 17:e202200775. [PMID: 36071031 DOI: 10.1002/asia.202200775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Indexed: 11/08/2022]
Abstract
Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.
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Affiliation(s)
- Lei Yang
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Jun Hu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Min-Chao Li
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Ming Xu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Zhi-Yuan Gu
- Nanjing Normal University, College of Chemistry and Materials Science, 1 Wenyuan Rd, 210023, Nanjing, CHINA
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Abstract
Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.
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Affiliation(s)
- Yuan Ju
- Sichuan University, Sichuan University Library, CHINA
| | - Mengjun Pu
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Ke Sun
- Sichuan University, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, CHINA
| | - Guiqin Song
- North Sichuan Medical College [Search North Sichuan Medical College]: North Sichuan Medical University, Shool of Basic Medical Sciences and Forensic Medicine, CHINA
| | - Jia Geng
- Sichuan University, State Key Laboratory of Biotherapy, No 17 Section 3 of South Renmin Rd, 610040, Chengdu, CHINA
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