1
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Zhao Y, Chen KL, Shen XY, Li MK, Wan YJ, Yang C, Yu RJ, Long YT, Yan F, Ying YL. HFM-Tracker: a cell tracking algorithm based on hybrid feature matching. Analyst 2024; 149:2629-2636. [PMID: 38563459 DOI: 10.1039/d4an00199k] [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: 04/04/2024]
Abstract
Cell migration is known to be a fundamental biological process, playing an essential role in development, homeostasis, and diseases. This paper introduces a cell tracking algorithm named HFM-Tracker (Hybrid Feature Matching Tracker) that automatically identifies cell migration behaviours in consecutive images. It combines Contour Attention (CA) and Adaptive Confusion Matrix (ACM) modules to accurately capture cell contours in each image and track the dynamic behaviors of migrating cells in the field of view. Cells are firstly located and identified via the CA module-based cell detection network, and then associated and tracked via a cell tracking algorithm employing a hybrid feature-matching strategy. This proposed HFM-Tracker exhibits superiorities in cell detection and tracking, achieving 75% in MOTA (Multiple Object Tracking Accuracy) and 65% in IDF1 (ID F1 score). It provides quantitative analysis of the cell morphology and migration features, which could further help in understanding the complicated and diverse cell migration processes.
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Affiliation(s)
- Yan Zhao
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, P. R. China.
| | - Ke-Le Chen
- School of Chemistry and Chemical Engineering, Molecular Sensing and Imaging Center (MSIC), Nanjing University, Nanjing 210023, P. R. China.
| | - Xin-Yu Shen
- School of Electronic Sciences and Engineering, Nanjing University, Nanjing, 210023, China
| | - Ming-Kang Li
- School of Chemistry and Chemical Engineering, Molecular Sensing and Imaging Center (MSIC), Nanjing University, Nanjing 210023, P. R. China.
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, P. R. China.
| | - Cheng Yang
- School of Electronic Sciences and Engineering, Nanjing University, Nanjing, 210023, China
| | - Ru-Jia Yu
- School of Chemistry and Chemical Engineering, Molecular Sensing and Imaging Center (MSIC), Nanjing University, Nanjing 210023, P. R. China.
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering, Molecular Sensing and Imaging Center (MSIC), Nanjing University, Nanjing 210023, P. R. China.
| | - Feng Yan
- School of Electronic Sciences and Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Lun Ying
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, P. R. China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
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2
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Li X, Fu YH, Wei N, Yu RJ, Bhatti H, Zhang L, Yan F, Xia F, Ewing AG, Long YT, Ying YL. Emerging Data Processing Methods for Single-Entity Electrochemistry. Angew Chem Int Ed Engl 2024; 63:e202316551. [PMID: 38411372 DOI: 10.1002/anie.202316551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ying-Huan Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nannan Wei
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
| | - Huma Bhatti
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Limin Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 430034, Wuhan, P. R. China
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296, Gothenburg, Sweden
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
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3
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Yang CN, Liu W, Liu HT, Zhang JC, Yu RJ, Ying YL, Long YT. Electrochemical Visualization of Single-Molecule Thiol Substitution with Nanopore Measurement. ACS Meas Sci Au 2024; 4:76-80. [PMID: 38404487 PMCID: PMC10885329 DOI: 10.1021/acsmeasuresciau.3c00046] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 02/27/2024]
Abstract
Reactions involving sulfhydryl groups play a critical role in maintaining the structure and function of proteins. However, traditional mechanistic studies have mainly focused on reaction rates and the efficiency in bulk solutions. Herein, we have designed a cysteine-mutated nanopore as a biological protein nanoreactor for electrochemical visualization of the thiol substitute reaction. Statistical analysis of characteristic current signals shows that the apparent reaction rate at the single-molecule level in this confined nanoreactor reached 1400 times higher than that observed in bulk solution. This substantial acceleration of thiol substitution reactions within the nanopore offers promising opportunities for advancing the design and optimization of micro/nanoreactors. Moreover, our results could shed light on the understanding of sulfhydryl reactions and the thiol-involved signal transduction mechanisms in biological systems.
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Affiliation(s)
- Chao-Nan Yang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Wei Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Hao-Tian Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Ji-Chang Zhang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Ru-Jia Yu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
- Chemistry
and Biomedicine Innovation Center, 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, 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, China
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4
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Jain A, Gosling J, Liu S, Wang H, Stone EM, Chakraborty S, Jayaraman PS, Smith S, Amabilino DB, Fromhold M, Long YT, Pérez-García L, Turyanska L, Rahman R, Rawson FJ. Wireless electrical-molecular quantum signalling for cancer cell apoptosis. Nat Nanotechnol 2024; 19:106-114. [PMID: 37709951 PMCID: PMC10796273 DOI: 10.1038/s41565-023-01496-y] [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: 03/26/2023] [Accepted: 08/01/2023] [Indexed: 09/16/2023]
Abstract
Quantum biological tunnelling for electron transfer is involved in controlling essential functions for life such as cellular respiration and homoeostasis. Understanding and controlling the quantum effects in biology has the potential to modulate biological functions. Here we merge wireless nano-electrochemical tools with cancer cells for control over electron transfer to trigger cancer cell death. Gold bipolar nanoelectrodes functionalized with redox-active cytochrome c and a redox mediator zinc porphyrin are developed as electric-field-stimulating bio-actuators, termed bio-nanoantennae. We show that a remote electrical input regulates electron transport between these redox molecules, which results in quantum biological tunnelling for electron transfer to trigger apoptosis in patient-derived cancer cells in a selective manner. Transcriptomics data show that the electric-field-induced bio-nanoantenna targets the cancer cells in a unique manner, representing electrically induced control of molecular signalling. The work shows the potential of quantum-based medical diagnostics and treatments.
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Affiliation(s)
- Akhil Jain
- Bioelectronics Laboratory, Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Jonathan Gosling
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Shaochuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Haowei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Eloise M Stone
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Sajib Chakraborty
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Stuart Smith
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
- Department of Neurosurgery, Nottingham University Hospitals, Nottingham, UK
| | - David B Amabilino
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus Universitari de Cerdanyola, Barcelona, Spain
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Mark Fromhold
- School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Lluïsa Pérez-García
- School of Pharmacy, University of Nottingham, Nottingham, UK
- Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
- Institut de Nanociència i Nanotecnologia, Universitat de Barcelona (IN2UB), Barcelona, Spain
| | | | - Ruman Rahman
- Children's Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Frankie J Rawson
- Bioelectronics Laboratory, Division of Regenerative Medicine and Cellular Therapies, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK.
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5
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Zhang R, Li L, Guo Y, Shi Y, Li JF, Long YT, Fang J. Confined-Enhanced Raman Spectroscopy. Nano Lett 2023; 23:11771-11777. [PMID: 38088915 DOI: 10.1021/acs.nanolett.3c03734] [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: 12/28/2023]
Abstract
In 1997, the discovery of single molecule-surface enhanced Raman spectroscopy (SM-SERS) rekindled broad interests owing to its ultrahigh enhancement factor up to the 1014-1015 level. However, regretfully, the advantage of SM-SERS with an ultralow detection limit has not yet been fully utilized in commercialized applications. Here, we report a strategy, which we name confined-enhanced Raman spectroscopy, in which the overall Raman properties can be remarkably improved with in situ-formed active nanoshell on the surface of silver or gold nanoparticles. The nanoshell can confine and anchor molecules onto the surface of plasmonic nanoparticles and avoid desorption from hot spots so that the "on and off" blinking effect can be eliminated. It is the first time the single-molecule detection of analytes with super sensitivity, high stability, and reproducibility based on gold nanoparticles has been realized. In addition, this strategy is suitable for SERS detection in diverse molecule systems, including biomedical diagnosis, catalytic reaction, etc.
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Affiliation(s)
- Ruiyuan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Lingwei Li
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yu Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yafei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Jian-Feng Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, College of Energy, and College of Materials, Xiamen University, Xiamen 361005, China
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Jixiang Fang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
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6
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Cao Y, Sun Y, Yu RJ, Long YT. Paper-based substrates for surface-enhanced Raman spectroscopy sensing. Mikrochim Acta 2023; 191:8. [PMID: 38052768 DOI: 10.1007/s00604-023-06086-2] [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: 06/21/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023]
Abstract
Surface-enhanced Raman scattering (SERS) has been recognized as one of the most sensitive analytical methods by adsorbing the target of interest onto a plasmonic surface. Growing attention has been directed towards the fabrication of various substrates to broaden SERS applications. Among these, flexible SERS substrates, particularly paper-based ones, have gained popularity due to their easy-to-use features by full contact with the sample surface. Herein, we reviewed the latest advancements in flexible SERS substrates, with a focus on paper-based substrates. Firstly, it begins by introducing various methods for preparing paper-based substrates and highlights their advantages through several illustrative examples. Subsequently, we demonstrated the booming applications of these paper-based SERS substrates in abiotic and biological matrix detection, with particular emphasis on their potential application in clinical diagnosis. Finally, the prospects and challenges of paper-based SERS substrates in broader applications are discussed.
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Affiliation(s)
- Yue Cao
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, 211166, People's Republic of China.
| | - Yang Sun
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, 211166, People's Republic of China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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7
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Abstract
Most relevant systems of interest to modern chemists rarely consist of a single phase. Real-world problems that require a rigorous understanding of chemical reactivity in multiple phases include the development of wearable and implantable biosensors, efficient fuel cells, single cell metabolic characterization techniques, and solar energy conversion devices. Within all of these systems, confinement effects at the nanoscale influence the chemical reaction coordinate. Thus, a fundamental understanding of the nanoconfinement effects of chemistry in multiphase environments is paramount. Electrochemistry is inherently a multiphase measurement tool reporting on a charged species traversing a phase boundary. Over the past 50 years, electrochemistry has witnessed astounding growth. Subpicoampere current measurements are routine, as is the study of single molecules and nanoparticles. This Perspective focuses on three nanoelectrochemical techniques to study multiphase chemistry under nanoconfinement: stochastic collision electrochemistry, single nanodroplet electrochemistry, and nanopore electrochemistry.
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Kathryn J Vannoy
- Department of Chemistry, Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jeffrey E Dick
- Department of Chemistry, Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - 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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8
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Wu XY, Li MY, Yang SJ, Jiang J, Ying YL, Chen PR, Long YT. Controlled Genetic Encoding of Unnatural Amino Acid in Protein Nanopore. Angew Chem Int Ed Engl 2023:e202300582. [PMID: 37195576 DOI: 10.1002/anie.202300582] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023]
Abstract
Conventional protein engineering methods for modifying protein nanopore are typically limited to 20 natural amino acids, which restricts the diversity of nanopore in structure and function. To enrich the chemical environment inside the nanopore, we employed the genetic code expansion (GCE) technique to site-specifically incorporate unnatural amino acid (UAA) into the sensing region of aerolysin nanopore. This approach leveraged the efficient pyrrolysine-based aminoacyl-tRNA synthetase-tRNA pair for a high yield of pore-forming protein. Both molecular dynamics (MD) simulations and single-molecule sensing experiments demonstrated that the conformation of UAA residues provided a favorable geometric orientation for the interactions of target molecules and the pore. This reasonably designed chemical environment enabled the direct discrimination of multiple peptides containing hydrophobic amino acids. Our work provides a new framework to endow unique sensing properties to nanopore that are difficult to achieve using classical protein engineering approaches.
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Affiliation(s)
- Xue-Yuan Wu
- Nanjing University, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, CHINA
| | - Meng-Yin Li
- Nanjing University, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, CHINA
| | - Shao-Jun Yang
- Peking University, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, CHINA
| | - Jie Jiang
- Nanjing University, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, CHINA
| | - Yi-Lun Ying
- Nanjing University, School of Chemistry and Chemical Engineering, 163 Xianlin Avenu, 210023, Nanjing, CHINA
| | - Peng R Chen
- Peking University, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, CHINA
| | - Yi-Tao Long
- Nanjing University, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, CHINA
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9
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Liu W, Yang CN, Yang ZL, Yu RJ, Long YT, Ying YL. Observing Confined Local Oxygen-induced Reversible Thiol/Disulfide Cycle with a Protein Nanopore. Angew Chem Int Ed Engl 2023:e202304023. [PMID: 37115672 DOI: 10.1002/anie.202304023] [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: 03/21/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
Disulfide bonds play an important role in thiol-based redox regulation. However, owing to the lack of analytical tools, little is known about how local O2 mediates the reversible thiol/disulfide cycle under protein confinement. In this study, a protein nanopore reactor inside a glove box is developed for O2 confinement, as well as a single-molecule sensor for real-time monitoring of the reversible thiol/disulfide cycle. The results demonstrate that the presence of local O2 molecules in protein nanopores can facilitate the redox cycle of disulfide formation and cleavage by promoting a higher fraction of effective reactant collisions owing to nanoconfinement. Further kinetic calculations indicate that negatively charged residues near the reactive sites facilitate proton-involved, oxygen-induced disulfide cleavage under protein confinement. The unexpectedly strong oxidation ability of confined local O2 may play an essential role in cellular redox signaling and enzyme reactions.
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Affiliation(s)
- Wei Liu
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Chao-Nan Yang
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Zhong-Lin Yang
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Ru-Jia Yu
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Yi-Tao Long
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Yi-Lun Ying
- Nanjing University, School of Chemistry and Chemical Engineering, 163 Xianlin Avenu, 210023, Nanjing, CHINA
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10
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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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11
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Wu XY, Jiang J, Li JG, Li MY, Long YT. Profiling the chemistry- and confinement-controlled sensing capability of an octameric aerolysin-like protein. Chem Commun (Camb) 2023; 59:5850-5853. [PMID: 37098687 DOI: 10.1039/d3cc01114c] [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: 04/27/2023]
Abstract
Octameric Aep1 was employed, for the first time to the best of our knowledge, as a nanopore to expand applications. After investigating the optimized conditions of Aep1 for single-channel recording, the sensing features were characterized. Cyclic and linear molecules of varying sizes and charges were employed to probe the radius and chemical environment of the pore, providing deep insights for expected future endeavors at predicting the structure of octameric Aep1. γ-CD showed unique suitability as an 8-subunit adapter in octameric Aep1, enabling the discrimination of β-nicotinamide mononucleotide.
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Affiliation(s)
- Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Jie Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Jun-Ge Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
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12
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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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13
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Abstract
Molecular structure conversion concomitant with mass transfer processes at the electrode-electrolyte interfaces plays a central role in energy electrochemistry. Mass spectrometry, as one of the most intuitive, sensitive techniques, provides the capability to collect transient intermediates and products and uncover reaction mechanisms and kinetics. In situ time-of-flight secondary ion electrochemical mass spectrometry with inherent high mass and spatiotemporal resolution has emerged as a promising strategy for investigating electrochemical processes at the electrode surface. This review illustrates the recent advancements in coupling time-of-flight secondary ion mass spectrometry and electrochemistry to visualize and quantify local dynamic electrochemical processes, identify solvated species distribution, and disclose hidden reaction pathways at the molecular level. Moreover, the key challenges in this field are further discussed to promote new applications and discoveries in operando studying the dynamic electrochemical interfaces of advanced energy systems.
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Affiliation(s)
- Jun-Gang Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, P. R. China
| | - 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.
| | - Xin Hua
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, 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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14
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Chen M, Lu SM, Wang HW, Long YT. Monitoring Photoinduced Interparticle Chemical Communication In Situ. Angew Chem Int Ed Engl 2023; 62:e202215631. [PMID: 36637164 DOI: 10.1002/anie.202215631] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023]
Abstract
Monitoring interparticle chemical communication plays a critical role in the nanomaterial synthesis as this communication controls the final structure and stability of global nanoparticles (NPs). Yet most ensemble analytical techniques, which could only reveal average macroscopic information, are unable to elucidate NP-to-NP interactions. Herein, we employ stochastic collision electrochemistry to track the morphology transformation of Ag NPs in photochemical process at the single NP level. By further statistical analysis of time-resolved current transients, we quantitatively determine the dynamic chemical potential difference and interparticle communication between populations of large and small Ag NPs. The high sensitivity of stochastic collision electrochemistry enables the in situ investigation of chemical communication-dependent transformation kinetics of NPs in photochemical process, shedding light on designing nanomaterials.
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Affiliation(s)
- Mengjie Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hao-Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, 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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15
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Gao Y, Jiang J, Li MY, Long YT. Exploring the water osmosis within physical and chemical controlled confinement for protein sensing. Biophys J 2023; 122:289a-290a. [PMID: 36783436 DOI: 10.1016/j.bpj.2022.11.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Yan Gao
- Nanjing University, Nanjing, China
| | | | - Meng-Yin Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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16
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Niu H, Li MY, Wu XY, Long YT. Directly mapping the O-sulfation sites within CCR2 via an engineered nanopore. Biophys J 2023; 122:319a. [PMID: 36783604 DOI: 10.1016/j.bpj.2022.11.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Meng-Yin Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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17
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Chen K, Xie Y, Yu RJ, Ying YL, Long YT. A confined nanopipette for time-resolved protein-lipid interactions. Biophys J 2023; 122:504a. [PMID: 36784603 DOI: 10.1016/j.bpj.2022.11.2685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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18
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Xin KL, Hu ZL, Ying YL, Long YT. Dense protein data storage based on nanopore sensing. Biophys J 2023; 122:438a. [PMID: 36784243 DOI: 10.1016/j.bpj.2022.11.2369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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19
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Jiang J, Li J, Gao Y, Li MY, Long YT. Direct identification of amino acid-derived hormones with single-atom resolution using an engineered aerolysin nanopore. Biophys J 2023; 122:288a. [PMID: 36783430 DOI: 10.1016/j.bpj.2022.11.1635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Jie Jiang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Junge Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yan Gao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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20
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Lu SM, Chen JF, Wang HF, Hu P, Long YT. Mass Transport and Electron Transfer at the Electrochemical-Confined Interface. J Phys Chem Lett 2023; 14:1113-1123. [PMID: 36705310 DOI: 10.1021/acs.jpclett.2c03479] [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: 06/18/2023]
Abstract
Single entity measurements based on the stochastic collision electrochemistry provide a promising and versatile means to study single molecules, single particles, single droplets, etc. Conceptually, mass transport and electron transfer are the two main processes at the electrochemically confined interface that underpin the most transient electrochemical responses resulting from the stochastic and discrete behaviors of single entities at the microscopic scale. This perspective demonstrates how to achieve controllable stochastic collision electrochemistry by effectively altering the two processes. Future challenges and opportunities for stochastic collision electrochemistry are also highlighted.
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Affiliation(s)
- Si-Min Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023P. R. China
| | - Jian-Fu Chen
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
| | - Hai-Feng Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
| | - Peijun Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
- School of Chemistry and Chemical Engineering, The Queen's University of Belfast, BelfastBT9 5AG, U.K
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023P. R. China
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21
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Long YT, Wanunu M, Winterhalter M. Editorial: Nanopore Electrochemistry. Chem Asian J 2023; 18:e202201253. [PMID: 36725362 DOI: 10.1002/asia.202201253] [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: 02/03/2023]
Abstract
This Special Collection highlights the most recent developments in nanopore electrochemistry and applications. In this Editorial, guest Editors Yi-Tao Long, Meni Wanunu, and Mathias Winterhalter briefly introduce the research published in this special collection.
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Affiliation(s)
- 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
| | - Meni Wanunu
- Department of Physics and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, 28759, Germany
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22
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Li S, Li X, Wan YJ, Ying YL, Yu RJ, Long YT. SmartImage: A Machine Learning Method for Nanopore Identifying Chemical Modifications on RNA. Chem Asian J 2023; 18:e202201144. [PMID: 36527379 DOI: 10.1002/asia.202201144] [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: 11/11/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
RNA modifications modulate essential cellular functions. However, it is challenging to quantitatively identify the differences in RNA modifications. To further improve the single-molecule sensing ability of nanopores, we propose a machine-learning algorithm called SmartImage for identifying and classifying nanopore electrochemical signals based on a combination of improved graph conversion methods and deep neural networks. SmartImage is effective for nearly all ranges of signal duration, which breaks the limitation of the current nanopore algorithm. The overall accuracy (OA) of our proposed recognition strategy exceeded 90% for identifying three types of RNAs. Prediction experiments show that the SmartImage owns the ability to recognize one modified RNA molecule from 1000 normal RNAs with OA >90%. Thus our proposed model and algorithm hold the potential application in clinical applications.
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Affiliation(s)
- Shijia Li
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
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23
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Chen M, Lu SM, Wang HW, Long YT. Monitoring Photoinduced Interparticle Chemical Communication In‐situ. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202215631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Mengjie Chen
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering No. 163, Xianlin Road 210046 Nanjing CHINA
| | - Si-Min Lu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering CHINA
| | - Hao-Wei Wang
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering CHINA
| | - Yi-Tao Long
- Nanjing University 163 Xianlin Avenue 210023 Nanjing CHINA
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24
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Ren J, Li HW, Chen L, Zhang M, Liu YX, Zhang BW, Xu R, Miao YY, Xu XM, Hua X, Sun XG, Yu RJ, Long YT, Hu SS. Mass Spectrometry Imaging-Based Single-Cell Lipidomics Profiles Metabolic Signatures of Heart Failure. Research 2023; 6:0019. [PMID: 37040505 PMCID: PMC10076023 DOI: 10.34133/research.0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 01/13/2023]
Abstract
Heart failure (HF), leading as one of the main causes of mortality, has become a serious public health issue with high prevalence around the world. Single cardiomyocyte (CM) metabolomics promises to revolutionize the understanding of HF pathogenesis since the metabolic remodeling in the human hearts plays a vital role in the disease progression. Unfortunately, current metabolic analysis is often limited by the dynamic features of metabolites and the critical needs for high-quality isolated CMs. Here, high-quality CMs were directly isolated from transgenic HF mice biopsies and further employed in the cellular metabolic analysis. The lipids landscape in individual CMs was profiled with a delayed extraction mode in time-of-flight secondary ion mass spectrometry. Specific metabolic signatures were identified to distinguish HF CMs from the control subjects, presenting as possible single-cell biomarkers. The spatial distributions of these signatures were imaged in single cells, and those were further found to be strongly associated with lipoprotein metabolism, transmembrane transport, and signal transduction. Taken together, we systematically studied the lipid metabolism of single CMs with a mass spectrometry imaging method, which directly benefited the identification of HF-associated signatures and a deeper understanding of HF-related metabolic pathways.
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Affiliation(s)
- Jie Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Hao-Wen Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yan-Xiang Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Bo-Wen Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yan-Yan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xue-Mei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xin Hua
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Xiao-Gang Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Ru-Jia Yu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Sheng-Shou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
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25
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. Nat Nanotechnol 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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26
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Cui LF, Ying YL, Yu RJ, Ma H, Hu P, Long YT. In Situ Characterization of Oxygen Evolution Electrocatalysis of Silver Salt Oxide on a Wireless Nanopore Electrode. Anal Chem 2022; 94:15033-15039. [PMID: 36255225 DOI: 10.1021/acs.analchem.2c03016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Silver salt oxide shows superior oxidation ability for the applications of superconductivity, sterilization, and catalysis. However, due to the easy decomposition, the catalytic properties of silver salt oxide are difficult to characterize by conventional methods. Herein, we used a closed-type wireless nanopore electrode (CWNE) to in situ and real-time monitor the electrocatalytic performance of Ag7NO11 in the oxygen evolution reaction. The real-time current recording revealed that the deposited Ag7NO11 on the CWNE tip greatly enhanced the oxidative capacity of the electrode, resulting in water splitting. The statistical event analysis reveals the periodic O2 bubble formation and dissolution at the Ag7NO11 interface, which ensures the characterization of the oxygen evolution electrocatalytic process at the nanoscale. The calculated kcat and Markov chain modeling suggest the anisotropy of Ag7NO11 at a low voltage may lead to multiple catalytic rates. Therefore, our results demonstrate the powerful capability of CWNE in direct and in situ characterization of gas-liquid-solid catalytic reactions for unstable catalysts.
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Affiliation(s)
- Ling-Fei Cui
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, P. R. China
| | - Hui Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
| | - Ping Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, P. R. China
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27
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Yu RJ, Hu YX, Chen KL, Gu Z, Ying YL, Long YT. Confined Nanopipet as a Versatile Tool for Precise Single Cell Manipulation. Anal Chem 2022; 94:12948-12953. [DOI: 10.1021/acs.analchem.2c02415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People’s Republic of China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People’s Republic of China
| | - Yong-Xu Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People’s Republic of China
| | - Ke-Le Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Zhen Gu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, People’s Republic of China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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Xin KL, Hu ZL, Liu SC, Li XY, Li JG, Niu H, Ying YL, Long YT. 3D Blockage Mapping for Identifying Familial Point Mutations in Single Amyloid‐β Peptides with a Nanopore. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kai-Li Xin
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science Nanjing University 210023 Nanjing CHINA
| | - Zheng-Li Hu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science; Shenzhen Research Institute of Nanjing University CHINA
| | - Shao-Chuang Liu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Xin-Yi Li
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science 210023 Nanjing CHINA
| | - Jun-Ge Li
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Hongyan Niu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Yi-Lun Ying
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science;Chemistry and Biomedicine Innovation Center 210023 Nanjing CHINA
| | - Yi-Tao Long
- Nanjing University 163 Xianlin Avenue 210023 Nanjing CHINA
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29
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Xin KL, Hu ZL, Liu SC, Li XY, Li JG, Niu H, Ying YL, Long YT. 3D Blockage Mapping for Identifying Familial Point Mutations in Single Amyloid‐β Peptides with a Nanopore. Angew Chem Int Ed Engl 2022; 61:e202209970. [DOI: 10.1002/anie.202209970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Kai-Li Xin
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science Nanjing University 210023 Nanjing CHINA
| | - Zheng-Li Hu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science; Shenzhen Research Institute of Nanjing University CHINA
| | - Shao-Chuang Liu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Xin-Yi Li
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science 210023 Nanjing CHINA
| | - Jun-Ge Li
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Hongyan Niu
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science CHINA
| | - Yi-Lun Ying
- Nanjing University State Key Laboratory of Analytical Chemistry for Life Science;Chemistry and Biomedicine Innovation Center 210023 Nanjing CHINA
| | - Yi-Tao Long
- Nanjing University 163 Xianlin Avenue 210023 Nanjing CHINA
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Ma H, Zhong CB, Ying YL, Long YT. Seeing Is Not Believing: Filtering Effects on Random Nature in Electrochemical Measurements of Single-Entity Collision. ACS Meas Sci Au 2022; 2:325-331. [PMID: 36785567 PMCID: PMC9885945 DOI: 10.1021/acsmeasuresciau.2c00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To clarify the discrete nature of electrochemistry, single-entity electrochemistry of collision (SEEC) utilizes a confinement space in a nanoscale local electric field at a microscale electrode interface for characterizing single freely diffusing entities. This promising method provides new insights at the single entity level. However, the precise measurement is challenging because of the short residence time and wide current fluctuations caused by the dynamic and stochastic motion of a single entity at the interface of the electrode. Moreover, the enormous noise in the electrochemical system would submerge these weak transient electrochemical signals. To increase the signal-to-noise ratio, the low-pass filter (LPF) is often used but at the cost of lower temporal resolution. Therefore, a deeper understanding of the filtering effects on the electrochemical signal is required in SEEC. Here, we build a random walk model to simulate the dynamic electrochemical oxidation of individual silver nanoparticles (AgNPs) in the local electric field near the electrode. This model considers the effect of the effective potential during the interaction between NP and electrode. Results reveal that the shape of the signal is seriously distorted as the cutoff frequency (f c) of LPF is set at <20 kHz. Due to the filtering effects, hundreds of subpeaks originating from the dynamic motion of NP are merged in a simple peak, which muddies our "believing" from the "seeing" signals. However, the entire interaction time of single NPs with the electrodes can be acquired at f c ≥ 10 kHz. Moreover, an integral charge of the signal is conserved at any LPF, which enables quantitative analysis of SEEC. Our understanding of the filtering effect on single AgNPs oxidation is generally applicable to nano-electrochemical techniques (e.g., nanopore electrochemistry and nanopipette sensing) that generate transient current signals.
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Affiliation(s)
- Hui Ma
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Cheng Bing Zhong
- 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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31
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Wang J, Prajapati JD, Gao F, Ying YL, Kleinekathöfer U, Winterhalter M, Long YT. Identification of Single Amino Acid Chiral and Positional Isomers Using an Electrostatically Asymmetric Nanopore. J Am Chem Soc 2022; 144:15072-15078. [PMID: 35953064 PMCID: PMC9413207 DOI: 10.1021/jacs.2c03923] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chirality is essential in nearly all biological organizations and chemical reactions but is rarely considered due to technical limitations in identifying L/D isomerization. Using OmpF, a membrane channel from Escherichia coli with an electrostatically asymmetric constriction zone, allows discriminating chiral amino acids in a single peptide. The heterogeneous distribution of charged residues in OmpF causes a strong lateral electrostatic field at the constriction. This laterally asymmetric constriction zone forces the sidechains of the peptides to specific orientations within OmpF, causing distinct ionic current fluctuations. Using statistical analysis of the respective ionic current variations allows distinguishing the presence and position of a single amino acid with different chiralities. To explore potential applications, the disease-related peptide β-Amyloid and its d-Asp1 isoform and a mixture of the icatibant peptide drug (HOE 140) and its d-Ser7 mutant have been discriminated. Both chiral isomers were not applicable to be distinguished by mass spectroscopy approaches. These findings highlight a novel sensing mechanism for identifying single amino acids in single peptides and even for achieving single-molecule protein sequencing.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | | | - Fan Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Abstract
Single-entity electrochemistry (SEE) provides powerful means to measure single cells, single particles, and even single molecules at the nanoscale by diverse well-defined interfaces. The nanoconfined electrode interface has significantly enhanced structural, electrical, and compositional characteristics that have great effects on the assay limitation and selectivity of single-entity measurement. In this Perspective, after introducing the dynamic chemistry interactions of the target and electrode interface, we present a fundamental understanding of how these dynamic interactions control the features of the electrode interface and thus the stochastic and discrete electrochemical responses of single entities under nanoconfinement. Both stochastic single-entity collision electrochemistry and nanopore electrochemistry as examples in this Perspective explore how these interactions alter the transient charge transfer and mass transport. Finally, we discuss the further challenges and opportunities in SEE, from the design of sensing interfaces to hybrid spectro-electrochemical methods, theoretical models, and advanced data processing.
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, 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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33
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Zhang LL, Zhong CB, Li JG, Niu HY, Ying YL, Long YT. A two-step calibration method for evaluation high bandwidth electrochemical instrument. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116266] [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: 10/18/2022]
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34
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Niu H, Li MY, Ying YL, Long YT. Correction: An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport. Chem Sci 2022; 13:6429. [PMID: 35733890 PMCID: PMC9159105 DOI: 10.1039/d2sc90101c] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/21/2022] Open
Abstract
Correction for ‘An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport’ by Hongyan Niu et al., Chem. Sci., 2022, 13, 2456–2461, https://doi.org/10.1039/D1SC06459B.
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Affiliation(s)
- Hongyan Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Meng-Yin Li
- 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-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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35
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Liu W, Yang ZL, Yang CN, Ying YL, Long YT. Profiling single-molecule reaction kinetics under nanopore confinement. Chem Sci 2022; 13:4109-4114. [PMID: 35440975 PMCID: PMC8985585 DOI: 10.1039/d1sc06837g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/13/2022] [Indexed: 02/02/2023] Open
Abstract
The study of a single-molecule reaction under nanoconfinement is beneficial for understanding the reactive intermediates and reaction pathways. However, the kinetics model of the single-molecule reaction under confinement remains elusive. Herein we engineered an aerolysin nanopore reactor to elaborate the single-molecule reaction kinetics under nanoconfinement. By identifying the bond-forming and non-bond-forming events directly, a four-state kinetics model is proposed for the first time. Our results demonstrated that the single-molecule reaction kinetics inside a nanopore depends on the frequency of individual reactants captured and the fraction of effective collision inside the nanopore confined space. This insight will guide the design of confined nanopore reactors for resolving the single-molecule chemistry, and shed light on the mechanistic understanding of dynamic covalent chemistry inside confined systems such as supramolecular cages, coordination cages, and micelles. A four-state kinetics model is proposed to reveal the kinetics of a single-molecule reaction under nanopore confinement.![]()
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Zhong-Lin Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Chao-Nan Yang
- 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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37
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Bohn PW, Cao XE, Chang S, Chen D, Confederat S, Duleba D, E P, Edwards MA, Ewing A, Gundry L, He J, Kamali AR, Kanoufi F, Kwon SR, Limani N, Linfield S, Liu X, Long YT, Lu SM, Mao BW, Minteer S, Pandey P, Ren H, Ross A, Slater B, Unwin P, Vakamulla Raghu SN, Venton J, Walcarius A, Wei H, Wu Y, Xiao L, Xu W, Ying YL, Yu P, Zhang Z. Advanced nanoelectrochemistry implementation: from concept to application: general discussion. Faraday Discuss 2022; 233:354-373. [PMID: 35302573 DOI: 10.1039/d2fd90004a] [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: 11/21/2022]
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38
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Buckingham MA, Cao XE, Chang S, Chen HY, Chen Q, Chinnathambi S, Edwards MA, Fornasaro S, Gooding J, Hill C, Hirano-Iwata A, Kamali AR, Kanoufi F, Krause S, Kurihara K, Lemay SG, Linfield S, Liu X, Long YT, Lu SM, Ma H, Mao BW, Meloni GN, Menkin S, Minteer S, O'Neill S, Pandey P, Ren H, Slater B, Tian Z, Unwin P, Valavanis D, Walcarius A, Willets KK, Wu Y, Xiao L, Xu W, Yang W, Ying YL, Zhang Z. Emerging electrochemical methods at the nanointerface: general discussion. Faraday Discuss 2022; 233:257-282. [PMID: 35302154 DOI: 10.1039/d2fd90003c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Li JG, Li MY, Li XY, Wu XY, Ying YL, Long YT. Full Width at Half Maximum of Nanopore Current Blockage Controlled by a Single-Biomolecule Interface. Langmuir 2022; 38:1188-1193. [PMID: 35019652 DOI: 10.1021/acs.langmuir.1c02900] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A biological nanopore is one of the predominant single-molecule approaches as a result of its controllable single-biomolecule interface, which could reflect the "intrinsic" information on an individual molecule in a label-free way. Because the current blockage is normally treated as the most important parameter for nanopore identification of every single molecule, the fluctuation of current blockage for certain types of molecules, defined as full width at half maximum (fwhm) of current blockage, actually owns a dominant influence on nanopore resolution. Therefore, controlling the fwhm of current blockage of molecules is critical for the sensing capability of the nanopore. Here, taking an aerolysin nanopore as a model, by precisely controlling the functional group in this single-biomolecule interface, we could narrow the fwhm of nanopore current blockage for DNA identification and prolong the duration inside the nanopore. Moreover, a substantial correlation between fwhm of current blockage and duration is established, showing a non-monotonic variation. Besides, the mechanism is also clarified with studying the detailed current blockage events. This proposed correlation is further demonstrated to be applied uniformly across different mutant aerolysins for a certain DNA. This study proposes a new strategy for regulating molecular sensing from the duration of the analyte, which could guide the resolution of heterogeneity analysis using nanopores.
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Affiliation(s)
- Jun-Ge Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xin-Yi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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40
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Ma H, Yu RJ, Ying YL, Long YT. Electrochemically Confined Effects on Single Enzyme Detection with Nanopipettes. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116086] [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: 10/19/2022]
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41
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Niu H, Li MY, Ying YL, Long YT. An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport. Chem Sci 2022; 13:2456-2461. [PMID: 35310483 PMCID: PMC8864703 DOI: 10.1039/d1sc06459b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
Reading the primary sequence directly using nanopores remains challenging due to the complex building blocks of 20 proteinogenic amino acids and the corresponding sophisticated structures. Compared to the uniformly negatively charged polynucleotides, biological nanopores hardly provide effective ionic current responses to all heterogeneously charged peptides under nearly physiological pH conditions. Herein, we precisely design a N226Q/S228K mutant aerolysin which creates a new electrostatic constriction named R3 in-between two natural sensing regions for controlling the capture and translocation of heterogeneously charged peptides. At nearly physiological pH, the decoration of positive charges at this constriction gives a large velocity of electroosmotic flow (EOF), leading to a maximum 8-fold increase in frequency for the heterogeneously charged peptides with the net charge from +1 to −3. Even the duration time of the negatively charged peptide Aβ35-25D4 in N226Q/S228K AeL also rises from 0.07 ± 0.01 ms to 0.63 ± 0.01 ms after introducing the third electrostatic constriction. Therefore, the N226Q/S228K aerolysin nanopore with three electrostatic constrictions realizes the dual goals of both capturing and decelerating heterogeneously charged peptides without labelling, even for the folded peptides. An engineered aerolysin nanopore captures all types of peptides despite the charges and folded structure, which facilitate the achievement of nanopore protein sequencing.![]()
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Affiliation(s)
- Hongyan Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Meng-Ying Li
- 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-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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42
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Zhong CB, Ma H, Wang JJ, Zhang LL, Ying YL, Wang R, Wan YJ, Long YT. An ultra-low noise amplifier array system for high throughput single entity analysis. Faraday Discuss 2021; 233:33-43. [PMID: 34913454 DOI: 10.1039/d1fd00055a] [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: 11/21/2022]
Abstract
Electrochemical measurements at the single entity level provide ultra-sensitive tools for the precise diagnosis and understanding of basic biological and chemical processes. By decoding current signatures, single-entity electrochemistry provides abundant information on charges, sizes, shapes, catalytic performances and compositions. The accuracy of single-entity electrochemistry highly relies on advanced instrumentation to achieve the amperometric resolution at the sub-picoampere level and the temporal resolution at the sub-microsecond level. Currently, it is still a challenge for paralleling amplifiers to allow low-noise and high bandwidth single-entity electrochemical measurements. Herein, we developed a low-noise four-channel electrochemical instrumentation that integrates an Au electrode array with amplifiers in the circuit board. With this amplifier array, we achieved a high bandwidth (>100 kHz) electrochemical measurement. The further practical experiments proved the capability of this amplifier array system in acquiring transient signals from both single-molecule detection with an aerolysin nanopore and single Pt nanoparticle catalysis during the dynamic collision process. Paired with appropriate microfluidic array systems, our instrumentation will enable an extraordinarily high-throughput feature for single-entity sensing.
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Affiliation(s)
- Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, 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.
| | - Jia-Jun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Lin-Lin Zhang
- 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
| | - Rong Wang
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China.
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, 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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43
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Chen H, Lin Y, Long YT, Minteer SD, Ying YL. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. Faraday Discuss 2021; 233:295-302. [PMID: 34889330 DOI: 10.1039/d1fd00042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
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Affiliation(s)
- Hui Chen
- Department of Chemistry, University of Utah, USA.
| | - Yao Lin
- Department of Chemistry, University of Utah, USA. .,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | | | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China. .,Chemistry and Biomedicine Innovation Center, Nanjing University, China
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44
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Liu SC, Xie BK, Zhong CB, Wang J, Ying YL, Long YT. An advanced optical-electrochemical nanopore measurement system for single-molecule analysis. Rev Sci Instrum 2021; 92:121301. [PMID: 34972456 DOI: 10.1063/5.0067185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Nanopore measurement has advanced in single-molecule analysis by providing a transient time and confined space window that only allows one interested molecule to exist. By optimization and integration of the electrical and optical analysis strategies in this transient window, the acquisition of comprehensive information could be achieved to resolve the intrinsic properties and heterogeneity of a single molecule. In this work, we present a roadmap to build a unified optical and electrochemical synchronous measurement platform for the research of a single molecule. We design a low-cost ultralow-current amplifier with low noise and high-bandwidth to measure the ionic current events as a single molecule translocates through a nanopore and combine a multi-functional optical system to implement the acquisition of the fluorescence, scattering spectrum, and photocurrent intensity of single molecule events in a nanopore confined space. Our system is a unified and unique platform for the protein nanopore, the solid-state nanopore, and the glass capillary nanopore, which has advantages in the comprehensive research of nanopore single-molecule techniques.
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Affiliation(s)
- Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Bao-Kang Xie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jia Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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Huo MZ, Hu ZL, Ying YL, Long YT. Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore. Proteomics 2021; 22:e2100041. [PMID: 34545670 DOI: 10.1002/pmic.202100041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/06/2021] [Revised: 08/08/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022]
Abstract
Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.
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Affiliation(s)
- Ming-Zhu Huo
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Zheng-Li Hu
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
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Abstract
The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.
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Chen M, Lu SM, Peng YY, Ding Z, Long YT. Tracking the Electrocatalytic Activity of a Single Palladium Nanoparticle for the Hydrogen Evolution Reaction. Chemistry 2021; 27:11799-11803. [PMID: 34101910 DOI: 10.1002/chem.202101263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 04/08/2021] [Indexed: 01/07/2023]
Abstract
The nanoparticle-based electrocatalysts' performance is directly related to their working conditions. In general, a number of nanoparticles are uncontrollably fixed on a millimetre-sized electrode for electrochemical measurements. However, it is hard to reveal the maximum electrocatalytic activity owing to the aggregation and detachment of nanoparticles on the electrode surface. To solve this problem, here, we take the hydrogen evolution reaction (HER) catalyzed by palladium nanoparticles (Pd NPs) as a model system to track the electrocatalytic activity of single Pd NPs by stochastic collision electrochemistry and ensemble electrochemistry, respectively. Compared with the nanoparticle fixed working condition, Pd NPs in the nanoparticle diffused working condition results in a 2-5 orders magnitude enhancement of electrocatalytic activity for HER at various bias potential. Stochastic collision electrochemistry with high temporal resolution gives further insights into the accurate study of NPs' electrocatalytic performance, enabling to dramatically enhance electrocatalytic efficiency.
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Affiliation(s)
- Mengjie Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Zhifeng Ding
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - 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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Li X, Ying YL, Fu XX, Wan YJ, Long YT. Single-Molecule Frequency Fingerprint for Ion Interaction Networks in a Confined Nanopore. Angew Chem Int Ed Engl 2021; 60:24582-24587. [PMID: 34390607 DOI: 10.1002/anie.202108226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/21/2021] [Indexed: 11/11/2022]
Abstract
The transport of molecules and ions through biological nanopores is governed by interaction networks among restricted ions, transported molecules, and residue moieties at pore inner walls. However, identification of such weak ion fluctuations from only few tens of ions inside nanopore is hard to achieve owing to electrochemical measurement limitations. Here, we developed an advanced frequency method to achieve qualitative and spectral analysis of ion interaction networks inside a nanopore. The peak frequency fm reveals the dissociation rate between nanopore and ions; the peak amplitude am depicts the amount of combined ions with the nanopore after interaction equilibrium. A mathematical model for single-molecule frequency fingerprint achieved the prediction of interaction characteristics of mutant nanopores. This single-molecule frequency fingerprint is important for classification, characterization, and prediction of synergetic interaction networks inside nanoconfinement.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
| | - Xi-Xin Fu
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, 210023, Nanjing, P. R. China
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Lu SM, Chen JF, Peng YY, Ma W, Ma H, Wang HF, Hu P, Long YT. Understanding the Dynamic Potential Distribution at the Electrode Interface by Stochastic Collision Electrochemistry. J Am Chem Soc 2021; 143:12428-12432. [PMID: 34347459 DOI: 10.1021/jacs.1c02588] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The potential distribution at the electrode interface is a core factor in electrochemistry, and it is usually treated by the classic Gouy-Chapman-Stern (G-C-S) model. Yet the G-C-S model is not applicable to nanosized particles collision electrochemistry as it describes steady-state electrode potential distribution. Additionally, the effect of single nanoparticles (NPs) on potential should not be neglected because the size of a NP is comparable to that of an electrode. Herein, a theoretical model termed as Metal-Solution-Metal Nanoparticle (M-S-MNP) is proposed to reveal the dynamic electrode potential distribution at the single-nanoparticle level. An explicit equation is provided to describe the size/distance-dependent potential distribution in single NPs stochastic collision electrochemistry, showing the potential distribution is influenced by the NPs. Agreement between experiments and simulations indicates the potential roles of the M-S-MNP model in understanding the charge transfer process at the nanoscale.
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Affiliation(s)
- Si-Min Lu
- 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
| | - Jian-Fu Chen
- State Key Laboratory of Chemical Engineering, Centre for Computational Chemistry & Research Institute of Industrial Catalysis, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yue-Yi Peng
- 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
| | - Wei Ma
- 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.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Hai-Feng Wang
- State Key Laboratory of Chemical Engineering, Centre for Computational Chemistry & Research Institute of Industrial Catalysis, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Peijun Hu
- State Key Laboratory of Chemical Engineering, Centre for Computational Chemistry & Research Institute of Industrial Catalysis, East China University of Science and Technology, Shanghai 200237, P. R. China.,School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast BT9 5AG, U.K
| | - 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.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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Li MY, Ying YL, Yu J, Liu SC, Wang YQ, Li S, Long YT. Revisiting the Origin of Nanopore Current Blockage for Volume Difference Sensing at the Atomic Level. JACS Au 2021; 1:967-976. [PMID: 34467343 PMCID: PMC8395674 DOI: 10.1021/jacsau.1c00109] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 05/21/2023]
Abstract
Changes in the nanopore ionic current during entry of a target molecule underlie the sensing capability and dominate the intensity and extent of applications of the nanopore approach. The volume exclusion model has been proposed and corrected to describe the nanopore current blockage. However, increasing evidence shows nonconformity with this model, suggesting that the ionic current within a nanopore should be entirely reconsidered. Here, we revisit the origin of nanopore current blockage from a theoretical perspective and propose that the noncovalent interactions between a nanopore and a target molecule affect the conductance of the solution inside the nanopore, leading to enhanced current blockage. Moreover, by considering the example of an aerolysin nanopore discriminating the cytosine DNA and methylcytosine DNA that differ by a single methyl group, we completely demonstrate, by nanopore experiments and molecular dynamics simulations, the essential nature of this noncovalent interaction for discrimination. Our conductance model suggests multiplicative effects of both volume exclusion and noncovalent interaction on the current blockage and provides a new strategy to achieve volume difference sensing at the atomic level with highly specific current events, which would promote the nanopore protein sequencing and its applications in real-life systems.
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Affiliation(s)
- Meng-Yin Li
- 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-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
| | - Jie Yu
- 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
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Shuang Li
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, 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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