1
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Rao YF, Sun LZ, Luo MB. Na +-Mg 2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition. Int J Biol Macromol 2024; 267:131273. [PMID: 38569994 DOI: 10.1016/j.ijbiomac.2024.131273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.
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Affiliation(s)
- Yi-Fan Rao
- School of Physics, Zhejiang University, Hangzhou 310027, China; Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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2
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Cao C, Magalhães P, Krapp LF, Bada Juarez JF, Mayer SF, Rukes V, Chiki A, Lashuel HA, Dal Peraro M. Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore. ACS NANO 2024; 18:1504-1515. [PMID: 38112538 PMCID: PMC10795472 DOI: 10.1021/acsnano.3c08623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level, and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection, in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish α-synuclein-derived peptides bearing single or multiple PTMs, namely, phosphorylation, nitration, and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the α-synuclein peptide and its PTM variants could be confidently identified by using a deep learning model for signal processing. We further demonstrate that this framework can quantify α-synuclein peptides at picomolar concentrations and detect the C-terminal peptides generated by digestion of full-length α-synuclein. Collectively, our work highlights the advantage of using nanopores as a tool for simultaneous detection of multiple PTMs and facilitates their use in biomarker discovery and diagnostics.
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Affiliation(s)
- Chan Cao
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
- Department
of Inorganic and Analytical Chemistry, Chemistry and Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Pedro Magalhães
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Lucien F. Krapp
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Juan F. Bada Juarez
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Simon Finn Mayer
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Verena Rukes
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Anass Chiki
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Hilal A. Lashuel
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Brain Mind
Institute, School of Life Sciences, Ecole
Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
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3
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Li H, Li Y, Gui C, Chen D, Chen L, Luo L, Huang G, Yuan Y, He R, Xia F, Wang J. Bare glassy nanopore for length-resolution reading of PCR amplicons from various pathogenic bacteria and viruses. Talanta 2023; 256:124275. [PMID: 36701856 DOI: 10.1016/j.talanta.2023.124275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/16/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
In this study, it is confirmed that without addition of organic solvent and embedding polymer hydrogel into glass nanopore, bare glass nanopore can faithfully measure various lengths of DNA duplexes from 200 to 3000 base pairs with 200 base pairs resolution, showing well-separated peak amplitudes of blockage currents. Furthermore, motivated by this readout capability of duplex DNA, amplicons from Polymerase Chain Reaction (PCR) amplification are straightforwardly discriminated by bare glassy nanopore without fluorescent labeling. Except simultaneous discrimination of up to 7 different segments of the same lambda genome, various pathogenic bacteria and viruses including SARS-CoV-2 and its mutants in clinical samples can be discriminated at high resolution. Moreover, quantitative measurement of PCR amplicons is obtained with detection range spanning from 0.75 aM to 7.5 pM and detection limit of 7.5 aM, which reveals that bare glass nanopore can faithfully disclose PCR results without any extra labeling.
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Affiliation(s)
- Huizhen Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yunhui Li
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Lanfang Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Le Luo
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Guobao Huang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, College of Chemistry and Food Science, Yulin Normal University, Yulin, Guangxi, 537000, China
| | - Yang Yuan
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Rong He
- Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, 510440, China.
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, 430074, China.
| | - Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
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4
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Sun LZ, Qian JL, Cai P, Hu HX, Xu X, Luo MB. Mg2+ effects on the single-stranded DNA conformations and nanopore translocation dynamics. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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5
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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6
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High sensitive electrochemical methamphetamine detection in serum and urine via atom transfer radical polymerization signal amplification. Talanta 2022; 238:123026. [PMID: 34857345 DOI: 10.1016/j.talanta.2021.123026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/25/2021] [Accepted: 10/31/2021] [Indexed: 01/06/2023]
Abstract
Herein we designed a highly sensitive and selective biosensor for methamphetamine (METH) detection based on aptamer recognition probe and atom transfer radical polymerization (ATRP) signal amplification strategy. In this experiment, METH aptamer and its complementary DNA strand were first attached to the electrode surface. In the presence of METH, the prioritized conjugation between METH and the aptamer will take one strand of DNA from the double-stranded DNA, so that the third segment of azide-modified DNA could be successfully modified onto the electrode surface. Through click chemistry and ATRP polymerization, the monomers with ferrocene were polymerized into a long chain, and the signal was amplified, then high-sensitivity detection of METH can be carried out. The result showed that the sensor could detect METH as low as 17 fM, which is about two orders of magnitude lower than that by traditional METH detection methods. Moreover, when different concentrations of METH were added to serum and urine, the recovery rate of the biosensor was as high as 93%. Therefore, using nucleic acid aptamer as capture probe and ATRP as signal amplification strategy can provide a promising application platform for sensitive detection of low concentration toxicants.
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7
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Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal. Biosens Bioelectron 2022; 197:113739. [PMID: 34781175 PMCID: PMC8553638 DOI: 10.1016/j.bios.2021.113739] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 02/07/2023]
Abstract
The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.
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8
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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9
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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] [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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10
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Guan T, Cheng M, Zeng L, Chen X, Xie Y, Lei Z, Ruan Q, Wang J, Cui S, Sun Y, Li H. Engineering the Redox-Driven Channel for Precisely Regulating Nanoconfined Glutathione Identification and Transport. ACS APPLIED MATERIALS & INTERFACES 2021; 13:49137-49145. [PMID: 34623797 DOI: 10.1021/acsami.1c12061] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bioinspired artificial nanochannels for molecular and ionic transport have extensive applications. However, it is still a huge challenge to achieve an intelligent transport system with high selectivity/efficiency and controllability. Inspired by glutathione transport across the plasma membrane via redox regulation, we herein designed and fabricated a redox-reactive artificial nanochannel based on the host-guest chemical strategy. The nanochannel platform achieved high selectivity/efficiency for the identification and transmission of glutathione in the confined space. In addition, this nanochannel can switch between the ON and OFF states through the redox reaction. This redox-regulated system can provide a potential application for detection/binding of biological analytes and redox-controlled drug release.
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Affiliation(s)
- Tianpei Guan
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Ming Cheng
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Lisi Zeng
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Xiaoya Chen
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Yuan Xie
- Guangdong Provincial Key Laboratory of Radioactive and Rare Resource Utilization, Shaoguan 512026, P. R. China
| | - Ziying Lei
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Qiang Ruan
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Jin Wang
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Shuzhong Cui
- Department 2 of Gastroentestinal Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, P. R. China
| | - Yao Sun
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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11
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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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [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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12
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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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13
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Xi D, Cui M, Zhou X, Zhuge X, Ge Y, Wang Y, Zhang S. Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures. ACS Sens 2021; 6:2691-2699. [PMID: 34237940 DOI: 10.1021/acssensors.1c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.
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Affiliation(s)
- Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
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14
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Qu LL, Ying YL, Yu RJ, Long YT. In situ food-borne pathogen sensors in a nanoconfined space by surface enhanced Raman scattering. Mikrochim Acta 2021; 188:201. [PMID: 34041602 PMCID: PMC8154335 DOI: 10.1007/s00604-021-04864-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/13/2021] [Indexed: 01/04/2023]
Abstract
The incidence of disease arising from food-borne pathogens is increasing continuously and has become a global public health problem. Rapid and accurate identification of food-borne pathogens is essential for adopting disease intervention strategies and controlling the spread of epidemics. Surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest due to the attractive features including simplicity, rapid measurement, and high sensitivity. It can be used for rapid in situ sensing of single and multicomponent samples within the nanostructure-based confined space by providing molecular fingerprint information and has been demonstrated to be an effective detection strategy for pathogens. This article aims to review the application of SERS to the rapid sensing of food-borne pathogens in food matrices. The mechanisms and advantages of SERS, and detection strategies are briefly discussed. The latest progress on the use of SERS for rapid detection of food-borne bacteria and viruses is considered, including both the labeled and label-free detection strategies. In closing, according to the current situation regarding detection of food-borne pathogens, the review highlights the challenges faced by SERS and the prospects for new applications in food safety. In this review, the advances on the SERS detection of pathogens over the past decades have been reviewed, focusing on the improvements in sensitivity, reproducibility, specificity, and the performance of the SERS-based assay in complex analytical scenarios. ![]()
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Affiliation(s)
- Lu-Lu Qu
- School of Chemistry and Materials Science, Jiangsu Normal University, 221116, Xuzhou, 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
| | - 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.
| | - 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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15
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Sun K, Chen P, Yan S, Yuan W, Wang Y, Li X, Dou L, Zhao C, Zhang J, Wang Q, Fu Z, Wei L, Xin Z, Tang Z, Yan Y, Peng Y, Ying B, Chen J, Geng J. Ultrasensitive Nanopore Sensing of Mucin 1 and Circulating Tumor Cells in Whole Blood of Breast Cancer Patients by Analyte-Triggered Triplex-DNA Release. ACS APPLIED MATERIALS & INTERFACES 2021; 13:21030-21039. [PMID: 33905228 DOI: 10.1021/acsami.1c03538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The characterization of circulating tumor cells (CTCs) by liquid biopsy has a great potential for precision medicine in oncology. Here, a universal and tandem logic-based strategy is developed by combining multiple nanomaterials and nanopore sensing for the determination of mucin 1 protein (MUC1) and breast cancer CTCs in real samples. The strategy consists of analyte-triggered signal conversion, cascaded amplification via nanomaterials including copper sulfide nanoparticles (CuS NPs), silver nanoparticles (Ag NPs), and biomaterials including DNA hydrogel and DNAzyme, and single-molecule-level detection by nanopore sensing. The amplification of the non-DNA nanomaterial gives this method considerable stability, significantly lowers the limit of detection (LOD), and enhances the anti-interference performance for complicated samples. As a result, the ultrasensitive detection of MUC1 could be achieved in the range of 0.0005-0.5 pg/mL, with an LOD of 0.1 fg/mL. Moreover, we further tested MUC1 as a biomarker for the clinical diagnosis of breast cancer CTCs under double-blind conditions on the basis of this strategy, and MCF-7 cells could be accurately detected in the range from 5 to 2000 cells/mL, with an LOD of 2 cells/mL within 6 h. The detection results of the 19 clinical samples were highly consistent with those of the clinical pathological sections, nuclear magnetic resonance imaging, and color ultrasound. These results demonstrate the validity and reliability of our method and further proved the feasibility of MUC1 as a clinical diagnostic biomarker for CTCs.
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Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Linqin Dou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jianfu Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Qiang Wang
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhoukai Fu
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Long Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhaodan Xin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhuoyun Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yiman Peng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jie Chen
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
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16
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Wei X, Zhang Z, Wang X, Lenhart B, Gambarini R, Gray J, Liu C. Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore. NANOTECHNOLOGY AND PRECISION ENGINEERING 2021; 3:2-8. [PMID: 33786424 PMCID: PMC8006565 DOI: 10.1016/j.npe.2019.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various molecules. However, the effect of several electrochemical factors on the host-guest interactions in nanopore still remains unknown. Here, we systematically studied host-guest interactions, especially oscillation of DNA-azide adamantane@cucurbit[6] in α-Hemolysin nanopore under varying pH, concentration of electrolytes and counterions (Li+, Na+, K+). Our results indicate correlations between the change of pH and the duration of the oscillation signal. In addition, the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals, and even the integrity of the protein nanopore. This study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Roberto Gambarini
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jonathan Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
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17
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Cai Y, Zhang B, Liang L, Wang S, Zhang L, Wang L, Cui HL, Zhou Y, Wang D. A solid-state nanopore-based single-molecule approach for label-free characterization of plant polysaccharides. PLANT COMMUNICATIONS 2021; 2:100106. [PMID: 33898974 PMCID: PMC8060702 DOI: 10.1016/j.xplc.2020.100106] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/22/2020] [Accepted: 08/28/2020] [Indexed: 05/07/2023]
Abstract
Polysaccharides are important biomacromolecules existing in all plants, most of which are integrated into a fibrillar structure called the cell wall. In the absence of an effective methodology for polysaccharide analysis that arises from compositional heterogeneity and structural flexibility, our knowledge of cell wall architecture and function is greatly constrained. Here, we develop a single-molecule approach for identifying plant polysaccharides with acetylated modification levels. We designed a solid-state nanopore sensor supported by a free-standing SiN x membrane in fluidic cells. This device was able to detect cell wall polysaccharide xylans at concentrations as low as 5 ng/μL and discriminate xylans with hyperacetylated and unacetylated modifications. We further demonstrated the capability of this method in distinguishing arabinoxylan and glucuronoxylan in monocot and dicot plants. Combining the data for categorizing polysaccharide mixtures, our study establishes a single-molecule platform for polysaccharide analysis, opening a new avenue for understanding cell wall structures, and expanding polysaccharide applications.
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Affiliation(s)
- Yao Cai
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin 130016, China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Liang Cui
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin 130016, China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
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18
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R SK, Puthumadathil N, Shaji AH, Santhosh Kumar K, Mohan G, Mahendran KR. Designed alpha-helical barrels for charge-selective peptide translocation. Chem Sci 2020; 12:639-649. [PMID: 34163795 PMCID: PMC8178987 DOI: 10.1039/d0sc04856a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022] Open
Abstract
Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously. Here, we report large transmembrane pores, pPorA formed from short synthetic alpha-helical peptides of tunable conductance and selectivity for single-molecule sensing of peptides. We quantified the selective translocation kinetics of differently charged cationic and anionic peptides through these synthetic pores at single-molecule resolution. The charged peptides are electrophoretically pulled into the pores resulting in an increase in the dissociation rate with the voltage indicating successful translocation of peptides. More specifically, we elucidated the charge pattern lining the pore lumen and the orientation of the pores in the membrane based on the asymmetry in the peptide-binding kinetics. The salt and pH-dependent measurements confirm the electrostatic dominance and charge selectivity in controlling target peptide interaction with the pores. Remarkably, we tuned the selectivity of the pores to charged peptides by modifying the charge composition of the pores, thus establishing the molecular and electrostatic basis of peptide translocation. We suggest that these synthetic pores that selectively conduct specific ions and biomolecules are advantageous for nanopore proteomics analysis and synthetic nanobiotechnology applications.
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Affiliation(s)
- Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
- Manipal Academy of Higher Education Manipal Karnataka India-576104
| | - Neethu Puthumadathil
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
- Manipal Academy of Higher Education Manipal Karnataka India-576104
| | - Amina H Shaji
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - K Santhosh Kumar
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - Gayathri Mohan
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology Thiruvananthapuram 695014 India
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19
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Li MY, Ying YL, Li S, Wang YQ, Wu XY, Long YT. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore. ACS NANO 2020; 14:12571-12578. [PMID: 32806044 DOI: 10.1021/acsnano.0c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
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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
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Xue-Yuan Wu
- 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
| | - 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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20
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Wang J, Prajapati JD, Kleinekathöfer U, Winterhalter M. Dynamic interaction of fluoroquinolones with magnesium ions monitored using bacterial outer membrane nanopores. Chem Sci 2020; 11:10344-10353. [PMID: 34094296 PMCID: PMC8162440 DOI: 10.1039/d0sc03486j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/30/2020] [Indexed: 01/05/2023] Open
Abstract
Divalent ions are known to have a severe effect on the translocation of several antibiotic molecules into (pathogenic) bacteria. In the present study we have investigated the effect of divalent ions on the permeability of norfloxacin across the major outer membrane channels from E. coli (OmpF and OmpC) and E. aerogenes (Omp35 and Omp36) at the single channel level. To understand the rate limiting steps in permeation, we reconstituted single porins into planar lipid bilayers and analyzed the ion current fluctuations caused in the presence of norfloxacin. Moreover, to obtain an atomistic view, we complemented the experiments with millisecond-long free energy calculations based on temperature-accelerated Brownian dynamics simulations to identify the most probable permeation pathways of the antibiotics through the respective pores. Both, the experimental analysis and the computational modelling, suggest that norfloxacin is able to permeate through the larger porins, i.e., OmpF, OmpC, and Omp35, whereas it only binds to the slightly narrower porin Omp36. Moreover, divalent ions can bind to negatively charged residues inside the porin, reversing the ion selectivity of the pore. In addition, the divalent ions can chelate with the fluoroquinolone molecules and alter their physicochemical properties. The results suggest that the conjugation with either pores or molecules must break when the antibiotic molecules pass the lumen of the porin, with the conjugation to the antibiotic being more stable than that to the respective pore. In general, the permeation or binding process of fluoroquinolones in porins occurs irrespective of the presence of divalent ions, but the presence of divalent ions can vary the kinetics significantly. Thus, a detailed investigation of the interplay of divalent ions with antibiotics and pores is of key importance in developing new antimicrobial drugs.
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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
| | | | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen 28759 Bremen Germany
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21
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Wang S, Wang Y, Yan S, Du X, Zhang P, Chen HY, Huang S. Retarded Translocation of Nucleic Acids through α-Hemolysin Nanopore in the Presence of a Calcium Flux. ACS APPLIED MATERIALS & INTERFACES 2020; 12:26926-26935. [PMID: 32432849 DOI: 10.1021/acsami.0c05626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Electrophysiological measurement of molecular translocation through a nanopore is the fundamental basis of nanopore sensing. Free translocation of nucleic acids however is normally so fast that the identities of the compounds are not clearly resolvable. Inspired by recent progress in fluorescence imaging based nanopore sensing, we found that during electrophysiology measurements, translocation of nucleic acids is also retarded whenever a calcium flux around the pore vicinity is established. The residence time of nucleic acids has been extended to tens of milliseconds, a result of the strong coupling between nucleic acids and free calcium ions. The methodology presented here is applicable to both DNAs and RNAs and is able to clearly discriminate between different RNA homopolymers. This offers new insights for calcium imaging based nanopore sensing and suggests a new strategy of electrophysiology-based nanopore sensing aimed at a retarded motion of nucleic acids.
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Affiliation(s)
- Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, P. R. China
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22
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Hu F, Angelov B, Li S, Li N, Lin X, Zou A. Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore. Chembiochem 2020; 21:2467-2473. [DOI: 10.1002/cbic.202000119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/09/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Fangzhou Hu
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Borislav Angelov
- Institute of Physics, ELI BeamlinesAcademy of Sciences of the Czech Republic Na Slovance 2 18221 Prague Czech Republic
| | - Shuang Li
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Na Li
- National Center for Protein Science in ShanghaiZhangjiang LabShanghai Advanced Research Institute, CAS Shanghai 200120 P. R. China
| | - Xubo Lin
- Institute of Single Cell EngineeringBeijing Advanced Innovation Center for Biomedical EngineeringBeihang University Beijing 100191 P. R. China
| | - Aihua Zou
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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23
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Yao F, Peng X, Su Z, Tian L, Guo Y, Kang XF. Crowding-Induced DNA Translocation through a Protein Nanopore. Anal Chem 2020; 92:3827-3833. [PMID: 32048508 DOI: 10.1021/acs.analchem.9b05249] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A crowded cellular environment is highly associated with many significant biological processes. However, the effect of molecular crowding on the translocation behavior of DNA through a pore has not been explored. Here, we use nanopore single-molecule analytical technique to quantify the thermodynamics and kinetics of DNA transport under heterogeneous cosolute PEGs. The results demonstrate that the frequency of the translocation event exhibits a nonmonotonic dependence on the crowding agent size, while both the event frequency and translocation time increase monotonically with increasing crowder concentration. In the presence of PEGs, the rate of DNA capture into the nanopore elevates 118.27-fold, and at the same time the translocation velocity decreases from 20 to 120 μs/base. Interestingly, the impact of PEG 4k on the DNA-nanopore interaction is the most notable, with up to ΔΔG = 16.27 kJ mol-1 change in free energy and 764.50-fold increase in the binding constant at concentration of 40% (w/v). The molecular crowding effect will has broad applications in nanopore biosensing and nanopore DNA sequencing in which the strategy to capture analyte and to control the transport is urgently required.
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Affiliation(s)
- Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao Peng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Zhuoqun Su
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
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24
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Wang J, Li MY, Yang J, Wang YQ, Wu XY, Huang J, Ying YL, Long YT. Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface. ACS CENTRAL SCIENCE 2020; 6:76-82. [PMID: 31989027 PMCID: PMC6978832 DOI: 10.1021/acscentsci.9b01129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 05/06/2023]
Abstract
DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.
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Affiliation(s)
- Jiajun Wang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Meng-Yin Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
| | - Jie Yang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Xue-Yuan Wu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Jin Huang
- School
of Pharmacy, East China University of Science
and Technology, 200237, Shanghai, China
| | - Yi-Lun Ying
- 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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25
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Fang Z, Liu L, Wang Y, Xi D, Zhang S. Unambiguous Discrimination of Multiple Protein Biomarkers by Nanopore Sensing with Double-Stranded DNA-Based Probes. Anal Chem 2019; 92:1730-1737. [DOI: 10.1021/acs.analchem.9b02965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhen Fang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Liping Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
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26
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Roozbahani GM, Zhang Y, Chen X, Soflaee MH, Guan X. Enzymatic reaction-based nanopore detection of zinc ions. Analyst 2019; 144:7432-7436. [PMID: 31691699 DOI: 10.1039/c9an01784d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a label-free nanopore sensor for the detection of Zn2+ ions. By taking advantage of the cleavage of a substrate peptide by zinc-dependent enzymes, nanomolar concentrations of Zn2+ ions could be detected within minutes. Furthermore, structurally similar transition metals such as Ni2+, Co2+, Hg2+, Cu2+, and Cd2+ did not interfere with their detection. The enzymatic reaction-based nanopore sensing strategy developed in this work may find potential applications in environmental monitoring and medical diagnosis.
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27
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Ying YL, Yang J, Meng FN, Li S, Li MY, Long YT. A Nanopore Phosphorylation Sensor for Single Oligonucleotides and Peptides. RESEARCH 2019; 2019:1050735. [PMID: 31912023 PMCID: PMC6944226 DOI: 10.34133/2019/1050735] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/07/2019] [Indexed: 11/07/2022]
Abstract
The phosphorylation of oligonucleotides and peptides plays a critical role in regulating virtually all cellular processes. To fully understand these complex and fundamental regulatory pathways, the cellular phosphorylate changes of both oligonucleotides and peptides should be simultaneously identified and characterized. Here, we demonstrated a single-molecule, high-throughput, label-free, general, and one-step aerolysin nanopore method to comprehensively evaluate the phosphorylation of both oligonucleotide and peptide substrates. By virtue of electrochemically confined effects in aerolysin, our results show that the phosphorylation accelerates the traversing speed of a negatively charged substrate for about hundreds of time while significantly enhances the translocation frequency of a positively charged substrate. Thereby, the kinase/phosphatase activity could be directly measured with the aerolysin nanopore from the characteristically dose-dependent event frequency of the substrates. By using this straightforward approach, a model T4 oligonucleotide kinase (PNK) further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a single-molecule level. Our study provides a step forward to nanopore enzymology for analyzing the phosphorylation of both oligonucleotides and peptides with significant feasibility in fundamental biochemical researches, clinical diagnosis, and kinase/phosphatase-targeted drug discovery.
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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 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing 210023, China
| | - Jie Yang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fu-Na Meng
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng-Ying Li
- 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 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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28
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Zhao Y, Fang X, Chen F, Bai M, Fan C, Zhao Y. Locus-patterned sequence oriented enrichment for multi-dimensional gene analysis. Chem Sci 2019; 10:8421-8427. [PMID: 31803421 PMCID: PMC6844269 DOI: 10.1039/c9sc02496d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/22/2019] [Indexed: 11/21/2022] Open
Abstract
Multi-dimensional gene analysis provides in-depth insights into gene sequence, locus variations and molecular abundance, whereas it is vulnerable to the perturbation of complex reaction networks and always compromises on the discrimination of analogous sequences. Here, we present a sequence oriented enrichment method patterned by the prescribed locus without crosstalk between concurrent reactions. Energetically favourable structures of nucleic acid probes are theoretically derived and oriented to a specific gene locus. We designed a pair of universal probes for multiple conserved loci to avoid side reactions from undesired interactions among increased probe sets. Furthermore, competitive probes were customized to sink analogues for differentiating the reaction equilibrium and kinetics of sequence enrichment from the target, so variant loci can be synchronously identified with nucleotide-level resolution. Thus, the gene locus guides sequence enrichment and combinatorial signals to create unique codes, which provides access to multidimensional and precise information for gene decoding.
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Affiliation(s)
- Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Xiaoxing Fang
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science , Key Laboratory of Biomedical Information Engineering of Ministry of Education , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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29
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Lu Y, Wu XY, Ying YL, Long YT. Simultaneous single-molecule discrimination of cysteine and homocysteine with a protein nanopore. Chem Commun (Camb) 2019; 55:9311-9314. [PMID: 31310244 DOI: 10.1039/c9cc04077c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Discrimination between cysteine and homocysteine at the single-molecule level is achieved within a K238Q mutant aerolysin nanopore, which provides a confined space for high spatial resolution to identify the amino acid difference with a 5'-benzaldehyde poly(dA)4 probe. Our strategy allows potential detection and characterization of various amino acids and their modifications, and provides a crucial step towards developing nanopore protein sequencing devices.
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Affiliation(s)
- Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Xue-Yuan Wu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China. and 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. and 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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Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
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Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
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32
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Zou Z, Yang H, Yan Q, Qi P, Qing Z, Zheng J, Xu X, Zhang L, Feng F, Yang R. Synchronous screening of multiplexed biomarkers of Alzheimer's disease by a length-encoded aerolysin nanopore-integrated triple-helix molecular switch. Chem Commun (Camb) 2019; 55:6433-6436. [DOI: 10.1039/c9cc02065a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A label-free triple-helix molecular switch-mediated nanopore sensor is developed for the synchronous screening of biomarkers of Alzheimer's disease.
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Affiliation(s)
- Zhen Zou
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Hua Yang
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Qi Yan
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Peng Qi
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Zhihe Qing
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- Hunan University
- Changsha 410082
- P. R. China
| | - Xuan Xu
- Children's Medical Center
- People's Hospital of Hunan Province
- Changsha
- P. R. China
| | - Lihua Zhang
- College of Chemistry and Environmental Engineering
- Shanxi Datong University
- Datong
- P. R. China
| | - Feng Feng
- College of Chemistry and Environmental Engineering
- Shanxi Datong University
- Datong
- P. R. China
| | - Ronghua Yang
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
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