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Cui R, Wang Z, Li L, Liu L, Li Z, Liu X, Chen T, Rauf A, Kang X, Guo Y. Bionic nanopore recognition receptors for single-molecule enantioselectivity studies of chiral drugs. Anal Chim Acta 2024; 1318:342960. [PMID: 39067929 DOI: 10.1016/j.aca.2024.342960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/09/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Enantiodiscrimination of chiral drugs is critical for understanding physiological phenomena and ensuring medical safety. Although enantiomers of these drugs share identical physicochemical properties, they exhibit significant differences in pharmacodynamic, pharmacokinetic, and toxicological properties due to the differences in their three-dimensional shapes. Therefore, the development of effective methods for chiral recognition is of great significance and has been a hot topic in chemo/biological studies. RESULTS In this study, we designed a recognition receptor comprising a α-hemolysin (α-HL) nanopore and sulfobutyl ether-β-cyclodextrin (SBEβCD) for identifying the enantiomers of the antidepressant duloxetine at the single-molecule level. Chiral molecules were discriminated based on the different current blockages within the recognition receptor. The results indicated a strong interaction between R-duloxetine and the recognition receptor. By combining the experimental data and molecular docking results, we explored the recognition mechanism of the designed nanopore recognition receptor for chiral drug molecules. It was found that hydrophobic and electrostatic interactions play key roles in chiral recognition. Additionally, by comparing the binding kinetics of enantiomers to cyclodextrins in confined nanospace and bulk solution, we found that enantiomeric identification was better facilitated in the confined nanospace. Finally, the enantiomeric excess (ee) of the enantiomeric duloxetine mixture was measured using this recognized receptor. SIGNIFICANCE This strategy has the advantages of low cost, high sensitivity, and no need for additional derivative modifications, providing a new perspective on the development of chiral recognition sensors with excellent enantioselectivity in drug design, pharmaceuticals, and biological applications.
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Affiliation(s)
- Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Tingting Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Ayesha Rauf
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China.
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2
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Ratinho L, Bacri L, Thiebot B, Cressiot B, Pelta J. Identification and Detection of a Peptide Biomarker and Its Enantiomer by Nanopore. ACS CENTRAL SCIENCE 2024; 10:1167-1178. [PMID: 38947203 PMCID: PMC11212137 DOI: 10.1021/acscentsci.4c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Until now, no fast, low-cost, and direct technique exists to identify and detect protein/peptide enantiomers, because their mass and charge are identical. They are essential since l- and d-protein enantiomers have different biological activities due to their unique conformations. Enantiomers have potential for diagnostic purposes for several diseases or normal bodily functions but have yet to be utilized. This work uses an aerolysin nanopore and electrical detection to identify vasopressin enantiomers, l-AVP and d-AVP, associated with different biological processes and pathologies. We show their identification according to their conformations, in either native or reducing conditions, using their specific electrical signature. To improve their identification, we used a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used the Monte Carlo prediction to assign each event type to a specific l- or d-AVP enantiomer.
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Affiliation(s)
- Laura Ratinho
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Laurent Bacri
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
| | - Bénédicte Thiebot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Benjamin Cressiot
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 95000, Cergy, France
| | - Juan Pelta
- Université
Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025, Evry-Courcouronnes, France
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3
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Zhang M, Tang C, Wang Z, Chen S, Zhang D, Li K, Sun K, Zhao C, Wang Y, Xu M, Dai L, Lu G, Shi H, Ren H, Chen L, Geng J. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. Nat Methods 2024; 21:609-618. [PMID: 38443507 PMCID: PMC11009107 DOI: 10.1038/s41592-024-02208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Biosafety Laboratory of West China Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Zichun Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shanchuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, China.
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4
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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Affiliation(s)
- Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Tian Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Hanhan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
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5
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Lee Y, Chong S, Lee C, Kim J, Choi SQ. Structural Determinants of Chirally Selective Transport of Amino Acids through the α-Hemolysin Protein Nanopores of Free-Standing Planar Lipid Membranes. NANO LETTERS 2024; 24:681-687. [PMID: 38185873 DOI: 10.1021/acs.nanolett.3c03976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite the importance of the enantioselective transport of amino acids through transmembrane protein nanopores from fundamental and practical perspectives, little has been explored to date. Here, we study the transport of amino acids through α-hemolysin (αHL) protein pores incorporated into a free-standing lipid membrane. By measuring the transport of 13 different amino acids through the αHL pores, we discover that the molecular size of the amino acids and their capability to form hydrogen bonds with the pore surface determine the chiral selectivity. Molecular dynamics simulations corroborate our findings by revealing the enantioselective molecular-level interactions between the amino acid enantiomers and the αHL pore. Our work is the first to present the determinants for chiral selectivity using αHL protein as a molecular filter.
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Affiliation(s)
- Yohan Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sanggyu Chong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Chiwoo Lee
- Chiral Technology Korea (CTK), Daejeon 34013, Republic of Korea
| | - Jihan Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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6
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Wang K, Zhang S, Zhou X, Yang X, Li X, Wang Y, Fan P, Xiao Y, Sun W, Zhang P, Li W, Huang S. Unambiguous discrimination of all 20 proteinogenic amino acids and their modifications by nanopore. Nat Methods 2024; 21:92-101. [PMID: 37749214 DOI: 10.1038/s41592-023-02021-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/21/2023] [Indexed: 09/27/2023]
Abstract
Natural proteins are composed of 20 proteinogenic amino acids and their post-translational modifications (PTMs). However, due to the lack of a suitable nanopore sensor that can simultaneously discriminate between all 20 amino acids and their PTMs, direct sequencing of protein with nanopores has not yet been realized. Here, we present an engineered hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore containing a sole Ni2+ modification. It enables full discrimination of all 20 proteinogenic amino acids and 4 representative modified amino acids, Nω,N'ω-dimethyl-arginine (Me-R), O-acetyl-threonine (Ac-T), N4-(β-N-acetyl-D-glucosaminyl)-asparagine (GlcNAc-N) and O-phosphoserine (P-S). Assisted by machine learning, an accuracy of 98.6% was achieved. Amino acid supplement tablets and peptidase-digested amino acids from peptides were also analyzed using this strategy. This capacity for simultaneous discrimination of all 20 proteinogenic amino acids and their PTMs suggests the potential to achieve protein sequencing using this nanopore-based strategy.
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Affiliation(s)
- Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiao Zhou
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Xian Yang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yunqi Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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7
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Bonini A, Sauciuc A, Maglia G. Engineered nanopores for exopeptidase protein sequencing. Nat Methods 2024; 21:16-17. [PMID: 38123862 DOI: 10.1038/s41592-023-02136-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Andrea Bonini
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Adina Sauciuc
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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8
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Jia W, Ouyang Y, Zhang S, Du X, Zhang P, Huang S. Nanopore Signatures of Nucleoside Drugs. NANO LETTERS 2023; 23:9437-9444. [PMID: 37818841 DOI: 10.1021/acs.nanolett.3c02872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Nucleoside drugs, which are analogues of natural nucleosides, have been widely applied in the clinical treatment of viral infections and cancers. The development of nucleoside drugs, repurposing of existing drugs, and combined use of multiple drug types have made the rapid sensing of nucleoside drugs urgently needed. Nanopores are emerging single-molecule sensors that have high resolution to resolve even minor structural differences between chemical compounds. Here, an engineered Mycobacterium smegmatis porin A hetero-octamer was used to perform general nucleoside drug analysis. Ten nucleoside drugs were simultaneously detected and fully discriminated. An accuracy of >99.9% was consequently reported. This sensing capacity was further demonstrated in direct nanopore analysis of ribavirin buccal tablets, confirming its sensing reliability against complex samples and environments. No sample separation is needed, however, significantly minimizing the complexity of the measurement. This technique may inspire nanopore applications in pharmaceutical production and pharmacokinetics measurements.
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Affiliation(s)
- Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yusheng Ouyang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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9
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Silva S, Singh S, Cao E, Fourkas JT, Siwy ZS. Gating ion and fluid transport with chiral solvent. Faraday Discuss 2023; 246:508-519. [PMID: 37427451 DOI: 10.1039/d3fd00063j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The development of modern membranes for ionic separations and energy-storage devices such as supercapacitors depends on the description of ions at solid interfaces, as is often provided by the electrical double layer (EDL) model. The classical EDL model ignores, however, important factors such as possible spatial organization of solvent at the interface and the influence of the solvent on the spatial dependence of the electrochemical potential; these effects in turn govern electrokinetic phenomena. Here we provide a molecular-level understanding of how solvent structure can dictate ionic distributions at interfaces using a model system of a polar, aprotic solvent, propylene carbonate, in its enantiomerically pure and racemic forms, at a silica interface. We link the interfacial structure to the tuning of ionic and fluid transport by the chirality of the solvent and the salt concentration. The results of nonlinear spectroscopic experiments and electrochemical measurements suggest that the solvent exhibits lipid-bilayer-like interfacial organization, with a structure that is dependent on the solvent chirality. The racemic form creates highly ordered layered structure that dictates local ionic concentrations, such that the effective surface potential becomes positive in a wide range of electrolyte concentrations. The enantiomerically pure form exhibits weaker ordering at the silica surface, which leads to a lower effective surface charge induced by ions partitioning into the layered structure. The surface charge in silicon nitride and polymer pores is probed through the direction of electroosmosis that the surface charges induce. Our findings add a new dimension to the nascent field of chiral electrochemistry, and emphasize the importance of including solvent molecules in descriptions of solid-liquid interfaces.
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Affiliation(s)
- Savannah Silva
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA.
| | - Siddharth Singh
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
| | - Ethan Cao
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA.
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Zuzanna S Siwy
- Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA.
- Department of Chemistry, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
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10
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Samineni L, Acharya B, Behera H, Oh H, Kumar M, Chowdhury R. Protein engineering of pores for separation, sensing, and sequencing. Cell Syst 2023; 14:676-691. [PMID: 37591205 DOI: 10.1016/j.cels.2023.07.004] [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: 02/27/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in 1833, a gamut of advanced experimental and computational tools has been developed and deployed for understanding protein structure and function. Recent studies have demonstrated the ability to redesign/alter natural proteins for applications in industrial processes of interest and to make customized, novel synthetic proteins in the laboratory through protein engineering. We comprehensively review the successes in engineering pore-forming proteins and correlate the amino acid-level biochemistry of different pore modification strategies to the intended applications limited to nucleotide/peptide sequencing, single-molecule sensing, and precise molecular separations.
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Affiliation(s)
- Laxmicharan Samineni
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Bibek Acharya
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Harekrushna Behera
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Hyeonji Oh
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Manish Kumar
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA; McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ratul Chowdhury
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
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11
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Zhang X, Lin M, Dai Y, Xia F. Stochastic Sensing of Dynamic Interactions and Chemical Reactions with Nanopores/Nanochannels. Anal Chem 2023. [PMID: 37413795 DOI: 10.1021/acs.analchem.3c00543] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Nanopore sensing technology is an emerging analysis method with the advantages of simple operation, high sensitivity, fast output and being label free, and it is widely used in protein analysis, gene sequencing, biomarker detection, and other fields. The confined space of the nanopore provides a place for dynamic interactions and chemical reactions between substances. The use of nanopore sensing technology to track these processes in real time is helpful to understand the interaction/reaction mechanism at the single-molecule level. According to nanopore materials, we summarize the development of biological nanopores and solid-state nanopores/nanochannels in the stochastic sensing of dynamic interactions and chemical reactions. The goal of this paper is to stimulate the interest of researchers and promote the development of this field.
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Affiliation(s)
- Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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12
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Liu M, Li J, Tan CS. Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End. BIOSENSORS 2023; 13:598. [PMID: 37366963 DOI: 10.3390/bios13060598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.
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Affiliation(s)
- Miao Liu
- Medical College, Tianjin University, Tianjin 300072, China
| | - Junyang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China
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13
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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14
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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. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [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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15
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Bayat P, Rambaud C, Priem B, Bourderioux M, Bilong M, Poyer S, Pastoriza-Gallego M, Oukhaled A, Mathé J, Daniel R. Comprehensive structural assignment of glycosaminoglycan oligo- and polysaccharides by protein nanopore. Nat Commun 2022; 13:5113. [PMID: 36042212 PMCID: PMC9427770 DOI: 10.1038/s41467-022-32800-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
Glycosaminoglycans are highly anionic functional polysaccharides with information content in their structure that plays a major role in the communication between the cell and the extracellular environment. The study presented here reports the label-free detection and analysis of glycosaminoglycan molecules at the single molecule level using sensing by biological nanopore, thus addressing the need to decipher structural information in oligo- and polysaccharide sequences, which remains a major challenge for glycoscience. We demonstrate that a wild-type aerolysin nanopore can detect and characterize glycosaminoglycan oligosaccharides with various sulfate patterns, osidic bonds and epimers of uronic acid residues. Size discrimination of tetra- to icosasaccharides from heparin, chondroitin sulfate and dermatan sulfate was investigated and we show that different contents and distributions of sulfate groups can be detected. Remarkably, differences in α/β anomerization and 1,4/1,3 osidic linkages can also be detected in heparosan and hyaluronic acid, as well as the subtle difference between the glucuronic/iduronic epimers in chondroitin and dermatan sulfate. Although, at this stage, discrimination of each of the constituent units of GAGs is not yet achieved at the single-molecule level, the resolution reached in this study is an essential step toward this ultimate goal.
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Affiliation(s)
- Parisa Bayat
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Charlotte Rambaud
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Bernard Priem
- CNRS, CERMAV, University Grenoble Alpes, Grenoble, France
| | | | - Mélanie Bilong
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Salomé Poyer
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | | | | | - Jérôme Mathé
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
| | - Régis Daniel
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
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16
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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: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [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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17
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Liu Y, Zhang S, Wang Y, Wang L, Cao Z, Sun W, Fan P, Zhang P, Chen HY, Huang S. Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products. J Am Chem Soc 2022; 144:13717-13728. [PMID: 35867993 DOI: 10.1021/jacs.2c04595] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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18
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Tajparast M, Glavinovic M. Current Flow in a Cylindrical Nanopore with an Object–Implications for Virus Sensing. BIONANOSCIENCE 2022; 12:927-945. [PMID: 35607652 PMCID: PMC9117592 DOI: 10.1007/s12668-022-00990-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2022] [Indexed: 11/18/2022]
Abstract
Interest is growing in nanopores as real-time, low-cost, label-free virus size sensors. To optimize their performance, we evaluate how external electric field and ion concentrations and pore wall charges influence currents and object (disk) radius-current relationship using simulations. The physics was described using the Poisson-Nernst-Planck and Navier–Stokes equations. In a charged cylindrical nanopore with a charged disk, elevated external electric field produces higher (and polarity independent) ion concentrations and greater ion current (largely migratory). Elevated external ion concentrations also lead to higher concentrations (mainly away from the pore wall), greater axial electric field especially in the disk-pore wall space, and finally larger current. At low concentrations, current is disk radius independent. The current rises as concentrations increase. Interestingly, the rise is greater for larger disks (except when the pore is blocked mechanically). Smaller cross-sectional area for current flow or volume exclusion of electrolyte by object thus cannot be universally accepted as explanations of current blockage. Ion current rises when pore wall charge density increases, but its direction is independent of charge sign. Current-disk radius relationship is also independent of pore wall charge sign. If the pore wall and disk charges have the same sign, larger current with bigger disk is due to higher counter-ion accumulation in the object-pore wall space. However, if their signs are opposite, it is largely due to elevated axial electric field in the object-pore wall space. Finally in uncharged nanopores, current diminishes when disk radius increases making them better sensors of virus size.
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19
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Jia W, Hu C, Wang Y, Liu Y, Wang L, Zhang S, Zhu Q, Gu Y, Zhang P, Ma J, Chen HY, Huang S. Identification of Single-Molecule Catecholamine Enantiomers Using a Programmable Nanopore. ACS NANO 2022; 16:6615-6624. [PMID: 35394745 DOI: 10.1021/acsnano.2c01017] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enantiomers, chiral isomers with opposite chirality, typically demonstrate differences in their pharmacological activity, metabolism, and toxicity. However, direct discrimination between enantiomers is challenging due to their similar physiochemical properties. Following the strategy of programmable nanoreactors for stochastic sensing (PNRSS), introduction of phenylboronic acid (PBA) to a Mycobacterium smegmatis porin A (MspA) assists in the identification of the enantiomers of norepinephrine and epinephrine. Using a machine learning algorithm, identification of the enantiomers has been achieved with an accuracy of 98.2%. The enantiomeric excess (ee) of a mixture of enantiomeric catecholamines was measured to determine the enantiomeric purity. This sensing strategy is a faster method for the determination of ee values than liquid chromatography-mass spectrometry and is useful as a quality control in the industrial production of enantiomeric drugs.
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Affiliation(s)
- Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Chengzhen Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Qiang Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yuming Gu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Jing Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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20
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Cairns-Gibson DF, Cockroft SL. Functionalised nanopores: chemical and biological modifications. Chem Sci 2022; 13:1869-1882. [PMID: 35308845 PMCID: PMC8848921 DOI: 10.1039/d1sc05766a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality. The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.![]()
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Affiliation(s)
- Dominic F. Cairns-Gibson
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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21
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Lucas FLR, Piso TRC, van der Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021; 60:22849-22855. [PMID: 34390104 PMCID: PMC8518494 DOI: 10.1002/anie.202107807] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/20/2021] [Indexed: 12/27/2022]
Abstract
The ability to measure the concentration of metabolites in biological samples is important, both in the clinic and for home diagnostics. Here we present a nanopore-based biosensor and automated data analysis for quantification of thiamine in urine in less than a minute, without the need for recalibration. For this we use the Cytolysin A nanopore and equip it with an engineered periplasmic thiamine binding protein (TbpA). To allow fast measurements we tuned the affinity of TbpA for thiamine by redesigning the π-π stacking interactions between the thiazole group of thiamine and TbpA. This substitution resulted furthermore in a marked difference between unbound and bound state, allowing the reliable discrimination of thiamine from its two phosphorylated forms by residual current only. Using an array of nanopores, this will allow the quantification within seconds, paving the way for next-generation single-molecule metabolite detection systems.
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Affiliation(s)
- Florian Leonardus Rudolfus Lucas
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747, AG Groningen, Netherlands
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22
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Lucas FLR, Piso TRC, Heide NJ, Galenkamp NS, Hermans J, Wloka C, Maglia G. Automated Electrical Quantification of Vitamin B1 in a Bodily Fluid using an Engineered Nanopore Sensor. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Tjemme Rinze Cornelis Piso
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nieck Jordy Heide
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Jos Hermans
- Analytical Biochemistry Department of Pharmacy University of Groningen Antonius Deusinglaan 1 Groningen 9713 AV The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen Groningen 9747 AG Groningen Netherlands
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23
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Tang Y, Zhong X, Yan S, Liu X, Cheng L, Wang Y, Liu X. Enantiospecific Detection of D‐Amino Acid through Synergistic Upconversion Energy Transfer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yongan Tang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
| | - Xiaoyan Zhong
- Institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow University Suzhou 215123 China
| | - Shuangqian Yan
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
| | - Xiaowang Liu
- MIIT Key Laboratory of Flexible Electronics (KLoFE) and Xi'an Institute of Flexible Electronics Northwestern Polytechnical University 710072 Xi'an Shaanxi China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow University Suzhou 215123 China
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
| | - Xiaogang Liu
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen 518060 China
- Department of Chemistry National University of Singapore Singapore 117549 Singapore
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24
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Tang Y, Zhong X, Yan S, Liu X, Cheng L, Wang Y, Liu X. Enantiospecific Detection of D-Amino Acid through Synergistic Upconversion Energy Transfer. Angew Chem Int Ed Engl 2021; 60:19648-19652. [PMID: 34224644 DOI: 10.1002/anie.202105297] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/20/2021] [Indexed: 01/23/2023]
Abstract
D-amino acids (DAAs) are indispensable in regulating diverse metabolic pathways. Selective and sensitive detection of DAAs is crucial for understanding the complexity of metabolic processes and managing associated diseases. However, current DAA detection strategies mainly rely on bulky instrumentation or electrochemical probes, limiting their cellular and animal applications. Here we report an enzyme-coupled nanoprobe that can detect enantiospecific DAAs through synergistic energy transfer. This nanoprobe offers near-infrared upconversion capability, a wide dynamic detection range, and a detection limit of 2.2 μM, providing a versatile platform for in vivo noninvasive detection of DAAs with high enantioselectivity. These results potentially allow real-time monitoring of biomolecular handedness in living animals, as well as developing antipsychotic treatment strategies.
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Affiliation(s)
- Yongan Tang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
| | - Xiaoyan Zhong
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, China
| | - Shuangqian Yan
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
| | - Xiaowang Liu
- MIIT Key Laboratory of Flexible Electronics (KLoFE) and Xi'an Institute of Flexible Electronics, Northwestern Polytechnical University, 710072, Xi'an, Shaanxi, China
| | - Liang Cheng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, China
| | - Yu Wang
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China
| | - Xiaogang Liu
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science & Technology, International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen, 518060, China.,Department of Chemistry, National University of Singapore, Singapore, 117549, Singapore
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25
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Liu Z, Li X, Masai H, Huang X, Tsuda S, Terao J, Yang J, Guo X. A single-molecule electrical approach for amino acid detection and chirality recognition. SCIENCE ADVANCES 2021; 7:eabe4365. [PMID: 33658198 PMCID: PMC7929498 DOI: 10.1126/sciadv.abe4365] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/15/2021] [Indexed: 05/27/2023]
Abstract
One of the ultimate goals of analytic chemistry is to efficiently discriminate between amino acids. Here we demonstrate this ability using a single-molecule electrical methodology based on molecular nanocircuits formed from stable graphene-molecule-graphene single-molecule junctions. These molecular junctions are fabricated by covalently bonding a molecular machine featuring a permethylated-β-cyclodextrin between a pair of graphene point contacts. Using pH to vary the type and charge of the amino acids, we find distinct multimodal current fluctuations originating from the different host-guest interactions, consistent with theoretical calculations. These conductance data produce characteristic dwell times and shuttling rates for each amino acid, and allow accurate, statistical real-time, in situ measurements. Testing four amino acids and their enantiomers shows the ability to distinguish between them within a few microseconds, thus paving a facile and precise way to amino acid identification and even single-molecule protein sequencing.
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Affiliation(s)
- Zihao Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xingxing Li
- Hefei National Laboratory for Physics Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Hiroshi Masai
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Xinyi Huang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Susumu Tsuda
- Department of Chemistry, Osaka Dental University, Osaka 573-1121, Japan
| | - Jun Terao
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan.
| | - Jinlong Yang
- Hefei National Laboratory for Physics Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, P. R. China
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26
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021; 60:14738-14749. [DOI: 10.1002/anie.202013462] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
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27
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
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28
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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29
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Yin YD, Zhang L, Leng XZ, Gu ZY. Harnessing biological nanopore technology to track chemical changes. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Wei X, Ma D, Jing L, Wang LY, Wang X, Zhang Z, Lenhart BJ, Yin Y, Wang Q, Liu C. Enabling nanopore technology for sensing individual amino acids by a derivatization strategy. J Mater Chem B 2020; 8:6792-6797. [PMID: 32495805 PMCID: PMC7429270 DOI: 10.1039/d0tb00895h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanopore technology holds remarkable promise for sequencing proteins and peptides. To achieve this, it is necessary to establish a characteristic profile for each individual amino acid through the statistical description of its translocation process. However, the subtle molecular differences among all twenty amino acids along with their unpredictable conformational changes at the nanopore sensing region result in very low distinguishability. Here we report the electrical sensing of individual amino acids using an α-hemolysin nanopore based on a derivatization strategy. Using derivatized amino acids as detection surrogates not only prolongs their interactions with the sensing region, but also improves their conformational variation. Furthermore, we show that distinct characteristics including current blockades and dwell times can be observed among all three classes of amino acids after 2,3-naphthalenedicarboxaldehyde (NDA)- and 2-naphthylisothiocyanate (NITC)-derivatization, respectively. These observable characteristics were applied towards the identification and differentiation of 9 of the 20 natural amino acids using their NITC derivatives. The method demonstrated herein will pave the way for the identification of all amino acids and further protein and peptide sequencing.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Lihong Jing
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing 100190, China
| | - Leon Y. Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
| | - Brian J. Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 20208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
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31
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Wei X, Ma D, Zhang Z, Wang LY, Gray JL, Zhang L, Zhu T, Wang X, Lenhart BJ, Yin Y, Wang Q, Liu C. N-Terminal Derivatization-Assisted Identification of Individual Amino Acids Using a Biological Nanopore Sensor. ACS Sens 2020; 5:1707-1716. [PMID: 32403927 PMCID: PMC7978492 DOI: 10.1021/acssensors.0c00345] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nanopore technology has been employed as a powerful tool for DNA sequencing and analysis. To extend this method to peptide sequencing, a necessary step is to profile individual amino acids (AAs) through their nanopore stochastic signals, which remains a great challenge because of the low signal-to-noise ratio and unpredictable conformational changes of AAs during their translocation through nanopores. We showed that the combination of an N-terminal derivatization strategy of AAs with nanopore technology could lead to effective in situ differentiation of AAs. Four different derivatization reactions have been tested with five selected AAs: Ala, Phe, Tyr, His, and Asp. Using an α-hemolysin nanopore, we demonstrated the feasibility of derivatization-assisted identification of AAs regardless of their charge composition and polarity. The method was further applied to discriminate each individual AA in testing data sets using their established nanopore profiles from training data sets. We envision that this proof-of-concept study will not only pave a way for identification of individual AAs but also lead to future applications in protein/peptide sequencing using the nanopore technology.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Dumei Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 Fujian, China
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Leon Y Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jonathan L Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Libo Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Tianyu Zhu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Brian J Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Yingwu Yin
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 Fujian, China
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, United States
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32
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Huang G, Willems K, Bartelds M, van Dorpe P, Soskine M, Maglia G. Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores. NANO LETTERS 2020; 20:3819-3827. [PMID: 32271587 PMCID: PMC7227020 DOI: 10.1021/acs.nanolett.0c00877] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Indexed: 05/19/2023]
Abstract
Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.
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Affiliation(s)
- Gang Huang
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
- imec, Kapeldreef 75, 3001 Leuven, Belgium
| | - Mart Bartelds
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol van Dorpe
- imec, Kapeldreef 75, 3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Misha Soskine
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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33
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Ramírez-Carreto S, Miranda-Zaragoza B, Rodríguez-Almazán C. Actinoporins: From the Structure and Function to the Generation of Biotechnological and Therapeutic Tools. Biomolecules 2020; 10:E539. [PMID: 32252469 PMCID: PMC7226409 DOI: 10.3390/biom10040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022] Open
Abstract
Actinoporins (APs) are a family of pore-forming toxins (PFTs) from sea anemones. These biomolecules exhibit the ability to exist as soluble monomers within an aqueous medium or as constitutively open oligomers in biological membranes. Through their conformational plasticity, actinoporins are considered good candidate molecules to be included for the rational design of molecular tools, such as immunotoxins directed against tumor cells and stochastic biosensors based on nanopores to analyze unique DNA or protein molecules. Additionally, the ability of these proteins to bind to sphingomyelin (SM) facilitates their use for the design of molecular probes to identify SM in the cells. The immunomodulatory activity of actinoporins in liposomal formulations for vaccine development has also been evaluated. In this review, we describe the potential of actinoporins for use in the development of molecular tools that could be used for possible medical and biotechnological applications.
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Affiliation(s)
| | | | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico; (S.R.-C.); (B.M.-Z.)
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34
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Zernia S, van der Heide NJ, Galenkamp NS, Gouridis G, Maglia G. Current Blockades of Proteins inside Nanopores for Real-Time Metabolome Analysis. ACS NANO 2020; 14:2296-2307. [PMID: 32003969 PMCID: PMC7045694 DOI: 10.1021/acsnano.9b09434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 05/14/2023]
Abstract
Biological nanopores are emerging as powerful and low-cost sensors for real-time analysis of biological samples. Proteins can be incorporated inside the nanopore, and ligand binding to the protein adaptor yields changes in nanopore conductance. In order to understand the origin of these conductance changes and develop sensors for detecting metabolites, we tested the signal originating from 13 different protein adaptors. We found that the quality of the protein signal depended on both the size and charge of the protein. The engineering of a dipole within the surface of the adaptor reduced the current noise by slowing the protein dynamics within the nanopore. Further, the charge of the ligand and the induced conformational changes of the adaptor defined the conductance changes upon metabolite binding, suggesting that the protein resides in an electrokinetic minimum within the nanopore, the position of which is altered by the ligand. These results represent an important step toward understanding the dynamics of the electrophoretic trapping of proteins inside nanopores and will allow developing next-generation sensors for metabolome analysis.
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Affiliation(s)
- Sarah Zernia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giorgos Gouridis
- Rega
Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Box 1037, 3000 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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35
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Ouldali H, Sarthak K, Ensslen T, Piguet F, Manivet P, Pelta J, Behrends JC, Aksimentiev A, Oukhaled A. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nat Biotechnol 2020; 38:176-181. [PMID: 31844293 PMCID: PMC7008938 DOI: 10.1038/s41587-019-0345-2] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 10/18/2019] [Accepted: 11/06/2019] [Indexed: 02/04/2023]
Abstract
Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.
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Affiliation(s)
- Hadjer Ouldali
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabien Piguet
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France
- DreamPore S.A.S., 33 Boulevard du Port 95000, Cergy, France
| | - Philippe Manivet
- APHP, GHU APHP.Nord, DMU BioGem, Hôpital Lariboisière, BIOBANK Lariboisière Department BB-0033-00064, Plateforme de BioPathologie et de Technologies Innovantes en Santé, Paris, France
- INSERM UMR 1141 "NeuroDiderot", Université de Paris, Paris, France
| | - Juan Pelta
- LAMBE UMR 8587, Université d'Evry-Val-d'Essonne, CNRS, CEA, Université Paris-Saclay, Evry, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Freiburg Materials Research Centre (FMF), University of Freiburg, Freiburg, Germany
- Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Abdelghani Oukhaled
- LAMBE UMR 8587, Université de Cergy-Pontoise, CNRS, CEA, Université Paris-Seine, Cergy-Pontoise, France.
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Giant single molecule chemistry events observed from a tetrachloroaurate(III) embedded Mycobacterium smegmatis porin A nanopore. Nat Commun 2019; 10:5668. [PMID: 31827098 PMCID: PMC6906327 DOI: 10.1038/s41467-019-13677-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
Biological nanopores are capable of resolving small analytes down to a monoatomic ion. In this research, tetrachloroaurate(III), a polyatomic ion, is discovered to bind to the methionine residue (M113) of a wild-type α-hemolysin by reversible Au(III)-thioether coordination. However, the cylindrical pore geometry of α-hemolysin generates shallow ionic binding events (~5–6 pA) and may have introduced other undesired interactions. Inspired by nanopore sequencing, a Mycobacterium smegmatis porin A (MspA) nanopore, which possesses a conical pore geometry, is mutated to bind tetrachloroaurate(III). Subsequently, further amplified blockage events (up to ~55 pA) are observed, which report the largest single ion binding event from a nanopore measurement. By taking the embedded Au(III) as an atomic bridge, the MspA nanopore is enabled to discriminate between different biothiols from single molecule readouts. These phenomena suggest that MspA is advantageous for single molecule chemistry investigations and has applications as a hybrid biological nanopore with atomic adaptors. Engineered biological nanopores enable observation of single molecule chemistry events; however a cylindrical pore geometry can have undesired effects. The authors report a conical biological pore which was embedded with tetrachloroaurate(III) to allow for discrimination between different biothiols.
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37
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Yuan C, Wu X, Gao R, Han X, Liu Y, Long Y, Cui Y. Nanochannels of Covalent Organic Frameworks for Chiral Selective Transmembrane Transport of Amino Acids. J Am Chem Soc 2019; 141:20187-20197. [DOI: 10.1021/jacs.9b10007] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Chen Yuan
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaowei Wu
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Gao
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xing Han
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yitao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yong Cui
- School of Chemistry and Chemical Engineering and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
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38
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Ding T, Chen AK, Lu Z. The applications of nanopores in studies of proteins. Sci Bull (Beijing) 2019; 64:1456-1467. [PMID: 36659703 DOI: 10.1016/j.scib.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023]
Abstract
Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.
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Affiliation(s)
- Taoli Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Zuhong Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Wang Y, Wang Y, Du X, Yan S, Zhang P, Chen HY, Huang S. Electrode-free nanopore sensing by DiffusiOptoPhysiology. SCIENCE ADVANCES 2019; 5:eaar3309. [PMID: 31523706 PMCID: PMC6731070 DOI: 10.1126/sciadv.aar3309] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/02/2019] [Indexed: 05/24/2023]
Abstract
A wide variety of single molecules can be identified by nanopore sensing. However, all reported nanopore sensing applications result from the same measurement configuration adapted from electrophysiology. Although urgently needed in commercial nanopore sequencing, parallel electrophysiology recording is limited in its cost and its throughput due to the introduced complexities from electronic integration. We present the first electrode-free nanopore sensing method defined as DiffusiOptoPhysiology (DOP), in which single-molecule events are monitored optically without any electrical connections. Single-molecule sensing of small molecules, macromolecules, and biomacromolecules was subsequently demonstrated. As a further extension, a fingertip-sized, multiplexed chip with single-molecule sensing capabilities has been introduced, which suggests a new concept of clinical diagnosis using disposable nanopore sensors. DOP, which is universally compatible with all types of channels and a variety of fluorescence imaging platforms, may benefit diverse areas such as nanopore sequencing, drug screening, and channel protein investigations.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, 210023 Nanjing, China
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40
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Yang X, Wang T, Zhang H, Chen Q, Wang B, Wang Y, Meng D. Chiral cysteine selective transport of proteins by CdS nanostructures modified anodic aluminum oxide template. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Sanganna Gari RR, Seelheim P, Liang B, Tamm LK. Quiet Outer Membrane Protein G (OmpG) Nanopore for Biosensing. ACS Sens 2019; 4:1230-1235. [PMID: 30990011 DOI: 10.1021/acssensors.8b01645] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interest in nanopore technology has been growing due to nanopores' unique capabilities in small molecule sensing, measurement of protein folding, and low-cost DNA and RNA sequencing. The E. coli β-barrel outer membrane protein OmpG is an excellent alternative to other protein nanopores because of its single polypeptide chain. However, the flexibility of its extracellular loops ultimately limits applications in traditional biosensing. We deleted several residues in and near loop 6 of OmpG. The dynamic structure of the new construct determined by NMR shows that loops 1, 2, 6, and 7 have reduced flexibilities compared to those of wild-type. Electrophysiological measurements show that the new design virtually eliminates flickering between open and closed states across a wide pH range. Modification of the pore lumen with a copper chelating moiety facilitates detection of small molecules. As proof of concept, we demonstrate concurrent single-molecule biosensing of glutamate and adenosine triphosphate.
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Affiliation(s)
- Raghavendar Reddy Sanganna Gari
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia 22908, United States
| | - Patrick Seelheim
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia 22908, United States
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia 22908, United States
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia 22908, United States
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42
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Anand D, Dhoke GV, Gehrmann J, Garakani TM, Davari MD, Bocola M, Zhu L, Schwaneberg U. Chiral separation of d/l-arginine with whole cells through an engineered FhuA nanochannel. Chem Commun (Camb) 2019; 55:5431-5434. [PMID: 30916680 DOI: 10.1039/c9cc00154a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Downstream processing to obtain enantiopure compounds from a racemic mixture relies mainly on crystallization. Natural transporters can specifically translocate enantiomers through membranes. Here a β-barrel transmembrane protein FhuA is re-engineered into a chiral channel protein (FhuAF4) to resolve racemic mixtures of d-/l-arginine. The engineered FhuAF4 variant exhibits an enantioselectivity (E-value) of 1.92 and an enantiomeric excess percentage (ee%) of 23.91 at 52.39% conversion. OmniChange mutant libraries at the computationally identified "filter-regions" likely help to identify FhuA variants for enantiomeric separation of other compounds.
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Affiliation(s)
- Deepak Anand
- Institute of Biotechnology, RWTH Aachen University Worringer Weg 3, D-52074 Aachen, Germany.
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43
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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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44
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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45
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Huang G, Voet A, Maglia G. FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution. Nat Commun 2019; 10:835. [PMID: 30783102 PMCID: PMC6381162 DOI: 10.1038/s41467-019-08761-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
A high throughput single-molecule method for identifying peptides and sequencing proteins based on nanopores could reduce costs and increase speeds of sequencing, allow the fabrication of portable home-diagnostic devices, and permit the characterization of low abundance proteins and heterogeneity in post-translational modifications. Here we engineer the size of Fragaceatoxin C (FraC) biological nanopore to allow the analysis of a wide range of peptide lengths. Ionic blockades through engineered nanopores distinguish a variety of peptides, including two peptides differing only by the substitution of alanine with glutamate. We also find that at pH 3.8 the depth of the peptide current blockades scales with the mass of the peptides irrespectively of the chemical composition of the analyte. Hence, this work shows that FraC nanopores allow direct readout of the mass of single peptide in solution, which is a crucial step towards the developing of a real-time and single-molecule protein sequencing device.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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46
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Ramsay WJ, Bell NAW, Qing Y, Bayley H. Single-Molecule Observation of the Intermediates in a Catalytic Cycle. J Am Chem Soc 2018; 140:17538-17546. [DOI: 10.1021/jacs.8b09282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- William J. Ramsay
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Nicholas A. W. Bell
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Yujia Qing
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
| | - Hagan Bayley
- University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA, United Kingdom
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47
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Study of the enantioselectivity and recognition mechanism of sulfhydryl-compound-functionalized gold nanochannel membranes. Anal Bioanal Chem 2018; 411:471-478. [DOI: 10.1007/s00216-018-1464-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/11/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
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48
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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49
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Enantioselective permeations of amino acids through l-proline-modified gold nanochannel membrane: an experimental and theoretical study. Amino Acids 2018; 50:1549-1556. [DOI: 10.1007/s00726-018-2629-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/24/2018] [Indexed: 01/29/2023]
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50
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Guo Y, Niu A, Jian F, Wang Y, Yao F, Wei Y, Tian L, Kang X. Metal-organic complex-functionalized protein nanopore sensor for aromatic amino acids chiral recognition. Analyst 2018; 142:1048-1053. [PMID: 28280809 DOI: 10.1039/c7an00097a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chiral recognition at single-molecule level for small active molecules is important, as exhibited by many nanostructures and molecular assemblies in biological systems, but it presents a significant challenge. We report a simple and rapid sensing strategy to discriminate all enantiomers of natural aromatic amino acids (AAA) using a metal-organic complex-functionalized protein nanopore, in which a chiral recognition element and a chiral recognition valve were equipped. A trifunctional molecule, heptakis-(6-deoxy-6-amino)-β-cyclodextrin (am7βCD), was non-covalently lodged within the nanopore of an α-hemolysin (αHL) mutant, (M113R)7-αHL. Copper(ii) ion reversibly bonds to the amino group of am7βCD to form an am7βCD-CuII complex, which allowed chiral recognition for each enantiomer in the mixture of AAA by distinct current signals. The CuII plugging valve plays a crucial rule that holds chiral molecules in the nanocavity for a sufficient registering time. Importantly, six enantiomers of all nature AAA could be simultaneously recognized at one time. Enantiomeric excess (ee) could also be accurately detected by this approach. It should be possible to generalize this approach for sensing of other chiral molecules.
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Affiliation(s)
- Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Aihua Niu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Feifei Jian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Ying Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China.
| | - Yongfeng Wei
- 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.
| | - Xiaofeng 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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