1
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Akhmadeev B, Retyunskaya O, Islamova L, Fazleeva G, Kalinin A, Katsyuba S, Elistratova J, Sinyashin O, Mustafina A. Biomimetic nanoplatforms constructed from dialkylaminostyryl hetarene dyes and phospholipids exhibiting selective fluorescent response to specific proteins. Colloids Surf B Biointerfaces 2024; 241:114046. [PMID: 38908044 DOI: 10.1016/j.colsurfb.2024.114046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/30/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
The present work explores the specificity of supramolecular assemblies comprising dialkylaminostyrylhetarene dye molecules incorporated into phosphatidylcholine (PC) or phosphatidylserine (PS) aggregates. In PS-based assemblies, the dyes demonstrate a concentration-dependent fluorescent response, distinguishing anionic proteins such as bovine serum albumin (BSA) and pepsin from lysozyme (LYZ) in aqueous solutions. Conversely, no significant response is observed when the dyes are incorporated into the well-organized bilayers of neutral PC. The fluorescent response arises from the binding of dyes to proteins, leading to the detachment of dye molecules from the assemblies, rather than from the binding of proteins to the assemblies, although the latter process is facilitated by electrostatic attraction. Thus, both the poor ordering of PS molecules and the interfacial arrangement of the dyes are prerequisites for the fluorescent response of dye-PS aggregates. The structure of the dyes significantly impacts the spectral features of dye-PS and dye-protein assemblies. An optimal dye structure has been identified for the recognition of BSA, with a limit of detection (LOD) of 10.8 nM.
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Affiliation(s)
- Bulat Akhmadeev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia; Kazan (Volga region) Federal University, Kremlyovskaya Str., 18, Kazan 420008, Russia.
| | - Olga Retyunskaya
- Kazan (Volga region) Federal University, Kremlyovskaya Str., 18, Kazan 420008, Russia
| | - Liliya Islamova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Guzyal Fazleeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Alexey Kalinin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Sergey Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Julia Elistratova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Oleg Sinyashin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
| | - Asiya Mustafina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov St. Kazan 420088, Russia
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2
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Baldelli M, Di Muccio G, Sauciuc A, Morozzo Della Rocca B, Viola F, Balme S, Bonini A, Maglia G, Chinappi M. Controlling Electroosmosis in Nanopores Without Altering the Nanopore Sensing Region. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2401761. [PMID: 38860821 DOI: 10.1002/adma.202401761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Indexed: 06/12/2024]
Abstract
Nanopores are powerful tools for single-molecule sensing of biomolecules and nanoparticles. The signal coming from the molecule to be analyzed strongly depends on its interaction with the narrower section of the nanopore (constriction) that may be tailored to increase sensing accuracy. Modifications of nanopore constriction have also been commonly used to induce electroosmosis, that favors the capture of molecules in the nanopore under a voltage bias and independently of their charge. However, engineering nanopores for increasing both electroosmosis and sensing accuracy is challenging. Here it is shown that large electroosmotic flows can be achieved without altering the nanopore constriction. Using continuum electrohydrodynamic simulations, it is found that an external charged ring generates strong electroosmosis in cylindrical nanopores. Similarly, for conical nanopores it is shown that moving charges away from the cone tip still results in an electroosmotic flow (EOF), whose intensity reduces increasing the diameter of the nanopore section where charges are placed. This paradigm is applied to engineered biological nanopores showing, via atomistic simulations and experiments, that mutations outside the constriction induce a relatively intense electroosmosis. This strategy provides much more flexibility in nanopore design since electroosmosis can be controlled independently from the constriction, which can be optimized to improve sensing accuracy.
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Affiliation(s)
- Matteo Baldelli
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
| | - Giovanni Di Muccio
- Department of Mechanical and Aerospace Engineering, University of Rome Sapienza, Roma, 00184, Italy
| | - Adina Sauciuc
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | | | | | - Sébastien Balme
- Institut Europeen des Membranes, UMR5635, University of Montpellier ENCSM CNRS, Montpellier, 34095, France
| | - Andrea Bonini
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
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3
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Zhang Y, Yi Y, Li Z, Zhou K, Liu L, Wu HC. Peptide sequencing based on host-guest interaction-assisted nanopore sensing. Nat Methods 2024; 21:102-109. [PMID: 37957431 DOI: 10.1038/s41592-023-02095-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Direct protein sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose an alternative method for peptide sequencing based on enzymatic cleavage and host-guest interaction-assisted nanopore sensing. We serendipitously discovered that the identity of any proteinogenic amino acid in a particular position of a phenylalanine-containing peptide could be determined via current blockage during translocation of the peptide through α-hemolysin nanopores in the presence of cucurbit[7]uril. Building upon this, we further present a proof-of-concept demonstration of peptide sequencing by sequentially cleaving off amino acids from C terminus of a peptide with carboxypeptidases, and then determining their identities and sequence with a peptide probe in nanopore. With future optimization, our results point to a different way of nanopore-based protein sequencing.
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Affiliation(s)
- Yun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yakun Yi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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4
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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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5
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Abraham Versloot R, Arias-Orozco P, Tadema MJ, Rudolfus Lucas FL, Zhao X, Marrink SJ, Kuipers OP, Maglia G. Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. J Am Chem Soc 2023; 145:18355-18365. [PMID: 37579582 PMCID: PMC10450680 DOI: 10.1021/jacs.3c04076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/16/2023]
Abstract
Mass spectrometry (MS) is widely used in proteomic analysis but cannot differentiate between molecules with the same mass-to-charge ratio. Nanopore technology might provide an alternative method for the rapid and cost-effective analysis and sequencing of proteins. In this study, we demonstrate that nanopore currents can distinguish between diastereomeric and enantiomeric differences in l- and d-peptides, not observed by conventional MS analysis, down to individual d-amino acids in small opioid peptides. Molecular dynamics simulations suggest that similar to chiral chromatography the resolution likely arises from multiple chiral interactions during peptide transport across the nanopore. Additionally, we used nanopore recordings to rapidly assess 4- and 11-amino acid ring formation in lanthipeptides, a process used in the synthesis of pharmaceutical peptides. The cyclization step requires distinguishing between constitutional isomers, which have identical MS signals and typically involve numerous tedious experiments to confirm. Hence, nanopore technology offers new possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
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Affiliation(s)
| | - Patricia Arias-Orozco
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | | | - Xinghong Zhao
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Oscar Paul Kuipers
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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6
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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: 106] [Impact Index Per Article: 53.0] [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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7
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Ge Y, Cui M, Zhang Q, Wang Y, Xi D. Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe. NANOSCALE ADVANCES 2022; 4:3883-3891. [PMID: 36133334 PMCID: PMC9470019 DOI: 10.1039/d2na00190j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Nanopore technology has attracted extensive attention due to its rapid, highly sensitive, and label-free performance. In this study, we aimed to identify proteinogenic amino acids using a wild-type aerolysin nanopore. Specifically, bipolar peptide probes were synthesised by linking four aspartic acid residues to the N-terminal and five arginine residues to the C-terminal of individual amino acids. With the help of the bipolar peptide carrier, 9 proteinogenic amino acids were reliably recognised based on current blockade and dwell time using an aerolysin nanopore. Furthermore, by changing the charge of the peptide probe, two of the five unrecognized amino acids above mentioned were identified. These findings promoted the application of aerolysin nanopores in proteinogenic amino acid recognition.
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Affiliation(s)
- Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Qiuqi Zhang
- The First School of Clinical Medicine, Southern Medical University Guangzhou 510515 P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University Linyi 276005 P. R. China
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8
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Zhou X, Tang R, Li Y, Zhang S, Xi D. Label-free Sensing of Main Protease Activity of SARS-CoV-2 with an Aerolysin Nanopore. Chem Asian J 2022; 17:e202200747. [PMID: 36029274 PMCID: PMC9539354 DOI: 10.1002/asia.202200747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/24/2022] [Indexed: 11/07/2022]
Abstract
The main protease (M pro ), which is highly conserved and plays a critical role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a natural biomarker for SARS-CoV-2. Accurate assessment of the M pro activity is crucial for the detection of SARS-CoV-2. Herein, we report a nanopore-based sensing strategy that uses an enzyme-catalyzed cleavage reaction of a peptide substrate to measure the M pro activity. The peptide was specifically cleaved by the M pro , thereby releasing the output products that, when translocated through aerolysin, quantitatively produced the signature current events. The proposed method exhibited high sensitivity, allowing the detection of M pro concentrations as low as 1 nM without the use of any signal amplification techniques. This simple, convenient, and label-free nanopore assay may expand the diagnostic tools for viruses.
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Affiliation(s)
- Xin Zhou
- Linyi University, department Shandong provincial key laboratory of detection technology for tumor markers, CHINA
| | - Ruping Tang
- Linyi University, Department Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, CHINA
| | - Yusen Li
- Linyi University, Department Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, CHINA
| | - Shusheng Zhang
- Linyi University, Department Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, CHINA
| | - Dongmei Xi
- Linyi University, Shandong Provincial laboratory of Detection technology for Tumor Markers, Middle section of Shuangling Road, 276000, linyi, CHINA
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9
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Spontaneous formation of nanopores within a nanofilm: phase diagram and multiple stable states. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Zhang LL, Zhong CB, Li JG, Niu HY, Ying YL, Long YT. A two-step calibration method for evaluation high bandwidth electrochemical instrument. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Versloot RA, Straathof SA, Stouwie G, Tadema MJ, Maglia G. β-Barrel Nanopores with an Acidic-Aromatic Sensing Region Identify Proteinogenic Peptides at Low pH. ACS NANO 2022; 16:7258-7268. [PMID: 35302739 PMCID: PMC9134492 DOI: 10.1021/acsnano.1c11455] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Biological nanopores are emerging as sensitive single-molecule sensors for proteins and peptides. The heterogeneous charge of a polypeptide chain, however, can complicate or prevent the capture and translocation of peptides and unfolded proteins across nanopores. Here, we show that two β-barrel nanopores, aerolysin and cytotoxin K, cannot efficiently detect proteinogenic peptides from a trypsinated protein under a wide range of conditions. However, the introduction of an acidic-aromatic sensing region in the β-barrel dramatically increased the dwell time and the discrimination of peptides in the nanopore at acidic pH. Surprisingly, despite the fact that the two β-barrel nanopores have a similar diameter and an acidic-aromatic construction, their capture mechanisms differ. The electro-osmotic flow played a dominant role for aerolysin, while the electrophoretic force dominated for cytotoxin K. Nonetheless, both β-barrel nanopores allowed the detection of mixtures of trypsinated peptides, with aerolysin nanopores showing a better resolution for larger peptides and cytotoxin K showing a better resolution for shorter peptides. Therefore, this work provides a generic strategy for modifying nanopores for peptide detection that will be most likely be applicable to other nanopore-forming toxins.
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Affiliation(s)
| | | | - Gemma Stouwie
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences
and Biotechnology Institute, University
of Groningen, Groningen, Groningen 9747AG, Netherlands
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12
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Chauhan N, Saxena K, Jain U. Single molecule detection; from microscopy to sensors. Int J Biol Macromol 2022; 209:1389-1401. [PMID: 35413320 DOI: 10.1016/j.ijbiomac.2022.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 01/31/2023]
Abstract
Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.
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Affiliation(s)
- Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Kirti Saxena
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India.
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13
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Lee H, Berk J, Webster A, Kim D, Foreman MR. Label-free detection of single nanoparticles with disordered nanoisland surface plasmon sensor. NANOTECHNOLOGY 2022; 33:165502. [PMID: 34915461 DOI: 10.1088/1361-6528/ac43e9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
We report sensing of single nanoparticles using disordered metallic nanoisland substrates supporting surface plasmon polaritons (SPPs). Speckle patterns arising from leakage radiation of elastically scattered SPPs provide a unique fingerprint of the scattering microstructure at the sensor surface. Experimental measurements of the speckle decorrelation are presented and shown to enable detection of sorption of individual gold nanoparticles and polystyrene beads. Our approach is verified through bright-field and fluorescence imaging of particles adhering to the nanoisland substrate.
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Affiliation(s)
- Hongki Lee
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Joel Berk
- Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2BW, United Kingdom
| | - Aaron Webster
- Independent Scholar, 187 Pinehurst Rd, Canyon, CA 94516, United States of America
| | - Donghyun Kim
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Matthew R Foreman
- Blackett Laboratory, Imperial College London, Prince Consort Road, London, SW7 2BW, United Kingdom
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14
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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15
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Niu H, Li MY, Ying YL, Long YT. An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport. Chem Sci 2022; 13:2456-2461. [PMID: 35310483 PMCID: PMC8864703 DOI: 10.1039/d1sc06459b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
Reading the primary sequence directly using nanopores remains challenging due to the complex building blocks of 20 proteinogenic amino acids and the corresponding sophisticated structures. Compared to the uniformly negatively charged polynucleotides, biological nanopores hardly provide effective ionic current responses to all heterogeneously charged peptides under nearly physiological pH conditions. Herein, we precisely design a N226Q/S228K mutant aerolysin which creates a new electrostatic constriction named R3 in-between two natural sensing regions for controlling the capture and translocation of heterogeneously charged peptides. At nearly physiological pH, the decoration of positive charges at this constriction gives a large velocity of electroosmotic flow (EOF), leading to a maximum 8-fold increase in frequency for the heterogeneously charged peptides with the net charge from +1 to −3. Even the duration time of the negatively charged peptide Aβ35-25D4 in N226Q/S228K AeL also rises from 0.07 ± 0.01 ms to 0.63 ± 0.01 ms after introducing the third electrostatic constriction. Therefore, the N226Q/S228K aerolysin nanopore with three electrostatic constrictions realizes the dual goals of both capturing and decelerating heterogeneously charged peptides without labelling, even for the folded peptides. An engineered aerolysin nanopore captures all types of peptides despite the charges and folded structure, which facilitate the achievement of nanopore protein sequencing.![]()
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Affiliation(s)
- Hongyan Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Meng-Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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16
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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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17
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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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18
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Abstract
Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification. Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.
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19
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Shorkey SA, Du J, Pham R, Strieter ER, Chen M. Real-Time and Label-Free Measurement of Deubiquitinase Activity with a MspA Nanopore. Chembiochem 2021; 22:2688-2692. [PMID: 34060221 PMCID: PMC8416795 DOI: 10.1002/cbic.202100092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/10/2021] [Indexed: 02/06/2023]
Abstract
Covalently attaching ubiquitin (Ub) to cellular proteins as a post-translational modification can result in altered function of modified proteins. Enzymes regulating Ub as a post-translational modification, such as ligases and deubiquitinases, are challenging to characterize in part due to the low throughput of in-vitro assays. Single-molecule nanopore based assays have the advantage of detecting proteins with high specificity and resolution, and in a label-free, real-time fashion. Here we demonstrate the use of a MspA nanopore for discriminating and quantifying Ub proteins. We further applied the MspA pore to measure the Ub-chain disassembly activity of UCH37, a proteasome associated deubiquitinase. The implementation of this MspA system into nanopore arrays could enable high throughput characterizations of unknown deubiquitinases as well as drug screening against disease related enzymes.
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Affiliation(s)
- Spencer A Shorkey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ryan Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Eric R Strieter
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Min Chen
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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20
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Huo MZ, Li MY, Ying YL, Long YT. Is the Volume Exclusion Model Practicable for Nanopore Protein Sequencing? Anal Chem 2021; 93:11364-11369. [PMID: 34379401 DOI: 10.1021/acs.analchem.1c00851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.
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21
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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22
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Miyagi M, Takiguchi S, Hakamada K, Yohda M, Kawano R. Single polypeptide detection using a translocon EXP2 nanopore. Proteomics 2021; 22:e2100070. [PMID: 34411416 DOI: 10.1002/pmic.202100070] [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: 06/26/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023]
Abstract
DNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites, and describe its pore-forming properties in the lipid bilayer. EXP2 mainly formed a nanopore with a diameter of 2.5 nm assembled from 7 monomers. Using the EXP2 nanopore allowed us to detect poly-L-lysine (PLL) at a single-molecule level. Furthermore, the EXP2 nanopore has sufficient resolution to distinguish the difference in molecular weight between two individual PLL, long PLL (Mw: 30,000-70,000) and short PLL (Mw: 10,000). Our results contribute to the accumulation of information for peptide-detectable nanopores.
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Affiliation(s)
- Mitsuki Miyagi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Kazuaki Hakamada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
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23
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Yan S, Zhang J, Wang Y, Guo W, Zhang S, Liu Y, Cao J, Wang Y, Wang L, Ma F, Zhang P, Chen HY, Huang S. Single Molecule Ratcheting Motion of Peptides in a Mycobacterium smegmatis Porin A (MspA) Nanopore. NANO LETTERS 2021; 21:6703-6710. [PMID: 34319744 DOI: 10.1021/acs.nanolett.1c02371] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diverse functions of proteins, including synthesis, catalysis, and signaling, result from their highly variable amino acid sequences. The technology allowing for direct analysis of protein sequences, however, is still unsatisfactory. Recent developments of nanopore sequencing of DNA or RNA have motivated attempts to realize nanopore sequencing of peptides in a similar manner. The core challenge has been to achieve a controlled ratcheting motion of the target peptide, which is currently restricted to a limited choice of compatible enzymes. By constructing peptide-oligonucleotide conjugates (POCs) and measurements with nanopore-induced phase-shift sequencing (NIPSS), direct observation of the ratcheting motion of peptides has been successfully achieved. The generated events show a clear sequence dependence on the peptide that is being tested. The method is compatible with peptides with either a conjugated N- or C-terminus. The demonstrated results suggest a proof of concept of nanopore sequencing of peptide and can be useful for peptide fingerprinting.
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Affiliation(s)
- Shuanghong Yan
- 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
| | - Jinyue 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
| | - Yu 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
| | - Weiming Guo
- 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
| | - 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
| | - Jiao 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
| | - 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
| | - Fubo Ma
- 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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24
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Wang J, Ying YL, Zhong CB, Zhang LM, Yan F, Long YT. Instrumentational implementation for parallelized nanopore electrochemical measurements. Analyst 2021; 146:4111-4120. [PMID: 34116564 DOI: 10.1039/d1an00471a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China. and Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Li-Min Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
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25
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Lucas FR, Sarthak K, Lenting EM, Coltan D, van der Heide NJ, Versloot RCA, Aksimentiev A, Maglia G. The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition. ACS NANO 2021; 15:9600-9613. [PMID: 34060809 PMCID: PMC8223486 DOI: 10.1021/acsnano.0c09958] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/21/2021] [Indexed: 05/21/2023]
Abstract
The detection of analytes and the sequencing of DNA using biological nanopores have seen major advances over recent years. The analysis of proteins and peptides with nanopores, however, is complicated by the complex physicochemical structure of polypeptides and the lack of understanding of the mechanism of capture and recognition of polypeptides by nanopores. In this work, we show that introducing aromatic amino acids at precise positions within the lumen of α-helical fragaceatoxin C (FraC) nanopores increased the capture frequency of peptides and largely improved the discrimination among peptides of similar size. Molecular dynamics simulations determined the sensing region of the nanopore, elucidated the microscopic mechanism enabling accurate characterization of the peptides via ionic current blockades in FraC, and characterized the effect of the pore modification on peptide discrimination. This work provides insights to improve the recognition and to augment the capture of peptides by nanopores, which is important for developing a real-time and single-molecule size analyzer for peptide recognition and identification.
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Affiliation(s)
| | - Kumar Sarthak
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Erica Mariska Lenting
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - David Coltan
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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26
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Sabirovas T, Valiūnienė A, Valincius G. Hybrid bilayer membranes on metallurgical polished aluminum. Sci Rep 2021; 11:9648. [PMID: 33958658 PMCID: PMC8102548 DOI: 10.1038/s41598-021-89150-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
In this work we describe the functionalization of metallurgically polished aluminum surfaces yielding biomimetic electrodes suitable for probing protein/phospholipid interactions. The functionalization involves two simple steps: silanization of the aluminum and subsequent fusion of multilamellar vesicles which leads to the formation of a hybrid bilayer lipid membrane (hBLM). The vesicle fusion was followed in real-time by fast Fourier transform electrochemical impedance spectroscopy (FFT EIS). The impedance-derived complex capacitance of the hBLMs was approximately 0.61 µF cm−2, a value typical for intact phospholipid bilayers. We found that the hBLMs can be readily disrupted if exposed to > 400 nM solutions of the pore-forming peptide melittin. However, the presence of cholesterol at 40% (mol) in hBLMs exhibited an inhibitory effect on the membrane-damaging capacity of the peptide. The melittin-membrane interaction was concentration dependent decreasing with concentration. The hBLMs on Al surface can be regenerated multiple times, retaining their dielectric and functional properties essentially intact.
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Affiliation(s)
- Tomas Sabirovas
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio ave. 7, 10257, Vilnius, Lithuania
| | - Aušra Valiūnienė
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko 24, 03225, Vilnius, Lithuania.
| | - Gintaras Valincius
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio ave. 7, 10257, Vilnius, Lithuania
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27
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021; 7:7/17/eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.
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Affiliation(s)
| | - Joseph W F Robertson
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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28
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Oh S, Lee MK, Chi SW. Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores. Chem Sci 2021; 12:5883-5891. [PMID: 34168813 PMCID: PMC8179679 DOI: 10.1039/d1sc00386k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.
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Affiliation(s)
- Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
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29
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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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30
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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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31
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Johnstone BA, Christie MP, Morton CJ, Parker MW. X-ray crystallography shines a light on pore-forming toxins. Methods Enzymol 2021; 649:1-46. [PMID: 33712183 DOI: 10.1016/bs.mie.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A common form of cellular attack by pathogenic bacteria is to secrete pore-forming toxins (PFTs). Capable of forming transmembrane pores in various biological membranes, PFTs have also been identified in a diverse range of other organisms such as sea anemones, earthworms and even mushrooms and trees. The mechanism of pore formation by PFTs is associated with substantial conformational changes in going from the water-soluble to transmembrane states of the protein. The determination of the crystal structures for numerous PFTs has shed much light on our understanding of these proteins. Other than elucidating the atomic structural details of PFTs and the conformational changes that must occur for pore formation, crystal structures have revealed structural homology that has led to the discovery of new PFTs and new PFT families. Here we review some key crystallographic results together with complimentary approaches for studying PFTs. We discuss how these studies have impacted our understanding of PFT function and guided research into biotechnical applications.
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Affiliation(s)
- Bronte A Johnstone
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michelle P Christie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.
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32
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Li MY, Ying YL, Li S, Wang YQ, Wu XY, Long YT. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore. ACS NANO 2020; 14:12571-12578. [PMID: 32806044 DOI: 10.1021/acsnano.0c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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33
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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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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35
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Hu F, Angelov B, Li S, Li N, Lin X, Zou A. Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore. Chembiochem 2020; 21:2467-2473. [DOI: 10.1002/cbic.202000119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/09/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Fangzhou Hu
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Borislav Angelov
- Institute of Physics, ELI BeamlinesAcademy of Sciences of the Czech Republic Na Slovance 2 18221 Prague Czech Republic
| | - Shuang Li
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Na Li
- National Center for Protein Science in ShanghaiZhangjiang LabShanghai Advanced Research Institute, CAS Shanghai 200120 P. R. China
| | - Xubo Lin
- Institute of Single Cell EngineeringBeijing Advanced Innovation Center for Biomedical EngineeringBeihang University Beijing 100191 P. R. China
| | - Aihua Zou
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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36
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Ying YL, Wang J, Leach AR, Jiang Y, Gao R, Xu C, Edwards MA, Pendergast AD, Ren H, Weatherly CKT, Wang W, Actis P, Mao L, White HS, Long YT. Single-entity electrochemistry at confined sensing interfaces. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9716-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Yuan B, Li S, Ying YL, Long YT. The analysis of single cysteine molecules with an aerolysin nanopore. Analyst 2020; 145:1179-1183. [DOI: 10.1039/c9an01965k] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biological nanopore technology has the advantages of high selectivity and high reproducibility for characterizing single biomolecules.
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Affiliation(s)
- Bo Yuan
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Shuang Li
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Yi-Lun Ying
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- P.R. China
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38
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Ying YL, Yang J, Meng FN, Li S, Li MY, Long YT. A Nanopore Phosphorylation Sensor for Single Oligonucleotides and Peptides. RESEARCH 2019; 2019:1050735. [PMID: 31912023 PMCID: PMC6944226 DOI: 10.34133/2019/1050735] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/07/2019] [Indexed: 11/07/2022]
Abstract
The phosphorylation of oligonucleotides and peptides plays a critical role in regulating virtually all cellular processes. To fully understand these complex and fundamental regulatory pathways, the cellular phosphorylate changes of both oligonucleotides and peptides should be simultaneously identified and characterized. Here, we demonstrated a single-molecule, high-throughput, label-free, general, and one-step aerolysin nanopore method to comprehensively evaluate the phosphorylation of both oligonucleotide and peptide substrates. By virtue of electrochemically confined effects in aerolysin, our results show that the phosphorylation accelerates the traversing speed of a negatively charged substrate for about hundreds of time while significantly enhances the translocation frequency of a positively charged substrate. Thereby, the kinase/phosphatase activity could be directly measured with the aerolysin nanopore from the characteristically dose-dependent event frequency of the substrates. By using this straightforward approach, a model T4 oligonucleotide kinase (PNK) further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a single-molecule level. Our study provides a step forward to nanopore enzymology for analyzing the phosphorylation of both oligonucleotides and peptides with significant feasibility in fundamental biochemical researches, clinical diagnosis, and kinase/phosphatase-targeted drug discovery.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing 210023, China
| | - Jie Yang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fu-Na Meng
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Meng-Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center, Nanjing 210023, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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39
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Li MY, Wang YQ, Ying YL, Long YT. Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore. Chem Sci 2019; 10:10400-10404. [PMID: 32110330 PMCID: PMC6988595 DOI: 10.1039/c9sc03163d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I 0) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China . .,School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
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40
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Pathirathna P, Balla RJ, Meng G, Wei Z, Amemiya S. Nanoscale electrostatic gating of molecular transport through nuclear pore complexes as probed by scanning electrochemical microscopy. Chem Sci 2019; 10:7929-7936. [PMID: 31673318 PMCID: PMC6788534 DOI: 10.1039/c9sc02356a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
The nuclear pore complex (NPC) is a large protein nanopore that solely mediates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. There is a long-standing consensus that selective transport barriers of the NPC are exclusively based on hydrophobic repeats of phenylalanine and glycine (FG) of nucleoporins. Herein, we reveal experimentally that charged residues of amino acids intermingled between FG repeats can modulate molecular transport through the NPC electrostatically and in a pathway-dependent manner. Specifically, we investigate the NPC of the Xenopus oocyte nucleus to find that excess positive charges of FG-rich nucleoporins slow down passive transport of a polycationic peptide, protamine, without affecting that of a polyanionic pentasaccharide, Arixtra, and small monovalent ions. Protamine transport is slower with a lower concentration of electrolytes in the transport media, where the Debye length becomes comparable to the size of water-filled spaces among the gel-like network of FG repeats. Slow protamine transport is not affected by the binding of a lectin, wheat germ agglutinin, to the peripheral route of the NPC, which is already blocked electrostatically by adjacent nucleoporins that have more cationic residues than anionic residues and even FG dipeptides. The permeability of NPCs to the probe ions is measured by scanning electrochemical microscopy using ion-selective tips based on liquid/liquid microinterfaces and is analysed by effective medium theory to determine the sizes of peripheral and central routes with distinct protamine permeability. Significantly, nanoscale electrostatic gating at the NPC can be relevant not only chemically and biologically, but also biomedically for efficient nuclear import of genetically therapeutic substances.
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Affiliation(s)
- Pavithra Pathirathna
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Ryan J Balla
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Guanqun Meng
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Zemeng Wei
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
| | - Shigeru Amemiya
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , Pennsylvania 15260 , USA .
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41
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Wei ZX, Ying YL, Li MY, Yang J, Zhou JL, Wang HF, Yan BY, Long YT. Learning Shapelets for Improving Single-Molecule Nanopore Sensing. Anal Chem 2019; 91:10033-10039. [PMID: 31083925 DOI: 10.1021/acs.analchem.9b01896] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high F1 score of 0.933. In comparison with the conventional statistical methods for the analysis of duration and residual current, the shapelet-transformed representation provides clearly discriminated distributions for multiple analytes. Taking advantage of the robust LTS algorithm, one could anticipate the real-time analysis of nanopore events for the direct identification and quantification of multiple biomolecules in a complex real sample (e.g., serum) without labels and time-consuming mutagenesis.
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Affiliation(s)
- Zi-Xuan Wei
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Yi-Lun Ying
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
| | - Meng-Yin Li
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jie Yang
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jia-Le Zhou
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hui-Feng Wang
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Bing-Yong Yan
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Yi-Tao Long
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , People's Republic of China
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Lu Y, Wu XY, Ying YL, Long YT. Simultaneous single-molecule discrimination of cysteine and homocysteine with a protein nanopore. Chem Commun (Camb) 2019; 55:9311-9314. [PMID: 31310244 DOI: 10.1039/c9cc04077c] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Discrimination between cysteine and homocysteine at the single-molecule level is achieved within a K238Q mutant aerolysin nanopore, which provides a confined space for high spatial resolution to identify the amino acid difference with a 5'-benzaldehyde poly(dA)4 probe. Our strategy allows potential detection and characterization of various amino acids and their modifications, and provides a crucial step towards developing nanopore protein sequencing devices.
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Affiliation(s)
- Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Xue-Yuan Wu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China. and State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China. and State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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44
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Li Q, Ying YL, Liu SC, Lin Y, Long YT. Detection of Single Proteins with a General Nanopore Sensor. ACS Sens 2019; 4:1185-1189. [PMID: 30860364 DOI: 10.1021/acssensors.9b00228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single protein sensing based on solid-state nanopores is promising but challenging, because the fast translocation velocity of a protein is beyond the bandwidth of nanopore instruments. To decelerate the translocation speed, here, we employed a common protein cross-link interaction to achieve a general and robust nanopore sensing platform for single-molecule detection of protein. Benefiting from the EDC/NHS coupling interaction between nanopore and proteins, a 10-fold decrease in speed has been achieved. The clearly distinguishable current signatures further reveal that the anisotropic translocation of a protein, which are horizontal, vertical, and flipping transit inside nanopore confinement. This strategy provides a general platform for rapid detection of proteins as well as exploring fundamental protein dynamics at the single-molecule level.
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Affiliation(s)
- Qiao Li
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yao Lin
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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45
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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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46
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Wang J, Fertig N, Ying YL. Real-time monitoring β-lactam/β-lactamase inhibitor (BL/BLI) mixture towards the bacteria porin pathway at single molecule level. Anal Bioanal Chem 2019; 411:4831-4837. [PMID: 30824965 DOI: 10.1007/s00216-019-01650-3] [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: 11/15/2018] [Revised: 01/09/2019] [Accepted: 01/28/2019] [Indexed: 02/07/2023]
Abstract
Multidrug-resistant bacteria are a great concern and a problem that must be addressed. Extended-spectrum β-lactamases are a common defence mechanism of bacteria to make β-lactam (BL) antibiotics ineffective. β-Lactamase inhibitors (BLIs) are consequently designed and are often clinically prescribed with a BL antibiotic to hinder degradation. Current studies focusing on how BL antibiotics or BLIs interact solely with the bacterial outer membrane nanopores (porins) on reaching the periplasmic side using a nanopore-based sensing technique. In electrochemical studies, the bias voltage allows real-time monitoring of BL antibiotics, BLIs and their mixture through the porin pathway at the single-molecule level. Here we consider the most abundant membrane protein from Escherichia coli (i.e. OmpF), purify and reconstitute the membrane protein in an artificial lipid bilayer and then study its ex vivo electrochemical behaviour. We show the piperacillin/tazobactam mixture interacts with OmpF, whereas the substrate interacts under the maximum bandwidth. The power spectrum analysis of the ionic current trace demonstrates the ampicillin/sulbactram mixture requires more energy than ampicillin alone to pass through the porin pathway. Our results demonstrate that clinically relevant combinations (e.g. piperacillin/tazobactam and ampicillin/sulbactam) interact more strongly with OmpF than either the BL antibiotic or the BLI alone. We suggest a quick and relatively cheap screening method to test the ability of BL antibiotics/BLIs to cross the bacterial cellular membrane.
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Affiliation(s)
- Jiajun Wang
- School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany.
| | - Niels Fertig
- Nanion Technologies GmbH, 80339, Munich, Germany
| | - Yi-Lun Ying
- School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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47
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Zou Z, Yang H, Yan Q, Qi P, Qing Z, Zheng J, Xu X, Zhang L, Feng F, Yang R. Synchronous screening of multiplexed biomarkers of Alzheimer's disease by a length-encoded aerolysin nanopore-integrated triple-helix molecular switch. Chem Commun (Camb) 2019; 55:6433-6436. [DOI: 10.1039/c9cc02065a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A label-free triple-helix molecular switch-mediated nanopore sensor is developed for the synchronous screening of biomarkers of Alzheimer's disease.
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Affiliation(s)
- Zhen Zou
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Hua Yang
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Qi Yan
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Peng Qi
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Zhihe Qing
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- Hunan University
- Changsha 410082
- P. R. China
| | - Xuan Xu
- Children's Medical Center
- People's Hospital of Hunan Province
- Changsha
- P. R. China
| | - Lihua Zhang
- College of Chemistry and Environmental Engineering
- Shanxi Datong University
- Datong
- P. R. China
| | - Feng Feng
- College of Chemistry and Environmental Engineering
- Shanxi Datong University
- Datong
- P. R. China
| | - Ronghua Yang
- Changsha University of Science and Technology
- School of Chemistry and Food Engineering
- Changsha
- P. R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
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48
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Yang J, Wang YQ, Li MY, Ying YL, Long YT. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14940-14945. [PMID: 30462509 DOI: 10.1021/acs.langmuir.8b03264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
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Affiliation(s)
- Jie Yang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
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49
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Zhu L, Xu Y, Ali I, Liu L, Wu H, Lu Z, Liu Q. Solid-State Nanopore Single-Molecule Sensing of DNAzyme Cleavage Reaction Assisted with Nucleic Acid Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26555-26565. [PMID: 30016075 DOI: 10.1021/acsami.8b09505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The detection and investigation of biomolecules at a single-molecule level is important for improving diagnosis in biomedicine. Solid-state nanopores are a unique tool that have the potential to accomplish this task because they are label-free and require only low sample consumption. However, the event-readouts of current small polymer molecules are still limited because of its relatively large size and low signal-to-noise ratios. Here, we present a rapid sensing approach for the detection of GR-5 DNAzyme cleaving specific substrate reactions using relatively larger size silicon nitride nanopores by introducing a type of nucleic acid nanostructure (DNA tetrahedron) as a carrier. The proposed method is convenient and sensitive enough to detect the cleavage reactions by identifying translocation events before and after reactions with nanomolar concentrations of the target sample. Furthermore, this assay was also carried out by using larger size nanopores (60 nm diameter) to achieve the DNAzyme cleavage sensing with the same sample concentration. This approach can improve event detectability of other smaller molecules' translocation, which opens up a wide range of applications for analytes detection by incorporating solid-state nanopores. Nucleic acid nanostructure-assisted nanopore sensing can promote the development of single-molecule studies.
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Affiliation(s)
- Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Ying Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Liping Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
- Guizhou Institute of Technology , Guiyang , Guizhou 550003 , People's Republic of China
| | - Hongwen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
- Department of Medical Devices , First Affiliated Hospital of Nanchang University , Nanchang 330006 , China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
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