1
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Greive SJ, Bacri L, Cressiot B, Pelta J. Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning. ACS NANO 2024; 18:539-550. [PMID: 38134312 DOI: 10.1021/acsnano.3c08433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.
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Affiliation(s)
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
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2
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Chen C, Song M, Li K, Yan S, Chen M, Geng J. E. coli outer membrane protein T (OmpT) nanopore for peptide sensing. Biochem Biophys Res Commun 2023; 677:132-140. [PMID: 37586211 DOI: 10.1016/j.bbrc.2023.05.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 08/18/2023]
Abstract
Peptide detection methods with facility and high sensitivity are essential for diagnosing disease associated with peptide biomarkers. Nanopore sensing technology had emerged as a low cost, high-throughput, and scalable tool for peptide detection. The omptins family proteins which can form β-barrel pores have great potentials to be developed as nanopore biosensor. However, there are no study about the channel properties of E. coli OmpT and the development of OmpT as a nanopore biosensor. In this study, the OmpT biological nanopore channel was constructed with a conductance of 1.49 nS in 500 mM NaCl buffer and a three-step gating phenomenon under negative voltage higher than 100 mV and then was developed as a peptide biosensor which can detect peptide without the interfere of ssDNA and dNTPs. The OmpT constructed in this study has potential application in peptide detection, and also provides a new idea for the detection of peptides using the specific binding ability of protease.
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Affiliation(s)
- Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, China
| | - Mengxiao Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China.
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3
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Chingarande RG, Tian K, Kuang Y, Sarangee A, Hou C, Ma E, Ren J, Hawkins S, Kim J, Adelstein R, Chen S, Gillis KD, Gu LQ. Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor. Proc Natl Acad Sci U S A 2023; 120:e2108118120. [PMID: 37276386 PMCID: PMC10268594 DOI: 10.1073/pnas.2108118120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 04/14/2023] [Indexed: 06/07/2023] Open
Abstract
Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.
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Affiliation(s)
- Rugare G. Chingarande
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Kai Tian
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Yu Kuang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Aby Sarangee
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Chengrui Hou
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Emily Ma
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Jarett Ren
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sam Hawkins
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Joshua Kim
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Ray Adelstein
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Sally Chen
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
| | - Kevin D. Gillis
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
| | - Li-Qun Gu
- Department of Chemical and Biomedical Engineering, University of Missouri, Columbia, MO65211
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO65211
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4
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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5
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Nemati S, Shalileh F, Mirjalali H, Omidfar K. Toward waterborne protozoa detection using sensing technologies. Front Microbiol 2023; 14:1118164. [PMID: 36910193 PMCID: PMC9999019 DOI: 10.3389/fmicb.2023.1118164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 03/14/2023] Open
Abstract
Drought and limited sufficient water resources will be the main challenges for humankind during the coming years. The lack of water resources for washing, bathing, and drinking increases the use of contaminated water and the risk of waterborne diseases. A considerable number of waterborne outbreaks are due to protozoan parasites that may remain active/alive in harsh environmental conditions. Therefore, a regular monitoring program of water resources using sensitive techniques is needed to decrease the risk of waterborne outbreaks. Wellorganized point-of-care (POC) systems with enough sensitivity and specificity is the holy grail of research for monitoring platforms. In this review, we comprehensively gathered and discussed rapid, selective, and easy-to-use biosensor and nanobiosensor technologies, developed for the early detection of common waterborne protozoa.
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Affiliation(s)
- Sara Nemati
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzaneh Shalileh
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular–Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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6
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Tan X, Lv C, Chen H. Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products. Crit Rev Food Sci Nutr 2022; 63:10866-10879. [PMID: 35687354 DOI: 10.1080/10408398.2022.2085238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.
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Affiliation(s)
- Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hai Chen
- College of Food Science, Southwest University, Chongqing, China
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7
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Bandara YMNDY, Farajpour N, Freedman KJ. Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point. J Am Chem Soc 2022; 144:3063-3073. [PMID: 35143193 DOI: 10.1021/jacs.1c11540] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
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8
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Su Z, Li T, Wu D, Wu Y, Li G. Recent Progress on Single-Molecule Detection Technologies for Food Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:458-469. [PMID: 34985271 DOI: 10.1021/acs.jafc.1c06808] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid and sensitive detection technologies for food contaminants play vital roles in food safety. Due to the complexity of the food matrix and the trace amount distribution, traditional methods often suffer from unsatisfying accuracy, sensitivity, or specificity. In past decades, single-molecule detection (SMD) has emerged as a way to realize the rapid and ultrasensitive measurement with low sample consumption, showing a great potential in food contaminants detection. For instance, based on the nanopore technique, simple and effective methods for single-molecule analysis of food contaminants have been developed. To our knowledge, there has been a rare review that focuses on SMD techniques for food safety. The present review attempts to cover some typical SMD methods in food safety, including electrochemistry, optical spectrum, and atom force microscopy. Then, recent applications of these techniques for detecting food contaminants such as biotoxins, pesticides, heavy metals, and illegal additives are reviewed. Finally, existing research challenges and future trends of SMD in food safety are also tentatively proposed.
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Affiliation(s)
- Zhuoqun Su
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Tong Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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9
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Current Developments in Diagnostic Assays for Laboratory Confirmation and Investigation of Botulism. J Clin Microbiol 2021; 60:e0013920. [PMID: 34586891 DOI: 10.1128/jcm.00139-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detection of botulinum neurotoxin or isolation of the toxin producing organism is required for the laboratory confirmation of botulism in clinical specimens. In an effort to reduce animal testing required by the gold standard method of botulinum neurotoxin detection, the mouse bioassay, many technologies have been developed to detect and characterize the causative agent of botulism. Recent advancements in these technologies have led to improvements in technical performance of diagnostic assays; however, many emerging assays have not been validated for the detection of all serotypes in complex clinical and environmental matrices. Improvements to culture protocols, endopeptidase-based assays, and a variety of immunological and molecular methods have provided laboratories with a variety of testing options to evaluate and incorporate into their testing algorithms. While significant advances have been made to improve these assays, additional work is necessary to evaluate these methods in various clinical matrices and to establish standardized criteria for data analysis and interpretation.
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10
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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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11
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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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12
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Ito Y, Izawa Y, Osaki T, Kamiya K, Misawa N, Fujii S, Mimura H, Miki N, Takeuchi S. A Lipid-Bilayer-On-A-Cup Device for Pumpless Sample Exchange. MICROMACHINES 2020; 11:mi11121123. [PMID: 33352964 PMCID: PMC7767076 DOI: 10.3390/mi11121123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/12/2023]
Abstract
Lipid-bilayer devices have been studied for on-site sensors in the fields of diagnosis, food and environmental monitoring, and safety/security inspection. In this paper, we propose a lipid-bilayer-on-a-cup device for serial sample measurements using a pumpless solution exchange procedure. The device consists of a millimeter-scale cylindrical cup with vertical slits which is designed to steadily hold an aqueous solution and exchange the sample by simply fusing and splitting the solution with an external solution. The slit design was experimentally determined by the capabilities of both the retention and exchange of the solution. Using the optimized slit, a planar lipid bilayer was reconstituted with a nanopore protein at a microaperture allocated to the bottom of the cup, and the device was connected to a portable amplifier. The solution exchangeability was demonstrated by observing the dilution process of a blocker molecule of the nanopore dissolved in the cup. The pumpless solution exchange by the proposed cup-like device presents potential as a lipid-bilayer system for portable sensing applications.
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Affiliation(s)
- Yoshihisa Ito
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
- School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yusuke Izawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
- School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Koki Kamiya
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
| | - Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
| | - Satoshi Fujii
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
| | - Hisatoshi Mimura
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
| | - Norihisa Miki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
- Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan; (Y.I.); (Y.I.); (T.O.); (K.K.); (N.M.); (S.F.); (H.M.); (N.M.)
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Correspondence: ; Tel.: +81-3-5841-7056; Fax: +81-3-5841-7104
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13
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Yin YD, Zhang L, Leng XZ, Gu ZY. Harnessing biological nanopore technology to track chemical changes. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Pauliukaite R, Voitechovič E. Multisensor Systems and Arrays for Medical Applications Employing Naturally-Occurring Compounds and Materials. SENSORS (BASEL, SWITZERLAND) 2020; 20:E3551. [PMID: 32585936 PMCID: PMC7349305 DOI: 10.3390/s20123551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 12/14/2022]
Abstract
The significant improvement of quality of life achieved over the last decades has stimulated the development of new approaches in medicine to take into account the personal needs of each patient. Precision medicine, providing healthcare customization, opens new horizons in the diagnosis, treatment and prevention of numerous diseases. As a consequence, there is a growing demand for novel analytical devices and methods capable of addressing the challenges of precision medicine. For example, various types of sensors or their arrays are highly suitable for simultaneous monitoring of multiple analytes in complex biological media in order to obtain more information about the health status of a patient or to follow the treatment process. Besides, the development of sustainable sensors based on natural chemicals allows reducing their environmental impact. This review is concerned with the application of such analytical platforms in various areas of medicine: analysis of body fluids, wearable sensors, drug manufacturing and screening. The importance and role of naturally-occurring compounds in the development of electrochemical multisensor systems and arrays are discussed.
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Affiliation(s)
- Rasa Pauliukaite
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanoriu Ave. 231, LT-02300 Vilnius, Lithuania;
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15
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Sun K, Ju Y, Chen C, Zhang P, Sawyer E, Luo Y, Geng J. Single‐Molecule Interaction of Peptides with a Biological Nanopore for Identification of Protease Activity. SMALL METHODS 2020. [DOI: 10.1002/smtd.201900892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Yuan Ju
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Chuan Chen
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Peng Zhang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Erica Sawyer
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
- Department of Biochemistry St. Lawrence University Canton NY 13617 USA
| | - Youfu Luo
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
| | - Jia Geng
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu Sichuan 610041 P. R. China
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16
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Omersa N, Aden S, Kisovec M, Podobnik M, Anderluh G. Design of Protein Logic Gate System Operating on Lipid Membranes. ACS Synth Biol 2020; 9:316-328. [PMID: 31995709 PMCID: PMC7308068 DOI: 10.1021/acssynbio.9b00340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Lipid membranes are becoming increasingly popular in synthetic biology due to their biophysical properties and crucial role in communication between different compartments. Several alluring protein-membrane sensors have already been developed, whereas protein logic gates designs on membrane-embedded proteins are very limited. Here we demonstrate the construction of a two-level protein-membrane logic gate with an OR-AND logic. The system consists of an engineered pH-dependent pore-forming protein listeriolysin O and its DARPin-based inhibitor, conjugated to a lipid vesicle membrane. The gate responds to low pH and removal of the inhibitor from the membrane either by switching to a reducing environment, protease cleavage, or any other signal depending on the conjugation chemistry used for inhibitor attachment to the membrane. This unique protein logic gate vesicle system advances generic sensing and actuator platforms used in synthetic biology and could be utilized in drug delivery.
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Affiliation(s)
- Neža Omersa
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Saša Aden
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Matic Kisovec
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
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17
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Ding T, Chen AK, Lu Z. The applications of nanopores in studies of proteins. Sci Bull (Beijing) 2019; 64:1456-1467. [PMID: 36659703 DOI: 10.1016/j.scib.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023]
Abstract
Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.
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Affiliation(s)
- Taoli Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Zuhong Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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18
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D Y Bandara YMN, Tang J, Saharia J, Rogowski LW, Ahn CW, Kim MJ. Characterization of Flagellar Filaments and Flagellin through Optical Microscopy and Label-Free Nanopore Responsiveness. Anal Chem 2019; 91:13665-13674. [PMID: 31525946 DOI: 10.1021/acs.analchem.9b02874] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In this study, we investigated the translocation characteristics of flagellar filaments (Salmonella typhimurium) and flagellin subunits through silicon nitride nanopores in tandem with optical microscopy analysis. Even though untagged flagella are dark to the optical method, the label-free nature of the nanopore sensor allows it to characterize both tagged (Cy3) and pristine forms of flagella (including real-time developments). Flagella were depolymerized to flagellin subunits at ∼65 °C (most commonly reported temperature), ∼70 °C, ∼75 °C, and ∼80 °C to investigate the effect of temperature (Tdepol) on depolymerization. The change in conductance (ΔG) profiles corresponding to Tdepol ∼65 °C and ∼70 °C were bracketed within the flagellin monomer profile whereas those of ∼75 °C and ∼80 °C extended beyond this profile, suggesting a change to the native protein state. The molecular radius calculated from the excluded electrolyte volume of flagellin through nanopore-based ΔG characteristics for each Tdepol of ∼65 °C, ∼70 °C, ∼75 °C, and ∼80 °C yielded ∼4.2 ± 0.2 nm, ∼4.3 ± 0.3 nm, ∼4.1 ± 0.2 nm, and ∼4.7 ± 0.5 nm, respectively. This, along with ΔG (plateaued values) and translocation time profiles, points to the possibility of flagellin misfolding at ∼80 °C.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Jiannan Tang
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Jugal Saharia
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Louis William Rogowski
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Chi Won Ahn
- Nano-Materials Laboratory , National NanoFab Center , Daejeon 34141 , Republic of Korea
| | - Min Jun Kim
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
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19
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Misawa N, Osaki T, Takeuchi S. Membrane protein-based biosensors. J R Soc Interface 2019; 15:rsif.2017.0952. [PMID: 29669891 DOI: 10.1098/rsif.2017.0952] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Affiliation(s)
- Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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20
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Omersa N, Podobnik M, Anderluh G. Inhibition of Pore-Forming Proteins. Toxins (Basel) 2019; 11:E545. [PMID: 31546810 PMCID: PMC6784129 DOI: 10.3390/toxins11090545] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/27/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022] Open
Abstract
Perforation of cellular membranes by pore-forming proteins can affect cell physiology, tissue integrity, or immune response. Since many pore-forming proteins are toxins or highly potent virulence factors, they represent an attractive target for the development of molecules that neutralize their actions with high efficacy. There has been an assortment of inhibitors developed to specifically obstruct the activity of pore-forming proteins, in addition to vaccination and antibiotics that serve as a plausible treatment for the majority of diseases caused by bacterial infections. Here we review a wide range of potential inhibitors that can specifically and effectively block the activity of pore-forming proteins, from small molecules to more specific macromolecular systems, such as synthetic nanoparticles, antibodies, antibody mimetics, polyvalent inhibitors, and dominant negative mutants. We discuss their mechanism of inhibition, as well as advantages and disadvantages.
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Affiliation(s)
- Neža Omersa
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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21
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Pham B, Eron SJ, Hill ME, Li X, Fahie MA, Hardy JA, Chen M. A Nanopore Approach for Analysis of Caspase-7 Activity in Cell Lysates. Biophys J 2019; 117:844-855. [PMID: 31427065 DOI: 10.1016/j.bpj.2019.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Caspases are an important protease family that coordinate inflammation and programmed cell death. Two closely related caspases, caspase-3 and caspase-7, exhibit largely overlapping substrate specificities. Assessing their proteolytic activities individually has therefore proven extremely challenging. Here, we constructed an outer membrane protein G (OmpG) nanopore with a caspase substrate sequence DEVDG grafted into one of the OmpG loops. Cleavage of the substrate sequence in the nanopore by caspase-7 generated a characteristic signal in the current recording of the OmpG nanopore that allowed the determination of the activity of caspase-7 in Escherichia coli cell lysates. Our approach may provide a framework for the activity-based profiling of proteases that share highly similar substrate specificity spectrums.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Maureen E Hill
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Xin Li
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts.
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22
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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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23
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Wang H, Kasianowicz JJ, Robertson JWF, Poster DL, Ettedgui J. A comparison of ion channel current blockades caused by individual poly(ethylene glycol) molecules and polyoxometalate nanoclusters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:83. [PMID: 31250227 DOI: 10.1140/epje/i2019-11838-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous nanometer-scale pores have been used to detect and physically characterize many different types of analytes at the single-molecule limit. The method is based on the ability to measure the transient reduction in the ionic channel conductance caused by molecules that partition into the pore. The distribution of blockade depth amplitudes and residence times of the analytes in the pore are used to physically and chemically characterize them. Here we compare the current blockade events caused by flexible linear polymers of ethylene glycol (PEGs) and structurally well-defined tungsten polyoxymetallate nanoparticles in the nanopores formed by Staphylococcus aureusα-hemolysin and Aeromonas hydrophila aerolysin. Surprisingly, the variance in the ionic current blockade depth values for the relatively rigid metallic nanoparticles is much greater than that for the flexible PEGs, possibly because of multiple charged states of the polyoxymetallate clusters.
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Affiliation(s)
- Haiyan Wang
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Shenzhen Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, 508060, Shenzhen, China
| | - John J Kasianowicz
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA.
- Columbia University, Department of Applied Physics Applied Mathematics, 10027, New York, NY, USA.
| | - Joseph W F Robertson
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Dianne L Poster
- National Institute of Standards and Technology, Material Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Jessica Ettedgui
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Columbia University, Department of Chemical Engineering, 10027, New York, NY, USA
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24
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Saharia J, Bandara YMNDY, Goyal G, Lee JS, Karawdeniya BI, Kim MJ. Molecular-Level Profiling of Human Serum Transferrin Protein through Assessment of Nanopore-Based Electrical and Chemical Responsiveness. ACS NANO 2019; 13:4246-4254. [PMID: 30844233 DOI: 10.1021/acsnano.8b09293] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we investigated the voltage and pH responsiveness of human serum transferrin (hSTf) protein using silicon nitride (Si xN y) nanopores. The Fe(III)-rich holo form of hSTf was dominant when pH > pI, while the Fe(III)-free apo form was dominant when pH < pI. The translocations of hSTf were purely in an electrophoretic sense, thus depended on its pI and the solution pH. With increasing voltage, voltage driven protein unfolding became prominent which was indicated by the trends associated with change in conductance, due to hSTf translocation, and in the excluded electrolyte volume. Additionally, analysis of the translocation events of the pure apo form of hSTf showed a clear difference in the event population compared to that of the holo form. The results obtained demonstrate the successful application of nanopore devices to distinguish between the holo and apo forms of hSTf in a mixture and to analyze its folding and unfolding phenomenon over a range of pH and applied voltages.
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Y M Nuwan D Y Bandara
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | - Gaurav Goyal
- Department of Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Jung Soo Lee
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
| | | | - Min Jun Kim
- Department of Mechanical Engineering , Southern Methodist University , Dallas , Texas 75275 , United States
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25
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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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26
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Harrington L, Alexander LT, Knapp S, Bayley H. Single-Molecule Protein Phosphorylation and Dephosphorylation by Nanopore Enzymology. ACS NANO 2019; 13:633-641. [PMID: 30588793 DOI: 10.1021/acsnano.8b07697] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reversible protein phosphorylation plays a crucial and ubiquitous role in the control of almost all cellular processes. The interplay of protein kinases and phosphatases acting in opposition ensures tight dynamic control of protein phosphorylation states within the cell. Previously, engineered α-hemolysin pores bearing kinase substrate peptides have been developed as single-molecule stochastic sensors for protein kinases. Here, we have used these pores to observe, label-free, the phosphorylation and dephosphorylation of a single substrate molecule. Further, we investigated the effect of Mg2+ and Mn2+ upon substrate and product binding and found that Mn2+ relaxes active-site specificity toward nucleotides and enhances product binding. In doing so, we demonstrate the power and versatility of nanopore enzymology to scrutinize a critical post-translational modification.
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Affiliation(s)
- Leon Harrington
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Leila T Alexander
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Hagan Bayley
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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27
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Wang J, Yang J, Ying YL, Long YT. Nanopore-Based Confined Spaces for Single-Molecular Analysis. Chem Asian J 2019; 14:389-397. [PMID: 30548206 DOI: 10.1002/asia.201801648] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Indexed: 11/07/2022]
Abstract
The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.
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Affiliation(s)
- Jiajun Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yang
- 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
| | - 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
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28
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Real-Time Monitoring of a Botulinum Neurotoxin Using All-Carbon Nanotube-Based Field-Effect Transistor Devices. SENSORS 2018; 18:s18124235. [PMID: 30513867 PMCID: PMC6308983 DOI: 10.3390/s18124235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 02/01/2023]
Abstract
The possibility of exposure to botulinum neurotoxin (BoNT), a powerful and potential bioterrorism agent, is considered to be ever increasing. The current gold-standard assay, live-mouse lethality, exhibits high sensitivity but has limitations including long assay times, whereas other assays evince rapidity but lack factors such as real-time monitoring or portability. In this study, we aimed to devise a novel detection system that could detect BoNT at below-nanomolar concentrations in the form of a stretchable biosensor. We used a field-effect transistor with a p-type channel and electrodes, along with a channel comprising aligned carbon nanotube layers to detect the type E light chain of BoNT (BoNT/E-Lc). The detection of BoNT/E-Lc entailed observing the cleavage of a unique peptide and the specific bonding between BoNT/E-Lc and antibody BoNT/E-Lc (Anti-BoNT/E-Lc). The unique peptide was cleaved by 60 pM BoNT/E-Lc; notably, 52 fM BoNT/E-Lc was detected within 1 min in the device with the antibody in the bent state. These results demonstrated that an all-carbon nanotube-based device (all-CNT-based device) could be produced without a complicated fabrication process and could be used as a biosensor with high sensitivity, suggesting its potential development as a wearable BoNT biosensor.
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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Wang Y, Gu LQ, Tian K. The aerolysin nanopore: from peptidomic to genomic applications. NANOSCALE 2018; 10:13857-13866. [PMID: 29998253 PMCID: PMC6157726 DOI: 10.1039/c8nr04255a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aerolysin pore (ARP) is a newly emerging nanopore that has been extensively used for peptide and protein sensing. Recently, several groups have explored the application of ARP in detecting genetic and epigenetic markers. This brief review summarizes the current applications of ARP, progressing from peptidomic to genomic detection; the recently reported site-directed mutagenesis of ARP; and new genomic DNA sensing approaches, and their advantages and disadvantages. This review will also discuss the perspectives and future applications of ARP for nucleic acid sequencing and biomolecule sensing.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
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31
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Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nat Commun 2018; 9:2823. [PMID: 30026547 PMCID: PMC6053387 DOI: 10.1038/s41467-018-05108-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/05/2018] [Indexed: 12/05/2022] Open
Abstract
Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing. Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.
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Wang YQ, Li MY, Qiu H, Cao C, Wang MB, Wu XY, Huang J, Ying YL, Long YT. Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis. Anal Chem 2018; 90:7790-7794. [PMID: 29882404 DOI: 10.1021/acs.analchem.8b01473] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.
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Affiliation(s)
- 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
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures , Nanjing University of Aeronautics and Astronautics , Nanjing , 210016 , P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Ming-Bo Wang
- School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Xue-Yuan Wu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Jin Huang
- School of Pharmacy , 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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ZHOU S, TANG P, WANG YJ, WANG L, WANG DQ. Applications of Nanopore Sensing in Detection of Toxic Molecules. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61089-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Li S, Cao C, Yang J, Long YT. Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore. ChemElectroChem 2018. [DOI: 10.1002/celc.201800288] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuang Li
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road 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; 130 Meilong Road Shanghai 200237 P.R. China
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35
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Zhou B, Wang YQ, Cao C, Li DW, Long YT. Monitoring disulfide bonds making and breaking in biological nanopore at single molecule level. Sci China Chem 2018. [DOI: 10.1007/s11426-018-9231-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Cao C, Long YT. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis. Acc Chem Res 2018; 51:331-341. [PMID: 29364650 DOI: 10.1021/acs.accounts.7b00143] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.
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Affiliation(s)
- Chan Cao
- 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
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37
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Wang Y, Tian K, Du X, Shi RC, Gu LQ. Remote Activation of a Nanopore for High-Performance Genetic Detection Using a pH Taxis-Mimicking Mechanism. Anal Chem 2017; 89:13039-13043. [PMID: 29183111 PMCID: PMC6174115 DOI: 10.1021/acs.analchem.7b03979] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerolysin protein pore has been widely used for sensing peptides and proteins. However, only a few groups explored this nanopore for nucleic acids detection. The challenge is the extremely low capture efficiency for nucleic acids (>10 bases), which severely lowers the sensitivity of an aerolysin-based genetic biosensor. Here we reported a simple and easy-to-operate approach to noncovalently transform aerolysin into a highly nucleic acids-sensitive nanopore. Through a remote pH-modulation mechanism, we simply lower the pH on one side of the pore, then aerolysin is immediately "activated" and enabled to capture target DNA/RNA efficiently from the opposite side of the pore. This mechanism also decelerates DNA translocation, a desired property for sequencing and gene detection, allowing temporal separation of DNAs in different lengths. This method provides insight into the nanopore engineering for biosensing, making aerolysin applicable in genetic and epigenetic detections of long nucleic acids.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiao Du
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Rui-Cheng Shi
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, United States
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38
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YANG J, LI S, WU XY, LONG YT. Development of Biological Nanopore Technique in Non-gene Sequencing Application. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61053-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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39
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Zhang X, Zhang D, Zhao C, Tian K, Shi R, Du X, Burcke AJ, Wang J, Chen SJ, Gu LQ. Nanopore electric snapshots of an RNA tertiary folding pathway. Nat Commun 2017; 8:1458. [PMID: 29133841 PMCID: PMC5684407 DOI: 10.1038/s41467-017-01588-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/29/2017] [Indexed: 12/22/2022] Open
Abstract
The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates. By identifying the nanopore signatures and measuring their time-dependent populations, we can “visualize” a series of kinetically important intermediates, track the kinetics of their inter-conversions, and derive the RNA pseudoknot folding pathway. This approach can potentially be developed into a single-molecule toolbox to investigate the biophysical mechanisms of RNA folding and unfolding, its interactions with ligands, and its functions. While RNA folding is critical for its function, study of this process is challenging. Here, the authors combine nanopore single-molecule manipulation with theoretical analysis to follow the folding of an RNA pseudoknot, monitoring the intermediate states and the kinetics of their interconversion.
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Affiliation(s)
- Xinyue Zhang
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dong Zhang
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA
| | - Chenhan Zhao
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA
| | - Kai Tian
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Xiao Du
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Andrew J Burcke
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Jing Wang
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Li-Qun Gu
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA. .,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.
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40
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Cao C, Yu J, Li MY, Wang YQ, Tian H, Long YT. Direct Readout of Single Nucleobase Variations in an Oligonucleotide. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13. [PMID: 29024329 DOI: 10.1002/smll.201702011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yu
- 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
| | - 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
| | - He Tian
- 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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Chavis AE, Brady KT, Hatmaker GA, Angevine CE, Kothalawala N, Dass A, Robertson JWF, Reiner JE. Single Molecule Nanopore Spectrometry for Peptide Detection. ACS Sens 2017; 2:1319-1328. [PMID: 28812356 DOI: 10.1021/acssensors.7b00362] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sensing and characterization of water-soluble peptides is of critical importance in a wide variety of bioapplications. Single molecule nanopore spectrometry (SMNS) is based on the idea that one can use biological protein nanopores to resolve different sized molecules down to limits set by the blockade duration and noise. Previous work has shown that this enables discrimination between polyethylene glycol (PEG) molecules that differ by a single monomer unit. This paper describes efforts to extend SMNS to a variety of biologically relevant, water-soluble peptides. We describe the use of Au25(SG)18 clusters, previously shown to improve PEG detection, to increase the on- and off-rate of peptides to the pore. In addition, we study the role that fluctuations play in the single molecule nanopore spectrometry (SMNS) methodology and show that modifying solution conditions to increase peptide flexibility (via pH or chaotropic salt) leads to a nearly 2-fold reduction in the current blockade fluctuations and a corresponding narrowing of the peaks in the blockade distributions. Finally, a model is presented that connects the current blockade depths to the mass of the peptides, which shows that our enhanced SMNS detection improves the mass resolution of the nanopore sensor more than 2-fold for the largest cationic peptides studied.
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Affiliation(s)
- Amy E. Chavis
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kyle T. Brady
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Grace A. Hatmaker
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Christopher E. Angevine
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nuwan Kothalawala
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Amala Dass
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Joseph W. F. Robertson
- Physical
Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8120, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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42
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Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nat Protoc 2017; 12:1901-1911. [PMID: 28837133 DOI: 10.1038/nprot.2017.077] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nanopore techniques offer the possibility to study biomolecules at the single-molecule level in a low-cost, label-free and high-throughput manner. By analyzing the level, duration and frequency of ionic current blockades, information regarding the structural conformation, mass, length and concentration of single molecules can be obtained in physiological conditions. Aerolysin monomers assemble into small pores that provide a confined space for effective electrochemical control of a single molecule interacting with the pore, which significantly improves the temporal resolution of this technique. In comparison with other reported protein nanopores, aerolysin maintains its functional stability in a wide range of pH conditions, which allows for the direct discrimination of oligonucleotides between 2 and 10 nt in length and the monitoring of the stepwise cleavage of oligonucleotides by exonuclease I (Exo I) in real time. This protocol describes the process of activating proaerolysin using immobilized trypsin to obtain the aerolysin monomer, the construction of a lipid membrane and the insertion of an individual aerolysin nanopore into this membrane. A step-by-step description is provided of how to perform single-oligonucleotide analyses and how to process the acquired data. The total time required for this protocol is ∼3 d.
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43
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Wang S, Zhou Z, Zhao Z, Zhang H, Haque F, Guo P. Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states. Biomaterials 2017; 126:10-17. [PMID: 28237908 PMCID: PMC5421631 DOI: 10.1016/j.biomaterials.2017.01.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
Abstract
Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the passage of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures. Utilizing single channel conductance assay and optical single molecule imaging, we observed translocation of peptides and quantitatively analyzed the dynamics of peptide oligomeric states in real-time at single molecule level. The oxidative and the reduced states of peptides were clearly differentiated based on their characteristic electronic signatures. A similar Gibbs free energy (ΔG0) was obtained when different concentrations of substrates were applied, suggesting that the use of SPP1 nanopore for real-time quantification of peptide oligomeric states is feasible. With the intrinsic nature of size and conjugation amenability, the SPP1 nanopore has the potential for development into a tool for the quantification of peptide and protein structures in real time.
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Affiliation(s)
- Shaoying Wang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhi Zhou
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zhengyi Zhao
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Hui Zhang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Farzin Haque
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.
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44
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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Affiliation(s)
- Toshihisa Osaki
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
| | - Shoji Takeuchi
- Artificial Cell
Membrane
Systems Group, Kanagawa Academy of Science and Technology, 3-2-1
Sakado, Takatsu, 213-0012 Kawasaki, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, 153-8505 Tokyo, Japan
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Fahie MA, Yang B, Pham B, Chen M. Tuning the selectivity and sensitivity of an OmpG nanopore sensor by adjusting ligand tether length. ACS Sens 2016; 1:614-622. [PMID: 27500277 DOI: 10.1021/acssensors.6b00014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have previously shown that a biotin ligand tethered to the rim of an OmpG nanopore can be used to detect biotin-binding proteins. Here, we investigate the effect of the length of the polyethylene glycol tether on the nanopore's sensitivity and selectivity. When the tether length was increased from 2 to 45 ethylene repeats, sensitivity decreased substantially for a neutral protein streptavidin and slightly for a positively charged protein (avidin). In addition, we found that two distinct avidin binding conformations were possible when using a long tether. These conformations were sensitive to the salt concentration and applied voltage. Finally, a longer tether resulted in reduced sensitivity due to slower association for a monoclonal anti-biotin antibody. Our results highlight the importance of electrostatic, electroosmotic and electrophoretic forces on nanopore binding kinetics and sensor readout.
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Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bib Yang
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bach Pham
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Zhou S, Wang L, Chen X, Guan X. Label-free nanopore single-molecule measurement of trypsin activity. ACS Sens 2016; 1:607-613. [PMID: 29130069 DOI: 10.1021/acssensors.6b00043] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trypsin is the most important digestive enzyme produced in the pancreas, and is a useful biomarker for pancreatitis. In this work, a rapid and sensitive method for the quantitative determination of trypsin activity is developed by using a biological alpha-hemolysin protein nanopore. Due to its much larger molecular diameter than the narrow pore constriction, trypsin itself cannot transport through the alpha-hemolysin channel. Hence, an indirect trypsin detection method is developed by monitoring its proteolytic cleavage of a lysine-containing peptide substrate. Based on the current modulations produced by the translocation of the substrate degradation products in the nanopore, the activity levels of trypsin could be determined. The method is rapid and highly sensitive, with picomolar concentrations of trypsin detected in minutes. In addition, the effects of cation and temperature on the sensor sensitivity, trypsin inhibition, and serum sample analysis are also investigated.
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Affiliation(s)
- Shuo Zhou
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Liang Wang
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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Schmidt J. Membrane platforms for biological nanopore sensing and sequencing. Curr Opin Biotechnol 2016; 39:17-27. [PMID: 26773300 DOI: 10.1016/j.copbio.2015.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
In the past two decades, biological nanopores have been developed and explored for use in sensing applications as a result of their exquisite sensitivity and easily engineered, reproducible, and economically manufactured structures. Nanopore sensing has been shown to differentiate between highly similar analytes, measure polymer size, detect the presence of specific genes, and rapidly sequence nucleic acids translocating through the pore. Devices featuring protein nanopores have been limited in part by the membrane support containing the nanopore, the shortcomings of which have been addressed in recent work developing new materials, approaches, and apparatus resulting in membrane platforms featuring automatability and increased robustness, lifetime, and measurement throughput.
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Affiliation(s)
- Jacob Schmidt
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA.
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50
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Blasutig IM. Miniaturization: The future of laboratory medicine. Clin Biochem 2016; 49:2-3. [DOI: 10.1016/j.clinbiochem.2015.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/10/2015] [Accepted: 11/12/2015] [Indexed: 10/22/2022]
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