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Zhao C, Wang Y, Chen C, Zhu Y, Miao Z, Mou X, Yuan W, Zhang Z, Li K, Chen M, Liang W, Zhang M, Miao W, Dong Y, Deng D, Wu J, Ke B, Bao R, Geng J. Direct and Continuous Monitoring of Multicomponent Antibiotic Gentamicin in Blood at Single-Molecule Resolution. ACS NANO 2024; 18:9137-9149. [PMID: 38470845 DOI: 10.1021/acsnano.4c00302] [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: 03/14/2024]
Abstract
Point-of-care monitoring of small molecules in biofluids is crucial for clinical diagnosis and treatment. However, the inherent low degree of recognition of small molecules and the complex composition of biofluids present significant obstacles for current detection technologies. Although nanopore sensing excels in the analysis of small molecules, the direct detection of small molecules in complex biofluids remains a challenge. In this study, we present a method for sensing the small molecule drug gentamicin in whole blood based on the mechanosensitive channel of small conductance in Pseudomonas aeruginosa (PaMscS) nanopore. PaMscS can directly detect gentamicin and distinguish its main components with only a monomethyl difference. The 'molecular sieve' structure of PaMscS enables the direct measurement of gentamicin in human whole blood within 10 min. Furthermore, a continuous monitoring device constructed based on PaMscS achieved continuous monitoring of gentamicin in live rats for approximately 2.5 h without blood consumption, while the drug components can be analyzed in situ. This approach enables rapid and convenient drug monitoring with single-molecule level resolution, which can significantly lower the threshold for drug concentration monitoring and promote more efficient drug use. Moreover, this work also lays the foundation for the future development of continuous monitoring technology with single-molecule level resolution in the living body.
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Affiliation(s)
- Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Chen Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Yibo Zhu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhuang Miao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhihao Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Weibo Liang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenqian Miao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuhan Dong
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
| | - Dong Deng
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, Sichuan, 610041 China
| | - Jianping Wu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Bowen Ke
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 610500, China
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2
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Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S, Suzuki H, Kambara F, Fukasawa G, Cooney A, Di Michele L, Elani Y, Matsuura T, Kawano R. Lipid vesicle-based molecular robots. LAB ON A CHIP 2024; 24:996-1029. [PMID: 38239102 PMCID: PMC10898420 DOI: 10.1039/d3lc00860f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.
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Affiliation(s)
- Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoji Iwabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Misa Yamaji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Shoko Fujita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Harune Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Fumika Kambara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
| | - Genki Fukasawa
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Aileen Cooney
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK
- FabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi, Tokyo185-8588, Japan.
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3
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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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4
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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5
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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6
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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7
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Huo MZ, Hu ZL, Ying YL, Long YT. Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore. Proteomics 2021; 22:e2100041. [PMID: 34545670 DOI: 10.1002/pmic.202100041] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/08/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022]
Abstract
Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.
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Affiliation(s)
- Ming-Zhu Huo
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Zheng-Li Hu
- Shenzhen Research Institute of Nanjing University, Shenzhen, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
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8
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Miyagi M, Takiguchi S, Hakamada K, Yohda M, Kawano R. Single polypeptide detection using a translocon EXP2 nanopore. Proteomics 2021; 22:e2100070. [PMID: 34411416 DOI: 10.1002/pmic.202100070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023]
Abstract
DNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites, and describe its pore-forming properties in the lipid bilayer. EXP2 mainly formed a nanopore with a diameter of 2.5 nm assembled from 7 monomers. Using the EXP2 nanopore allowed us to detect poly-L-lysine (PLL) at a single-molecule level. Furthermore, the EXP2 nanopore has sufficient resolution to distinguish the difference in molecular weight between two individual PLL, long PLL (Mw: 30,000-70,000) and short PLL (Mw: 10,000). Our results contribute to the accumulation of information for peptide-detectable nanopores.
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Affiliation(s)
- Mitsuki Miyagi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Sotaro Takiguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Kazuaki Hakamada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
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9
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Li X, Song G, Dou L, Yan S, Zhang M, Yuan W, Lai S, Jiang X, Li K, Sun K, Zhao C, Geng J. The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing. NANOSCALE 2021; 13:11827-11835. [PMID: 34152351 DOI: 10.1039/d0nr08729g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hairpin structures play an essential role in DNA replication, transcription, and recombination. Single-molecule studies enable the real-time measurement and observation of the energetics and dynamics of hairpin structures, including folding and DNA-protein interactions. Nanopore sensing is emerging as a powerful tool for DNA sensing and sequencing, and previous research into hairpins using an α-hemolysin (α-HL) nanopore suggested that hairpin DNA enters from its stem side. In this work, the translocation and interaction of hairpin and dumbbell DNA samples with varying stems, loops, and toeholds were investigated systematically using a Mycobacterium smegmatis porin A (MspA) nanopore. It was found that these DNA constructs could translocate through the pore under a bias voltage above +80 mV, and blockage events with two conductance states could be observed. The events of the lower blockage were correlated with the loop size of the hairpin or dumbbell DNA (7 nt to 25 nt), which could be attributed to non-specific collisions with the pore, whereas the dwell time of events with the higher blockage were correlated with the stem length, thus indicating effective translocation. Furthermore, dumbbell DNA with and without a stem opening generated different dwell times when driven through the MspA nanopore. Finally, a new strategy based on the dwell time difference was developed to detect single nucleotide polymorphisms (SNPs). These results demonstrated that the unzipping behaviors and DNA-protein interactions of hairpin and dumbbell DNA could be revealed using nanopore technology, and this could be further developed to create sensors for the secondary structures of nucleic acids.
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Affiliation(s)
- Xinqiong 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.
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10
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Sun K, Chen P, Yan S, Yuan W, Wang Y, Li X, Dou L, Zhao C, Zhang J, Wang Q, Fu Z, Wei L, Xin Z, Tang Z, Yan Y, Peng Y, Ying B, Chen J, Geng J. Ultrasensitive Nanopore Sensing of Mucin 1 and Circulating Tumor Cells in Whole Blood of Breast Cancer Patients by Analyte-Triggered Triplex-DNA Release. ACS APPLIED MATERIALS & INTERFACES 2021; 13:21030-21039. [PMID: 33905228 DOI: 10.1021/acsami.1c03538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The characterization of circulating tumor cells (CTCs) by liquid biopsy has a great potential for precision medicine in oncology. Here, a universal and tandem logic-based strategy is developed by combining multiple nanomaterials and nanopore sensing for the determination of mucin 1 protein (MUC1) and breast cancer CTCs in real samples. The strategy consists of analyte-triggered signal conversion, cascaded amplification via nanomaterials including copper sulfide nanoparticles (CuS NPs), silver nanoparticles (Ag NPs), and biomaterials including DNA hydrogel and DNAzyme, and single-molecule-level detection by nanopore sensing. The amplification of the non-DNA nanomaterial gives this method considerable stability, significantly lowers the limit of detection (LOD), and enhances the anti-interference performance for complicated samples. As a result, the ultrasensitive detection of MUC1 could be achieved in the range of 0.0005-0.5 pg/mL, with an LOD of 0.1 fg/mL. Moreover, we further tested MUC1 as a biomarker for the clinical diagnosis of breast cancer CTCs under double-blind conditions on the basis of this strategy, and MCF-7 cells could be accurately detected in the range from 5 to 2000 cells/mL, with an LOD of 2 cells/mL within 6 h. The detection results of the 19 clinical samples were highly consistent with those of the clinical pathological sections, nuclear magnetic resonance imaging, and color ultrasound. These results demonstrate the validity and reliability of our method and further proved the feasibility of MUC1 as a clinical diagnostic biomarker for CTCs.
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Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Weidan Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Linqin Dou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jianfu Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Qiang Wang
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhoukai Fu
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Long Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhaodan Xin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Zhuoyun Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yiman Peng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jie Chen
- Department of Breast Surgery, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
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11
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Oh S, Lee MK, Chi SW. Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores. Chem Sci 2021; 12:5883-5891. [PMID: 34168813 PMCID: PMC8179679 DOI: 10.1039/d1sc00386k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.
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Affiliation(s)
- Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
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12
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Zhang X, Dou L, Zhang M, Wang Y, Jiang X, Li X, Wei L, Chen Y, Zhou C, Geng J. Real-time sensing of neurotransmitters by functionalized nanopores embedded in a single live cell. MOLECULAR BIOMEDICINE 2021; 2:6. [PMID: 35006433 PMCID: PMC8607392 DOI: 10.1186/s43556-021-00026-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/12/2021] [Indexed: 02/08/2023] Open
Abstract
Interface between neuron cells and biomaterials is the key to real-time sensing, transmitting and manipulating of neuron activities, which are the long-term pursue of scientists and gain intense research focus recently. It is of great interest to develop a sensor with exquisite sensitivity and excellent selectivity for real-time monitoring neurotransmitters transport through single live cell. Sensing techniques including electrode-based methods, optogenetics, and nanowire cell penetration systems have been developed to monitor the neuron activities. However, their biocompatibilities remain a challenge. Protein nanopores with membrane compatibility and lumen tunability provide real-time, single-molecule sensitivities for biosensing of DNA, RNA, peptides and small molecules. In this study, an engineered protein nanopore MspA (Mycobacterium smegmatis porin A) through site-directed mutation with histidine selectively bind with Cu2+ in its internal lumen. Chelation of neurotransmitters such as L-glutamate (L-Glu), dopamine (DA) and norepinephrine (NE) with the Cu2+ creates specific current signals, showing different transient current blockade and dwell time in single channel electrophysiological recording. Furthermore, the functionalized M2MspA-N91H nanopores have been embedded in live HEK293T cell membrane for real-time, in situ monitoring of extracellular L-glutamate translocating through the nanopore. This biomimetic neurotransmitter nanopore has provided a new platform for future development of neuron sensors, drug carrier and artificial synapse.
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Affiliation(s)
- Xialin Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Linqin Dou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Xin Jiang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Long Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Yuejia 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
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, 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.
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13
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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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14
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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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15
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Zhuang X, Wu Q, Zhang A, Liao L, Fang B. Single-molecule biotechnology for protein researches. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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