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Algharagholy LA, García-Suárez VM, Bardan KH. Robust nanotube-based nanosensor designed for the detection of explosive molecules. NANOSCALE ADVANCES 2024; 6:3553-3565. [PMID: 38989522 PMCID: PMC11232540 DOI: 10.1039/d4na00166d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/29/2024] [Indexed: 07/12/2024]
Abstract
The adequate determination and detection of explosive molecules is key to introducing improvements in areas related to safety, whose progress depends on an adequate and rapid determination of dangerous substances. To detect explosives down to the molecular level and accurately discriminate between different but somehow similar substances, it is necessary to design sensors that can differentiate them uniquely and efficiently. In this study, we present a new generation nanoscale sensor based on carbon nanotubes with an adapted nanopore shape that is capable of effectively discriminating between five types of explosive compounds (TATP, RDX, PENT, HMX and DNT). We show that the interaction of each compound with the walls of the nanotubes induces changes in transmission and current that allows clear differentiation of each type of molecule. Interestingly, the transport properties do not depend on the orientation of the molecules within the nanopore in most cases, making it a robust device with high reproducibility and stability. The results also show that these systems can lead to relatively high thermoelectric performances and, furthermore, the Seebeck coefficient can be used to discriminate between them.
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Affiliation(s)
- Laith A Algharagholy
- Department of Physics, College of Science, University of Sumer Al Rifaee Zip: 64005 Thi-Qar Iraq
| | | | - Kareem Hasan Bardan
- Department of Physics, College of Science, University of Sumer Al Rifaee Zip: 64005 Thi-Qar Iraq
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2
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Jia W, Ouyang Y, Zhang S, Du X, Zhang P, Huang S. Nanopore Signatures of Nucleoside Drugs. NANO LETTERS 2023; 23:9437-9444. [PMID: 37818841 DOI: 10.1021/acs.nanolett.3c02872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Nucleoside drugs, which are analogues of natural nucleosides, have been widely applied in the clinical treatment of viral infections and cancers. The development of nucleoside drugs, repurposing of existing drugs, and combined use of multiple drug types have made the rapid sensing of nucleoside drugs urgently needed. Nanopores are emerging single-molecule sensors that have high resolution to resolve even minor structural differences between chemical compounds. Here, an engineered Mycobacterium smegmatis porin A hetero-octamer was used to perform general nucleoside drug analysis. Ten nucleoside drugs were simultaneously detected and fully discriminated. An accuracy of >99.9% was consequently reported. This sensing capacity was further demonstrated in direct nanopore analysis of ribavirin buccal tablets, confirming its sensing reliability against complex samples and environments. No sample separation is needed, however, significantly minimizing the complexity of the measurement. This technique may inspire nanopore applications in pharmaceutical production and pharmacokinetics measurements.
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Affiliation(s)
- Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Yusheng Ouyang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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3
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [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: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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4
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da Silva AAR, da Silva Júnior JJ, Cavalcanti MIDS, Machado DC, Medeiros PL, Rodrigues CG. Alphatoxin Nanopore Detection of Aflatoxin, Ochratoxin and Fumonisin in Aqueous Solution. Toxins (Basel) 2023; 15:toxins15030183. [PMID: 36977074 PMCID: PMC10058818 DOI: 10.3390/toxins15030183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023] Open
Abstract
Mycotoxins are toxic and carcinogenic metabolites produced by groups of filamentous fungi that colonize food crops. Aflatoxin B1 (AFB1), ochratoxin A (OTA) and fumonisin B1 (FB1) are among the most relevant agricultural mycotoxins, as they can induce various toxic processes in humans and animals. To detect AFB1, OTA and FB1 in the most varied matrices, chromatographic and immunological methods are primarily used; however, these techniques are time-consuming and expensive. In this study, we demonstrate that unitary alphatoxin nanopore can be used to detect and differentiate these mycotoxins in aqueous solution. The presence of AFB1, OTA or FB1 inside the nanopore induces reversible blockage of the ionic current flowing through the nanopore, with distinct characteristics of blockage that are unique to each of the three toxins. The process of discrimination is based on the residual current ratio calculation and analysis of the residence time of each mycotoxin inside the unitary nanopore. Using a single alphatoxin nanopore, the mycotoxins could be detected at the nanomolar level, indicating that alphatoxin nanopore is a promising molecular tool for discriminatory analysis of mycotoxins in aqueous solution.
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Affiliation(s)
- Artur Alves Rodrigues da Silva
- Education and Health Center, Federal University of Campina Grande, Rua Aprígio Veloso, 882, Universitário, Campina Grande 58429-900, Brazil
- Postgraduate Program in Therapeutic Innovation, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Janilson José da Silva Júnior
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Maria Isabel dos Santos Cavalcanti
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Dijanah Cota Machado
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Paloma Lys Medeiros
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
| | - Claudio Gabriel Rodrigues
- Postgraduate Program in Therapeutic Innovation, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
- Department of Biophysics and Radiobiology, Federal University of Pernambuco, Avenida Professor Moraes Rego, s/n, Cidade Universitária, Recife 50670-901, Brazil
- Correspondence: ; Tel.: +55-81-2126-8535
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5
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Ghanem N, Kanagami N, Matsui T, Takeda K, Kaneko J, Shiraishi Y, Choe CA, Uchikubo‐Kamo T, Shirouzu M, Hashimoto T, Ogawa T, Matsuura T, Huang P, Yokoyama T, Tanaka Y. Chimeric mutants of staphylococcal hemolysin, which act as both one‐component and two‐component hemolysin, created by grafting the stem domain. FEBS J 2022; 289:3505-3520. [DOI: 10.1111/febs.16354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/03/2021] [Accepted: 01/12/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Nouran Ghanem
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Laboratory for Protein Functional and Structural Biology RIKEN Center for Biosystems Dynamics Research Yokohama Japan
| | - Natsuki Kanagami
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Takashi Matsui
- Graduate School of Life Sciences Tohoku University Sendai Japan
- School of Science Kitasato University Sagamihara Japan
| | - Kein Takeda
- Department of Microbial Biotechnology Graduate School of Agricultural Science Tohoku University Sendai Japan
| | - Jun Kaneko
- Department of Microbial Biotechnology Graduate School of Agricultural Science Tohoku University Sendai Japan
| | - Yasuyuki Shiraishi
- Pre‐Clinical Research Center Institute of Development, Aging and Cancer Tohoku University Sendai Japan
| | | | - Tomomi Uchikubo‐Kamo
- Laboratory for Protein Functional and Structural Biology RIKEN Center for Biosystems Dynamics Research Yokohama Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology RIKEN Center for Biosystems Dynamics Research Yokohama Japan
| | | | - Tomohisa Ogawa
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Department of Microbial Biotechnology Graduate School of Agricultural Science Tohoku University Sendai Japan
| | - Tomoaki Matsuura
- Department of Biotechnology Graduate School of Engineering Osaka University Suita Japan
| | - Po‐Ssu Huang
- Department of Bioengineering Stanford University CA USA
| | - Takeshi Yokoyama
- Graduate School of Life Sciences Tohoku University Sendai Japan
- Laboratory for Protein Functional and Structural Biology RIKEN Center for Biosystems Dynamics Research Yokohama Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences Tohoku University Sendai Japan
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6
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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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7
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Control of subunit stoichiometry in single-chain MspA nanopores. Biophys J 2022; 121:742-754. [PMID: 35101416 PMCID: PMC8943699 DOI: 10.1016/j.bpj.2022.01.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/18/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Transmembrane protein channels enable fast and highly sensitive detection of single molecules. Nanopore sequencing of DNA was achieved using an engineered Mycobacterium smegmatis porin A (MspA) in combination with a motor enzyme. Due to its favorable channel geometry, the octameric MspA pore exhibits the highest current level compared with other pore proteins. To date, MspA is the only protein nanopore with a published record of DNA sequencing. While widely used in commercial devices, nanopore sequencing of DNA suffers from significant base-calling errors due to stochastic events of the complex DNA-motor-pore combination and the contribution of up to five nucleotides to the signal at each position. Different mutations in specific subunits of a pore protein offer an enormous potential to improve nucleotide resolution and sequencing accuracy. However, individual subunits of MspA and other oligomeric protein pores are randomly assembled in vivo and in vitro, preventing the efficient production of designed pores with different subunit mutations. In this study, we converted octameric MspA into a single-chain pore by connecting eight subunits using peptide linkers. Lipid bilayer experiments demonstrated that single-chain MspA formed membrane-spanning channels and discriminated all four nucleotides identical to MspA produced from monomers in DNA hairpin experiments. Single-chain constructs comprising three, five, six, and seven connected subunits assembled to functional channels, demonstrating a remarkable plasticity of MspA to different subunit stoichiometries. Thus, single-chain MspA constitutes a new milestone in the optimization of MspA as a biosensor for DNA sequencing and many other applications by enabling the production of pores with distinct subunit mutations and pore diameters.
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8
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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9
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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10
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Schwieters MS, Mathieu-Gaedke M, Westphal M, Dalpke R, Dirksen M, Qi D, Grull M, Bick T, Taßler S, Sauer DF, Bonn M, Wendler P, Hellweg T, Beyer A, Gölzhäuser A, Schwaneberg U, Glebe U, Böker A. Protein Nanopore Membranes Prepared by a Simple Langmuir-Schaefer Approach. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102975. [PMID: 34643032 DOI: 10.1002/smll.202102975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Filtration through membranes with nanopores is typically associated with high transmembrane pressures and high energy consumption. This problem can be addressed by reducing the respective membrane thickness. Here, a simple procedure is described to prepare ultrathin membranes based on protein nanopores, which exhibit excellent water permeance, two orders of magnitude superior to comparable, industrially applied membranes. Furthermore, incorporation of either closed or open protein nanopores allows tailoring the membrane's ion permeability. To form such membranes, the transmembrane protein ferric hydroxamate uptake protein component A (FhuA) or its open-pore variant are assembled at the air-water interface of a Langmuir trough, compressed to a dense film, crosslinked by glutaraldehyde, and transferred to various support materials. This approach allows to prepare monolayer or multilayer membranes with a very high density of protein nanopores. Freestanding membranes covering holes up to 5 μm in diameter are visualized by atomic force microscopy (AFM), helium ion microscopy, and transmission electron microscopy. AFM PeakForce quantitative nanomechanical property mapping (PeakForce QNM) demonstrates remarkable mechanical stability and elastic properties of freestanding monolayer membranes with a thickness of only 5 nm. The new protein membrane can pave the way to energy-efficient nanofiltration.
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Affiliation(s)
- Magnus S Schwieters
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
- Polymer Engineering/Polymer Physics, Berlin Institute of Technology (TU Berlin), Ernst-Reuter-Platz 1, 10587, Berlin, Germany
| | - Maria Mathieu-Gaedke
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
- Chair of Polymer Materials and Polymer Technologies, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Michael Westphal
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Raphael Dalpke
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Maxim Dirksen
- Department of Physical and Biophysical Chemistry, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Daizong Qi
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Marco Grull
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Thomas Bick
- Department of Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Stephanie Taßler
- Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Gif-Sur-Yvette, Saint-Aubin, 91192, France
| | - Daniel F Sauer
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Petra Wendler
- Department of Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
| | - Thomas Hellweg
- Department of Physical and Biophysical Chemistry, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - André Beyer
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Armin Gölzhäuser
- Physics of Supramolecular Systems and Surfaces, Faculty of Physics, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials e.V., Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Ulrich Glebe
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
| | - Alexander Böker
- Fraunhofer Institute for Applied Polymer Research IAP, Geiselbergstr. 69, 14476, Potsdam-Golm, Germany
- Chair of Polymer Materials and Polymer Technologies, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam-Golm, Germany
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11
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Arora G, Maman P, Sharma A, Verma N, Puri V. Systemic Overview of Microstrip Patch Antenna's for Different Biomedical Applications. Adv Pharm Bull 2021; 11:439-449. [PMID: 34513618 PMCID: PMC8421620 DOI: 10.34172/apb.2021.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/16/2020] [Accepted: 06/30/2020] [Indexed: 02/01/2023] Open
Abstract
Timely diagnosis is the most important parameter for the detection and hindrance with tissues (infected). Many conventional techniques are used for the determination of the chronic disease like MRI, X-ray, mammography, ultrasound and other diagnosing methods. Nevertheless, they have some limitations. We epitomize between 4 and 34 % of all carcinogenic tissues are lacking because of weak, in adequate malignant/benign cancer tissue on the contrary. So, an effective alternative method is the valid concern in the field of medical right now. Imaging with the help of patch antenna to detect chronic disease like breast cancer, oxidative stress syndrome etc. it has been proved to be a suitable potential method, and there are many works in this area. All materials have different conductivity and permittivity. With the help of these antennas, a 3D tissue structure which has different conductivity and permittivity is modelled in high-frequency structure simulator through finite element method which resolves electromagnetic field values and a microstrip patch antenna operation process. As compared with conventional antennas, micro strip patch antennas have enhanced benefits and better prospects. An integrated Antenna plays an important or crucial role for supporting many applications in biomedical, commercial and in military fields. The Antenna designed for these applications should be wideband, not sensitive to the human body. In this present review, the precise application of the Antenna in different biomedical aspects is considered. Furthermore, the author has also discussed the analytical results using simulation models and experimental results for some of the significantdisease.
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Affiliation(s)
- Govind Arora
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | | | - Ameya Sharma
- Chitkara University School of Pharmacy, Chitkara University, Himachal Pradesh, India
| | - Nitin Verma
- Chitkara University School of Pharmacy, Chitkara University, Himachal Pradesh, India
| | - Vivek Puri
- Chitkara University School of Pharmacy, Chitkara University, Himachal Pradesh, India
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12
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Liu X, Feng W, Yao F, Zhang J, Ayesha R, Chen T, Shi X, Qiao X, Ma L, Yu S, Kang XF. Biomimetic Molecular Clamp Nanopores for Simultaneous Quantifications of NAD + and NADH. Anal Chem 2021; 93:7118-7124. [PMID: 33905222 DOI: 10.1021/acs.analchem.1c00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
NADH/NAD+ is pivotal to fundamental biochemistry research and molecular diagnosis, but recognition and detection for them are a big challenge at the single-molecule level. Inspired by the biological system, here, we designed and synthesized a biomimetic NAD+/NADH molecular clamp (MC), octakis-(6-amino-6-deoxy)-γ-cyclomaltooctaose, and harbored in the engineered α-HL(M113R)7 nanopore, forming a novel single-molecule biosensor. The single-molecule measurement possesses high selectivity and a high signal-to-noise ratio, allowing to simultaneously recognize and detect for sensing NADH/NAD+ and their transformations.
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Affiliation(s)
- Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Wanyue Feng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Jinlei Zhang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Rauf Ayesha
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Tingting Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiaoyu Shi
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xixi Qiao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Luping Ma
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Sha Yu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
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13
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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14
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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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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Nanopore Enzymology to Study Protein Kinases and Their Inhibition by Small Molecules. Methods Mol Biol 2020. [PMID: 32918732 DOI: 10.1007/978-1-0716-0806-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Nanopore enzymology is a powerful single-molecule technique for the label-free study of enzymes using engineered protein nanopore sensors. The technique has been applied to protein kinases, where it has enabled the full repertoire of kinase function to be observed, including: kinetics of substrate binding and dissociation, product binding and dissociation, nucleotide binding, and reversible phosphorylation. Further, minor modifications enable the screening of type I kinase inhibitors and the determination of inhibition constants in a facile and label-free manner. Here, we describe the design and production of suitably engineered protein nanopores and their use for the determination of key mechanistic parameters of kinases. We also provide procedures for the determination of inhibition constants of protein kinase inhibitors.
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17
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Su Z, Wei Y, Kang XF. Simultaneous High-Resolution Detection of Bioenergetic Molecules using Biomimetic-Receptor Nanopore. Anal Chem 2019; 91:15255-15259. [PMID: 31665602 DOI: 10.1021/acs.analchem.9b04268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel artificial receptor, heptakis-[6-deoxy-6-(2-hydroxy-3-trimethylammonion-propyl) amino]-beta-cyclomaltoheptaose, with similar functions of mitochondrial ADP/ATP carrier protein, was synthesized and harbored in the engineered α-HL (M113R)7 nanopore, forming a single-molecule biosensor for sensing bioenergetic molecules and their transformations. The strategy significantly elevates both selectivity and signal-to-noise, which enables simultaneous recognition and detection of ATP, ADP, and AMP by real-time single-molecule measurement.
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Affiliation(s)
- Zhuoqun Su
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
| | - Yongfeng Wei
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science , Northwest University , Xi'an 710069 , P. R. China
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18
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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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19
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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20
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Lang C, Ye D, Song W, Yao C, Tu YM, Capparelli C, LaNasa JA, Hickner MA, Gomez EW, Gomez ED, Hickey RJ, Kumar M. Biomimetic Separation of Transport and Matrix Functions in Lamellar Block Copolymer Channel-Based Membranes. ACS NANO 2019; 13:8292-8302. [PMID: 31251576 DOI: 10.1021/acsnano.9b03659] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cell membranes control mass, energy, and information flow to and from the cell. In the cell membrane a lipid bilayer serves as the barrier layer, with highly efficient molecular machines, membrane proteins, serving as the transport elements. In this way, highly specialized transport properties are achieved by these composite materials by segregating the matrix function from the transport function using different components. For example, cell membranes containing aquaporin proteins can transport ∼4 billion water molecules per second per aquaporin while rejecting all other molecules including salts, a feat unmatched by any synthetic system, while the impermeable lipid bilayer provides the barrier and matrix properties. True separation of functions between the matrix and the transport elements has been difficult to achieve in conventional solute separation synthetic membranes. In this study, we created membranes with distinct matrix and transport elements through designed coassembly of solvent-stable artificial (peptide-appended pillar[5]arene, PAP5) or natural (gramicidin A) model channels with block copolymers into lamellar multilayered membranes. Self-assembly of a lamellar structure from cross-linkable triblock copolymers was used as a scalable replacement for lipid bilayers, offering better stability and mechanical properties. By coassembly of channel molecules with block copolymers, we were able to synthesize nanofiltration membranes with sharp selectivity profiles as well as uncharged ion exchange membranes exhibiting ion selectivity. The developed method can be used for incorporation of different artificial and biological ion and water channels into synthetic polymer membranes. The strategy reported here could promote the construction of a range of channel-based membranes and sensors with desired properties, such as ion separations, stimuli responsiveness, and high sensitivity.
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21
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Chen X, Zhang Y, Roozbahani GM, Guan X. Salt-Mediated Nanopore Detection of ADAM-17. ACS APPLIED BIO MATERIALS 2018; 2:504-509. [PMID: 32529174 DOI: 10.1021/acsabm.8b00689] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ADAM-17 (a disintegrin and metalloproteinase 17) plays an important role in various physiological and pathophysiological processes. Overexpression/underexpression of ADAM-17 could lead to various diseases. In this work, by taking advantage of ionic strength and salt gradient, and monitoring the cleavage of a substrate peptide by ADAM-17 in a nanopore, we developed a label-free sensor for the rapid detection of ADAM-17. The sensor was highly sensitive and selective: picomolar concentrations of ADAM-17 could be detected within minutes, while structure similar proteases such as ADAM-9 and MMP-9 did not interfere with its detection. Our developed nanopore sensing strategy should find useful applications in the development of nanopore sensors for other proteases of biological, pharmaceutical, and medical importance.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | | | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
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23
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Wang L, Chen X, Zhou S, Roozbahani GM, Zhang Y, Wang D, Guan X. Displacement chemistry-based nanopore analysis of nucleic acids in complicated matrices. Chem Commun (Camb) 2018; 54:13977-13980. [PMID: 30480311 PMCID: PMC6800042 DOI: 10.1039/c8cc07944g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To overcome the effect of other components of complicated biological samples on nanopore stochastic sensing, displacement chemical reaction was utilized to selectively extract the target nucleic acid from whole blood. Given its simplicity and high sensitivity for detecting nucleic acids, our developed displacement chemistry-based nanopore sensing strategy offers the potential for fieldable/point-of-care diagnostic applications.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China.
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24
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Chen X, Wang L, Roozbahani GM, Zhang Y, Xiang J, Guan X. Nanopore label-free detection of single-nucleotide deletion in Baxα/BaxΔ2. Electrophoresis 2018; 39:2410-2416. [PMID: 29998460 PMCID: PMC6168411 DOI: 10.1002/elps.201800193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
Baxα, a key tumor suppressor gene, will not be expressed correctly as a result of single nucleotide mutation in its microsatellite region; Instead, BaxΔ2, an isoform of Baxα, is often produced. In addition, lack of the exon 2 due to an alternative splicing, BaxΔ2 has the same sequence as Baxα except single base deletion from eight continuous guanines (G8) to G7. Most of the currently available methods for Bax∆2 detection are inefficient and time-consuming, and/or require the use of labels or dyes. In this work, we reported a label-free nanopore sensing strategy to differentiate between Baxα and BaxΔ2 with a DNA polymer as a molecular probe based on alternative spliced sequences. Two DNA molecules were designed to selectively detect Baxα and BaxΔ2, respectively. The method was rapid, accurate, and highly sensitive: picomolar concentrations of target nucleic acids could be detected in minutes. Our developed simple and fast nanopore-based detection strategy is not only useful for distinguishing between Baxα and Bax∆2, but also provides a useful tool for detection of other single-base mutations in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
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25
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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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26
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Roozbahani GM, Chen X, Zhang Y, Juarez O, Li D, Guan X. Computation-Assisted Nanopore Detection of Thorium Ions. Anal Chem 2018; 90:5938-5944. [PMID: 29648804 DOI: 10.1021/acs.analchem.8b00848] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Thorium is a well-known radioactive and chemically toxic contaminant in the environment. The continuous exposure to thorium may cause an increased risk of developing lung and liver diseases as well as lung, pancreas, and bone cancer. Due to its use in nuclear industry and other industrial applications, thorium may be accidentally released to the environment from its mining and processing plants. In this work, we developed a rapid, real-time, and label-free nanopore sensor for Th4+ detection by using an aspartic acid containing peptide as a chelating agent and tuning the electrolyte solution pH to control the net charges of the peptide ligand and its metal ion complex. The method is highly sensitive with a detection limit of 0.45 nM. Furthermore, the sensor is selective: other metal ions (e.g., UO22+, Pb2+, Cu2+, Ni2+, Hg2+, Zn2+, As3+, Mg2+, and Ca2+) with concentrations of up to 3 orders of magnitude greater than that of Th4+ would not interfere with Th4+detection. In addition, simulated water samples were successfully analyzed. Our developed computation-assisted sensing strategy should find useful applications in the development of nanopore sensors for other metal ions.
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Affiliation(s)
- Golbarg M Roozbahani
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Xiaohan Chen
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Youwen Zhang
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Oscar Juarez
- Department of Biology , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
| | - Dien Li
- Environmental Sciences and Biotechnology , Savannah River National Laboratory , Aiken , South Carolina 29808 , United States
| | - Xiyun Guan
- Department of Chemistry , Illinois Institute of Technology , Chicago , Illinois 60616 , United States
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27
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Chen X, Roozbahani GM, Ye Z, Zhang Y, Ma R, Xiang J, Guan X. Label-Free Detection of DNA Mutations by Nanopore Analysis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:11519-11528. [PMID: 29537824 PMCID: PMC6760912 DOI: 10.1021/acsami.7b19774] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Zijing Ye
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Rui Ma
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
- Corresponding author: Tel: 312-567-8922. Fax: 312-567-3494.
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28
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Cressiot B, Greive SJ, Si W, Pascoa TC, Mojtabavi M, Chechik M, Jenkins HT, Lu X, Zhang K, Aksimentiev A, Antson AA, Wanunu M. Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. ACS NANO 2017; 11:11931-11945. [PMID: 29120602 PMCID: PMC5963890 DOI: 10.1021/acsnano.7b06980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics, and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein's insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal's DNA-ratchet function.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J. Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Wei Si
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Tomas C. Pascoa
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Huw T. Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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29
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Lazenby RA, Macazo FC, Wormsbecher RF, White RJ. Quantitative Framework for Stochastic Nanopore Sensors Using Multiple Channels. Anal Chem 2017; 90:903-911. [PMID: 29185715 DOI: 10.1021/acs.analchem.7b03845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Membrane protein channels employed as stochastic sensors offer large signal-to-noise ratios and high specificity in single molecule binding measurements. Stochastic events in a single ion channel system can be measured using current-time traces, which are straightforward to analyze. Signals arising from measurement using multiple ion channels are more complicated to interpret. We show that multiple independent ion channels offer improved detection sensitivity compared to single channel measurements and that increased signal complexity can be accounted for using binding event frequency. More specifically, the leading edge of binding events follows a Poisson point process, which means signals from multiple channels can be superimposed and the association times (between each binding event leading edge), allow for sensitive and quantitative measurements. We expand our calibration to high ligand concentrations and high numbers of ion channels to demonstrate that there is an upper limit of quantification, defined by the time resolution of the measurement. The upper limit is a combination of the instrumental time resolution and the dissociation time of a ligand and protein which limits the number of detectable events. This upper limit also allows us to predict, in general, the measurement requirements needed to observe any process as a Poisson point process. The nanopore-based sensing analysis has wide implications for stochastic sensing platforms that operate using multiple simultaneous superimposable signals.
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Affiliation(s)
- Robert A Lazenby
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
| | - Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
| | - Richard F Wormsbecher
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
| | - Ryan J White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , Baltimore, Maryland 21250, United States
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30
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Wang S, Zhao Z, Haque F, Guo P. Engineering of protein nanopores for sequencing, chemical or protein sensing and disease diagnosis. Curr Opin Biotechnol 2017; 51:80-89. [PMID: 29232619 DOI: 10.1016/j.copbio.2017.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/17/2022]
Abstract
Biological systems contain highly-ordered structures performing diverse functions. The elegant structures of biomachines have inspired the development of nanopores as single molecule sensors. Over the years, the utility of nanopores for detecting a wide variety of analytes have rapidly emerged for sensing, sequencing and diagnostic applications. Several protein channels with diverse shapes and sizes, such as motor channels from bacteriophage Phi29, SPP1, T3, and T4, as well as α-hemolysin, MspA, aerolysin, FluA, OmpF/G, CsgG, ClyA, have been continually investigated and developed as nanopores. Herein, we focus on advances in biological nanopores for single molecule sensing and DNA sequencing from a protein engineering standpoint for changing pore sizes, altering charge distributions, enhancing sensitivity, improving stability, and imparting new detection capabilities.
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Affiliation(s)
| | - Zhengyi Zhao
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | | | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics & Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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31
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Roozbahani GM, Chen X, Zhang Y, Xie R, Ma R, Li D, Li H, Guan X. Peptide-Mediated Nanopore Detection of Uranyl Ions in Aqueous Media. ACS Sens 2017; 2:703-709. [PMID: 28580428 PMCID: PMC5450019 DOI: 10.1021/acssensors.7b00210] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/04/2017] [Indexed: 01/31/2023]
Abstract
![]()
Uranium
is one of the most common radioactive contaminants in the
environment. As a major nuclear material in production, environmental
samples (like soil and groundwater) can provide signatures on uranium
production activity inside the facility. Thus, developing a new and
portable analytical technology for uranium in aqueous media is significant
not only for environmental monitoring, but also for nonproliferation.
In this work, a label-free method for the detection of uranyl (UO22+) ions is developed by monitoring the translocation
of a peptide probe in a nanopore. Based on the difference in the number
of peptide events in the absence and presence of uranyl ions, nanomolar
concentration of UO22+ ions could be detected
in minutes. The method is highly selective; micromolar concentrations
of Cd2+, Cu2+, Zn2+, Ni2+, Pb2+, Hg2+, Th4+, Mg2+, and Ca2+ would not interfere with the detection of UO22+ ions. In addition, simulated water samples were
successfully analyzed.
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Affiliation(s)
- Golbarg M. Roozbahani
- 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
| | - Youwen Zhang
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Ruiqi Xie
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Rui Ma
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Dien Li
- Environmental
Sciences and Biotechnology, Savannah River National Laboratory, Aiken, South Carolina 29808, United States
| | - Huazhong Li
- Henan Jintai Biological Technology Co., Ltd., ZhengZhou, Henan, 450016, PR China
| | - Xiyun Guan
- Department
of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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32
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Wloka C, Van Meervelt V, van Gelder D, Danda N, Jager N, Williams CP, Maglia G. Label-Free and Real-Time Detection of Protein Ubiquitination with a Biological Nanopore. ACS NANO 2017; 11:4387-4394. [PMID: 28353339 PMCID: PMC5444049 DOI: 10.1021/acsnano.6b07760] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/17/2017] [Indexed: 05/18/2023]
Abstract
The covalent addition of ubiquitin to target proteins is a key post-translational modification that is linked to a myriad of biological processes. Here, we report a fast, single-molecule, and label-free method to probe the ubiquitination of proteins employing an engineered Cytolysin A (ClyA) nanopore. We show that ionic currents can be used to recognize mono- and polyubiquitinated forms of native proteins under physiological conditions. Using defined conjugates, we also show that isomeric monoubiquitinated proteins can be discriminated. The nanopore approach allows following the ubiquitination reaction in real time, which will accelerate the understanding of fundamental mechanisms linked to protein ubiquitination.
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Affiliation(s)
- Carsten Wloka
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | | | - Dewi van Gelder
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Natasha Danda
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Nienke Jager
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
| | - Chris P. Williams
- Molecular
Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
| | - Giovanni Maglia
- Chemical
Biology I, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
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33
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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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34
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Campos EJ, McVey CE, Astier Y. Stochastic Detection of MPSA-Gold Nanoparticles Using a α-Hemolysin Nanopore Equipped with a Noncovalent Molecular Adaptor. Anal Chem 2016; 88:6214-22. [PMID: 27238076 DOI: 10.1021/acs.analchem.5b03558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present the first study of a novel, more sensitive method for the characterization of nanoparticles (NPs). This approach combines detection via a protein nanopore with modification of its interaction behavior using a molecular adaptor. We identify different populations of 3-mercapto-1-propanesulfonate (MPSA)-modified-gold NPs using the biological nanopores α-hemolysin (αHL) and its M113N mutant equipped with a noncovalently bound γ-cyclodextrin molecule as a stochastic sensor. Identification takes place on the basis of the extent of current blockades and residence times. Here, we demonstrate that noncovalently attached adaptors can be used to change the sensing properties of αHL nanopores, allowing the detection and characterization of different populations of MPSA NPs. This is an advance in sensitivity and diversity of NP sensing, as well as a promising and reliable technology to characterize NPs by using protein nanopores.
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Affiliation(s)
- Elisa J Campos
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - Colin E McVey
- Structural Virology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - Yann Astier
- Single Molecule Processes Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
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35
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Macazo F, White RJ. Bioinspired Protein Channel-Based Scanning Ion Conductance Microscopy (Bio-SICM) for Simultaneous Conductance and Specific Molecular Imaging. J Am Chem Soc 2016; 138:2793-801. [PMID: 26848947 PMCID: PMC4778544 DOI: 10.1021/jacs.5b13252] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 01/24/2023]
Abstract
The utility of stochastic single-molecule detection using protein nanopores has found widespread application in bioanalytical sensing as a result of the inherent signal amplification of the resistive pulse method. Integration of protein nanopores with high-resolution scanning ion conductance microscopy (SICM) extends the utility of SICM by enabling selective chemical imaging of specific target molecules, while simultaneously providing topographical information about the net ion flux through a pore under a concentration gradient. In this study, we describe the development of a bioinspired scanning ion conductance microscopy (bio-SICM) approach that couples the imaging ability of SICM with the sensitivity and chemical selectivity of protein channels to perform simultaneous pore imaging and specific molecule mapping. To establish the framework of the bio-SICM platform, we utilize the well-studied protein channel α-hemolysin (αHL) to map the presence of β-cyclodextrin (βCD) at a substrate pore opening. We demonstrate concurrent pore and specific molecule imaging by raster scanning an αHL-based probe over a glass membrane containing a single 25-μm-diameter glass pore while recording the lateral positions of the probe and channel activity via ionic current. We use the average channel current to create a conductance image and the raw current-time traces to determine spatial localization of βCD. With further optimization, we believe that the bio-SICM platform will provide a powerful analytical methodology that is generalizable, and thus offers significant utility in a myriad of bioanalytical applications.
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Affiliation(s)
- Florika
C. Macazo
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Ryan J. White
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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36
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Liu L, Li Y, Li T, Xie J, Chen C, Liu Q, Zhang S, Wu HC. Selective Detection of 8-Oxo-2'-deoxyguanosine in Single-Stranded DNA via Nanopore Sensing Approach. Anal Chem 2015; 88:1073-7. [PMID: 26699617 DOI: 10.1021/acs.analchem.5b04102] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have developed a nanopore sensing approach for the selective detection of 8-oxo-2'-deoxyguanosine (8-oxoG) in single-stranded DNA. First, 1,12-dodecanediamine is coupled with 8-oxoG-containing DNA molecules in high yield which leaves a free amine group for subsequent attaching of an adamantane moiety. After incubation with cucurbit[7]uril, the host-guest complex-modified DNA hybrid is translocated through an α-hemolysin nanopore. Highly characteristic events can be recorded and used to quantify the 8-oxoG-DNA content in a DNA mixture. Compared with the existing methods, this study provides a reliable, quick, and low-cost approach for the detection of 8-oxoG site in single-stranded DNA at the single-molecule level, particularly suitable for high-throughput screening of a massive number of samples.
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Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Yuru Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Ting Li
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Jiani Xie
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Chaofei Chen
- Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Quansheng Liu
- Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Shouwen Zhang
- Epilepsy Department, Beijing ChaoYang Emergency Medical Center , Beijing 100021, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
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37
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Zhang D, Zhang Q, Lu Y, Yao Y, Li S, Jiang J, Liu GL, Liu Q. Peptide Functionalized Nanoplasmonic Sensor for Explosive Detection. NANO-MICRO LETTERS 2015; 8:36-43. [PMID: 30464992 PMCID: PMC6223917 DOI: 10.1007/s40820-015-0059-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/21/2015] [Indexed: 05/12/2023]
Abstract
In this study, a nanobiosensor for detecting explosives was developed, in which the peptide was synthesized with trinitrotoluene (TNT)-specific sequence and immobilized on nanodevice by Au-S covalent linkage, and the nanocup arrays were fabricated by nanoimprint and deposited with Au nanoparticles to generate localized surface plasmon resonance (LSPR). The device was used to monitor slight change from specific binding of 2,4,6-TNT to the peptide. With high refractive index sensing of ~104 nm/RIU, the nanocup device can detect the binding of TNT at concentration as low as 3.12 × 10-7 mg mL-1 by optical transmission spectrum modulated by LSPR. The nanosensor is also able to distinguish TNT from analogs of 2,4-dinitrotoluene and 3-nitrotoluene in the mixture with great selectivity. The peptide-based nanosensor provides novel approaches to design versatile biosensor assays by LSPR for chemical molecules.
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Affiliation(s)
- Diming Zhang
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Qian Zhang
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Yanli Lu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Yao Yao
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Shuang Li
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
| | - Jing Jiang
- Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Champaign, IL 61801 USA
| | - Gang Logan Liu
- Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Champaign, IL 61801 USA
| | - Qingjun Liu
- Biosensor National Special Laboratory, Key Laboratory for Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027 People’s Republic of China
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38
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Jakova E, Lee JS. Superposition of an AC field improves the discrimination between peptides in nanopore analysis. Analyst 2015; 140:4813-9. [PMID: 25699656 DOI: 10.1039/c4an02180k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In standard nanopore analysis a constant DC voltage is used to electrophoretically drive small molecules and peptides towards a pore. Superposition of an AC voltage at particular frequencies causes molecules to oscillate as they approach the pore which can alter the event parameters, the blockade current (I) and blockade time (T). Four peptides with similar structures were studied. Alpha-helical peptides A10 (FmocDDA10KK), A14, A18 and retro-inverso A10. It was shown that the ratio of translocations to bumping events could be manipulated by a combination of AC voltages and frequencies. In particular, A10 could be studied without interference from retro-inverso A10. Similarly, a large, intrinsically disordered protein of 140 amino acids, α-synuclein, which translocates the pore readily in a DC field could be prevented from doing so by application of an AC field of 200 mV at 100 MHz.
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Affiliation(s)
- Elisabet Jakova
- Department of Biochemistry, 107, Wiggins Road, University of Saskatchewan, Saskatoon, SK, S7N 0W0 Canada.
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39
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Feng Y, Zhang Y, Ying C, Wang D, Du C. Nanopore-based fourth-generation DNA sequencing technology. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:4-16. [PMID: 25743089 PMCID: PMC4411503 DOI: 10.1016/j.gpb.2015.01.009] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/23/2015] [Indexed: 12/24/2022]
Abstract
Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than $100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.
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Affiliation(s)
- Yanxiao Feng
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuechuan Zhang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Cuifeng Ying
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; MOE Key Laboratory of Weak-light Nonlinear Photonics, School of Physics, Nankai University, Tianjin 300071, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chunlei Du
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; University of Chinese Academy of Sciences, Beijing 100049, China
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40
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Ferrier DC, Shaver MP, Hands PJW. Micro- and nano-structure based oligonucleotide sensors. Biosens Bioelectron 2015; 68:798-810. [PMID: 25655465 DOI: 10.1016/j.bios.2015.01.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 12/26/2022]
Abstract
This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.
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Affiliation(s)
- David C Ferrier
- School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK
| | - Michael P Shaver
- School of Chemistry, David Brewster Road, University of Edinburgh, Edinburgh EH9 3FJ, UK
| | - Philip J W Hands
- School of Engineering, University of Edinburgh, Edinburgh EH9 3JL, UK.
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41
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Trick JL, Wallace EJ, Bayley H, Sansom MSP. Designing a hydrophobic barrier within biomimetic nanopores. ACS NANO 2014; 8:11268-11279. [PMID: 25317664 DOI: 10.1021/nn503930p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanopores in membranes have a range of potential applications. Biomimetic design of nanopores aims to mimic key functions of biological pores within a stable template structure. Molecular dynamics simulations have been used to test whether a simple β-barrel protein nanopore can be modified to incorporate a hydrophobic barrier to permeation. Simulations have been used to evaluate functional properties of such nanopores, using water flux as a proxy for ionic conductance. The behavior of these model pores has been characterized as a function of pore size and of the hydrophobicity of the amino acid side chains lining the narrow central constriction of the pore. Potential of mean force calculations have been used to calculate free energy landscapes for water and for ion permeation in selected models. These studies demonstrate that a hydrophobic barrier can indeed be designed into a β-barrel protein nanopore, and that the height of the barrier can be adjusted by modifying the number of consecutive rings of hydrophobic side chains. A hydrophobic barrier prevents both water and ion permeation even though the pore is sterically unoccluded. These results both provide insights into the nature of hydrophobic gating in biological pores and channels, and furthermore demonstrate that simple design features may be computationally transplanted into β-barrel membrane proteins to generate functionally complex nanopores.
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Affiliation(s)
- Jemma L Trick
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, Oxford, United Kingdom
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42
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Han Y, Zhou S, Wang L, Guan X. Nanopore back titration analysis of dipicolinic acid. Electrophoresis 2014; 36:467-70. [PMID: 25074707 DOI: 10.1002/elps.201400255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/07/2022]
Abstract
Here, we report a novel label-free nanopore back titration method for the detection of dipicolinic acid, a marker molecule for bacterial spores. By competitive binding of the target analyte and a large ligand probe to metal ions, dipicolinic acid could be sensitively and selectively detected. This nanopore back titration approach should find useful applications in the detection of other species of medical, biological, or environmental importance if their direct detection is difficult to achieve.
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Affiliation(s)
- Yujing Han
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, IL, USA
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43
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Single-molecule study of proteins by biological nanopore sensors. SENSORS 2014; 14:18211-22. [PMID: 25268917 PMCID: PMC4239869 DOI: 10.3390/s141018211] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 08/31/2014] [Accepted: 09/19/2014] [Indexed: 01/27/2023]
Abstract
Nanopore technology has been developed for detecting properties of proteins through monitoring of ionic current modulations as protein passes via a nanosize pore. As a real-time, sensitive, selective and stable technology, biological nanopores are of widespread concern. Here, we introduce the background of nanopore researches in the area of α-hemolysin (α-HL) nanopores in protein conformation detections and protein-ligand interactions. Moreover, several original biological nanopores are also introduced with various features and functions.
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44
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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45
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Bell NA, Keyser UF. Nanopores formed by DNA origami: A review. FEBS Lett 2014; 588:3564-70. [DOI: 10.1016/j.febslet.2014.06.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/03/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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46
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Boreyko JB, Polizos G, Datskos PG, Sarles SA, Collier CP. Air-stable droplet interface bilayers on oil-infused surfaces. Proc Natl Acad Sci U S A 2014; 111:7588-93. [PMID: 24821774 PMCID: PMC4040577 DOI: 10.1073/pnas.1400381111] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Droplet interface bilayers are versatile model membranes useful for synthetic biology and biosensing; however, to date they have always been confined to fluid reservoirs. Here, we demonstrate that when two or more water droplets collide on an oil-infused substrate, they exhibit noncoalescence due to the formation of a thin oil film that gets squeezed between the droplets from the bottom up. We show that when phospholipids are included in the water droplets, a stable droplet interface bilayer forms between the noncoalescing water droplets. As with traditional oil-submerged droplet interface bilayers, we were able to characterize ion channel transport by incorporating peptides into each droplet. Our findings reveal that droplet interface bilayers can function in ambient environments, which could potentially enable biosensing of airborne matter.
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Affiliation(s)
| | - Georgios Polizos
- Energy and Transportation Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; and
| | - Panos G Datskos
- Energy and Transportation Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; and
| | - Stephen A Sarles
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN 37996
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47
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Macazo FC, White RJ. Monitoring charge flux to quantify unusual ligand-induced ion channel activity for use in biological nanopore-based sensors. Anal Chem 2014; 86:5519-25. [PMID: 24794413 PMCID: PMC4051251 DOI: 10.1021/ac500832a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The
utility of biological nanopores for the development of sensors
has become a growing area of interest in analytical chemistry. Their
emerging use in chemical analysis is a result of several ideal characteristics.
First, they provide reproducible control over nanoscale pore sizes
with an atomic level of precision. Second, they are amenable to resistive-pulse
type measurement systems when embedded into an artificial lipid bilayer.
A single binding event causes a change in the flow of millions of
ions across the membrane per second that is readily measured as a
change in current with excellent signal-to-noise ratio. To date, ion
channel-based biosensors have been limited to well-behaved proteins.
Most demonstrations of using ion channels as sensors have been limited
to proteins that remain in the open, conducting state, unless occupied
by an analyte of interest. Furthermore, these proteins are nonspecific,
requiring chemical, biochemical, or genetic manipulations to impart
chemical specificity. Here, we report on the use of the pore-forming
abilities of heat shock cognate 70 (Hsc70) to quantify a specific
analyte. Hsc70 reconstitutes into phospholipid membranes and opens
to form multiple conductance states specifically in the presence of
ATP. We introduce the measurement of “charge flux” to
characterize the ATP-regulated multiconductance nature of Hsc70, which
enables sensitive quantification of ATP (100 μM–4 mM).
We believe that monitoring protein-induced charge flux across a bilayer
membrane represents a universal method for quantitatively monitoring
ion-channel activity. This measurement has the potential to broaden
the library of usable proteins in the development of nanopore-based
biosensors.
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Affiliation(s)
- Florika C Macazo
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County , 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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48
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Wang G, Wang L, Han Y, Zhou S, Guan X. Nanopore stochastic detection: diversity, sensitivity, and beyond. Acc Chem Res 2013; 46:2867-77. [PMID: 23614724 DOI: 10.1021/ar400031x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanopore sensors have emerged as a label-free and amplification-free technique for measuring single molecules. First proposed in the mid-1990s, nanopore detection takes advantage of the ionic current modulations produced by the passage of target analytes through a single nanopore at a fixed applied potential. Over the last 15 years, these nanoscale pores have been used to sequence DNA, to study covalent and non-covalent bonding interactions, to investigate biomolecular folding and unfolding, and for other applications. A major issue in the application of nanopore sensors is the rapid transport of target analyte molecules through the nanopore. Current recording techniques do not always accurately detect these rapid events. Therefore, researchers have looked for methods that slow molecular and ionic transport. Thus far, several strategies can improve the resolution and sensitivity of nanopore sensors including variation of the experimental conditions, use of a host compound, and modification of the analyte molecule and the nanopore sensor. In this Account, we highlight our recent research efforts that have focused on applications of nanopore sensors including the differentiation of chiral molecules, the study of enzyme kinetics, and the determination of sample purity and composition. Then we summarize our efforts to regulate molecular transport. We show that the introduction of various surface functional groups such as hydrophobic, aromatic, positively charged, and negatively charged residues in the nanopore interior, an increase in the ionic strength of the electrolyte solution, and the use of ionic liquid solutions as the electrolyte instead of inorganic salts may improve the resolution and sensitivity of nanopore stochastic sensors. Our experiments also demonstrate that the introduction of multiple functional groups into a single nanopore and the development of a pattern-recognition nanopore sensor array could further enhance sensor resolution. Although we have demonstrated the feasibility of nanopore sensors for various applications, challenges remain before nanopore sensing is deployed for routine use in applications such as medical diagnosis, homeland security, pharmaceutical screening, and environmental monitoring.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Yujing Han
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Shuo Zhou
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc Natl Acad Sci U S A 2013; 110:E4417-26. [PMID: 24194548 DOI: 10.1073/pnas.1312739110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In stochastic sensing, the association and dissociation of analyte molecules is observed as the modulation of an ionic current flowing through a single engineered protein pore, enabling the label-free determination of rate and equilibrium constants with respect to a specific binding site. We engineered sensors based on the staphylococcal α-hemolysin pore to allow the single-molecule detection and characterization of protein kinase-peptide interactions. We enhanced this approach by using site-specific proteolysis to generate pores bearing a single peptide sensor element attached by an N-terminal peptide bond to the trans mouth of the pore. Kinetics and affinities for the Pim protein kinases (Pim-1, Pim-2, and Pim-3) and cAMP-dependent protein kinase were measured and found to be independent of membrane potential and in good agreement with previously reported data. Kinase binding exhibited a distinct current noise behavior that forms a basis for analyte discrimination. Finally, we observed unusually high association rate constants for the interaction of Pim kinases with their consensus substrate Pimtide (~10(7) to 10(8) M(-1) · s(-1)), the result of electrostatic enhancement, and propose a cellular role for this phenomenon.
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50
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Wang G, Wang L, Han Y, Zhou S, Guan X. Nanopore detection of copper ions using a polyhistidine probe. Biosens Bioelectron 2013; 53:453-8. [PMID: 24211457 DOI: 10.1016/j.bios.2013.10.013] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 01/14/2023]
Abstract
We report a stochastic nanopore sensing method for the detection of Cu(2+) ions. By employing a polyhistidine molecule as a chelating agent, and based on the different signatures of the events produced by the translocation of the chelating agent through an α-hemolysin pore in the absence and presence of target analytes, trace amounts of copper ions could be detected with a detection limit of 40 nM. Importantly, although Co(2+), Ni(2+), and Zn(2+) also interacts with the polyhistidine molecule, since the event residence times and/or blockage amplitudes for these metal chelates are significantly different from those of copper chelates, these metal ions do not interfere with Cu(2+) detection. This chelating reaction approach should find useful application in the development of nanopore sensors for other metal ions.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
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