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Ge Y, Li W, Tian J, Yu H, Wang Z, Wang M, Dong Z. Single-Stranded Nucleic Acid Transmembrane Molecular Carriers Based on Positively Charged Helical Foldamers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400678. [PMID: 38757406 PMCID: PMC11267351 DOI: 10.1002/advs.202400678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Transmembrane delivery of biologically active nucleic acids is an important process in cells and has inspired one to develop advanced drug delivery techniques. In this contribution, molecular-level single-stranded nucleic acid transmembrane carriers are reported based on 3.2 nm long Huc's foldamers (AOrnQ3Q3)8 and (mQ3Q2)8 with linearly and helically aligned positive charges, respectively. These two foldamers not only show very strong DNA affinity via electrostatic interactions but also discriminatively bind single-stranded DNA (ss-DNA) and double-stranded DNA (ds-DNA), corroborating the importance of precise charge arrangement in the electrostatic interactions. More importantly, these two foldamers are capable of efficiently transporting ss-DNA across the lipid membranes, and the ss-DNA transport activity of (AOrnQ3Q3)8 with linearly aligned charges is higher than that of (mQ3Q2)8 with helically aligned charges. Thus a type of novel single-stranded nucleic acid transmembrane molecular carriers based on positively charged helical foldamers are introduced. Further, effective and enhanced expression in EGFP-mRNA transfection experiments strongly demonstrates the potential of positively charged foldamers for RNA transmembrane transport and therapy.
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Affiliation(s)
- Yunpeng Ge
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
- Center for Supramolecular Chemical BiologyJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Wencan Li
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
- Center for Supramolecular Chemical BiologyJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Jun Tian
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
- Center for Supramolecular Chemical BiologyJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Hao Yu
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Zhenzhu Wang
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
- Center for Supramolecular Chemical BiologyJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
| | - Zeyuan Dong
- State Key Laboratory of Supramolecular Structure and MaterialsCollege of ChemistryJilin University2699 Qianjin StreetChangchun130012P. R. China
- Center for Supramolecular Chemical BiologyJilin University2699 Qianjin StreetChangchun130012P. R. China
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2
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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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3
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Sihorwala AZ, Lin AJ, Stachowiak JC, Belardi B. Light-Activated Assembly of Connexon Nanopores in Synthetic Cells. J Am Chem Soc 2023; 145:3561-3568. [PMID: 36724060 PMCID: PMC10188233 DOI: 10.1021/jacs.2c12491] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During developmental processes and wound healing, activation of living cells occurs with spatiotemporal precision and leads to rapid release of soluble molecular signals, allowing communication and coordination between neighbors. Nonliving systems capable of similar responsive release hold great promise for information transfer in materials and site-specific drug delivery. One nonliving system that offers a tunable platform for programming release is synthetic cells. Encased in a lipid bilayer structure, synthetic cells can be outfitted with molecular conduits that span the bilayer and lead to material exchange. While previous work expressing membrane pore proteins in synthetic cells demonstrated content exchange, user-defined control over release has remained elusive. In mammalian cells, connexon nanopore structures drive content release and have garnered significant interest since they can direct material exchange through intercellular contacts. Here, we focus on connexon nanopores and present activated release of material from synthetic cells in a light-sensitive fashion. To do this, we re-engineer connexon nanopores to assemble after post-translational processing by a protease. By encapsulating proteases in light-sensitive liposomes, we show that assembly of nanopores can be triggered by illumination, resulting in rapid release of molecules encapsulated within synthetic cells. Controlling connexon nanopore activity provides an opportunity for initiating communication with extracellular signals and for transferring molecular agents to the cytoplasm of living cells in a rapid, light-guided manner.
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Affiliation(s)
- Ahmed Z Sihorwala
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander J Lin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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5
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Qiao D, Chen Y, Tan H, Zhou R, Feng J. De novo design of transmembrane nanopores. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
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7
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Puthumadathil N, Krishnan R S, Nair GS, Mahendran KR. Assembly of alpha-helical transmembrane pores through an intermediate state. NANOSCALE 2022; 14:6507-6517. [PMID: 35420118 DOI: 10.1039/d2nr00556e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pore-forming alpha-helical proteins are well known for their dynamic assembly mechanism and it has been challenging to delineate the pore-forming structures in membranes. Previously, attempts have been made to elucidate their assembly mechanism and there is a large gap due to complex pathways by which these membrane-active pores impart their effect. Here we demonstrate a multi-step structural assembly pathway of alpha-helical peptide pores formed by a 37 amino acid synthetic peptide, pPorU, based on the natural porin from Corynebacterium urealyticum using single-channel electrical recordings. More specifically, we report detectable intermediate states during the membrane insertion and pore formation of pPorU. The fully assembled pore exhibited unusually large stable conductance, voltage-dependent gating, and functional blockage by cyclic sugars generally applicable to a range of transmembrane pores. Furthermore, we used rationally designed mutants to understand the role of specific amino acids in the assembly of these peptide pores. Mutant peptides that differ from wild-type peptides produced noisy and unstable intermediate states and low conductance pores, demonstrating sequence specificity in the pore-formation process supported by molecular dynamics simulations. We suggest that our study contributes to understanding the mechanism of action of naturally occurring alpha-helical pore-forming proteins and should be of broad interest to build peptide-based nanopore sensors.
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Affiliation(s)
- Neethu Puthumadathil
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Smrithi Krishnan R
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
- Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Greeshma S Nair
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
| | - Kozhinjampara R Mahendran
- Membrane Biology Laboratory, Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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8
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Sowlati-Hashjin S, Gandhi A, Garton M. Dawn of a New Era for Membrane Protein Design. BIODESIGN RESEARCH 2022; 2022:9791435. [PMID: 37850134 PMCID: PMC10521746 DOI: 10.34133/2022/9791435] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/20/2022] [Indexed: 10/19/2023] Open
Abstract
A major advancement has recently occurred in the ability to predict protein secondary structure from sequence using artificial neural networks. This new accessibility to high-quality predicted structures provides a big opportunity for the protein design community. It is particularly welcome for membrane protein design, where the scarcity of solved structures has been a major limitation of the field for decades. Here, we review the work done to date on the membrane protein design and set out established and emerging tools that can be used to most effectively exploit this new access to structures.
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Affiliation(s)
- Shahin Sowlati-Hashjin
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Aanshi Gandhi
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
| | - Michael Garton
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, Canada, M5S 3E2
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9
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Cytolysin A (ClyA): A Bacterial Virulence Factor with Potential Applications in Nanopore Technology, Vaccine Development, and Tumor Therapy. Toxins (Basel) 2022; 14:toxins14020078. [PMID: 35202106 PMCID: PMC8880466 DOI: 10.3390/toxins14020078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022] Open
Abstract
Cytolysin A (ClyA) is a pore-forming toxin that is produced by some bacteria from the Enterobacteriaceae family. This review provides an overview of the current state of knowledge regarding ClyA, including the prevalence of the encoding gene and its transcriptional regulation, the secretion pathway used by the protein, and the mechanism of protein assembly, and highlights potential applications of ClyA in biotechnology. ClyA expression is regulated at the transcriptional level, primarily in response to environmental stressors, and ClyA can exist stably both as a soluble monomer and as an oligomeric membrane complex. At high concentrations, ClyA induces cytolysis, whereas at low concentrations ClyA can affect intracellular signaling. ClyA is secreted in outer membrane vesicles (OMVs), which has important implications for biotechnology applications. For example, the native pore-forming ability of ClyA suggests that it could be used as a component of nanopore-based technologies, such as sequencing platforms. ClyA has also been exploited in vaccine development owing to its ability to present antigens on the OMV surface and provoke a robust immune response. In addition, ClyA alone or OMVs carrying ClyA fusion proteins have been investigated for their potential use as anti-tumor agents.
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10
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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11
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Bayoumi M, Nomidis SK, Willems K, Carlon E, Maglia G. Autonomous and Active Transport Operated by an Entropic DNA Piston. NANO LETTERS 2021; 21:762-768. [PMID: 33342212 PMCID: PMC7809690 DOI: 10.1021/acs.nanolett.0c04464] [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: 05/14/2023]
Abstract
We present a synthetic nanoscale piston that uses chemical energy to perform molecular transport against an applied bias. Such a device comprises a 13 by 5 nm protein cylinder, embedded in a biological membrane enclosing a single-stranded DNA (ssDNA) rod. Hybridization with DNA cargo rigidifies the rod, allowing for transport of a selected DNA molecule across the nanopore. A strand displacement reaction from ssDNA fuel on the other side of the membrane then liberates the DNA cargo back into solution and regenerates the initial configuration. The entropic penalty of ssDNA confinement inside the nanopore drives DNA transport regardless of the applied bias. Multiple automated and reciprocating cycles are observed, in which the DNA piston moves through the 10 nm length of the nanopore. In every cycle, a single DNA molecule is transported across the nanopore against an external bias force, which is the hallmark of biological transporters.
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Affiliation(s)
- Mariam Bayoumi
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, Leuven 3001, Belgium
- Center for
Brain & Disease Research, VIB-KU Leuven, Leuven 3000, Belgium
| | - Stefanos K. Nomidis
- Flemish
Institute for Technological Research (VITO), Boeretang 200, Mol B-2400, Belgium
- KU Leuven, Soft Matter and Biophysics Unit,
Department of Physics
and Astronomy, Celestijnenlaan
200D, 3001 Leuven, Belgium
| | | | - Enrico Carlon
- KU Leuven, Soft Matter and Biophysics Unit,
Department of Physics
and Astronomy, Celestijnenlaan
200D, 3001 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen 9747 AG , The Netherlands
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, Leuven 3001, Belgium
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12
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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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13
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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14
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Zhou W, Qiu H, Guo Y, Guo W. Molecular Insights into Distinct Detection Properties of α-Hemolysin, MspA, CsgG, and Aerolysin Nanopore Sensors. J Phys Chem B 2020; 124:1611-1618. [PMID: 32027510 DOI: 10.1021/acs.jpcb.9b10702] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein nanopores have been widely used as single-molecule sensors for the detection and characterization of biological polymers such as DNA, RNA, and polypeptides. A variety of protein nanopores with various geometries have been exploited for this purpose, which usually exhibit distinct sensing capabilities, but the underlying molecular mechanism remains elusive. Here, we systematically characterize the molecular transport properties of four widely studied protein nanopores, α-hemolysin, MspA, CsgG, and aerolysin, by extensive molecular dynamics simulations. It is found that a sudden drop in electrostatic potentials occurs at the sole constriction in MspA and CsgG nanopores in contrast to the gradual potential change inside α-hemolysin and aerolysin pores, indicating the crucial role of pore geometry in ionic and molecular transport. We further demonstrate that these protein nanopores exhibit open-pore currents and ssDNA-induced current blockades both in the order MspA > α-hemolysin > CsgG > aerolysin, but an equivalent blockade percentage around 80%. In addition, the substitution of key amino acids at the pore constriction, especially by charged ones, provides an efficient way to modulate the pore electrostatic potential and ionic current. This work sheds new light on the search for high-performance nanopores, engineering of protein nanopores, and design of bioinspired solid-state nanopores.
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Affiliation(s)
- Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yufeng Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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15
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Pallares RM, Thanh NTK, Su X. Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods. Chem Commun (Camb) 2019; 55:15041-15044. [PMID: 31696164 DOI: 10.1039/c9cc07511a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of transcription factors to DNA is one of the main mechanisms in gene regulation. While transcription factors frequently bind to unwrapped long DNA sequences known as open chromatin structures, most bioassays that study protein-DNA binding rely on short oligonucleotide probes. In this work, we develop a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After the determination of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance and compared it to other established techniques.
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Affiliation(s)
- Roger M Pallares
- Biophysics Group, Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.
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16
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Synthetic protein-conductive membrane nanopores built with DNA. Nat Commun 2019; 10:5018. [PMID: 31685824 PMCID: PMC6828756 DOI: 10.1038/s41467-019-12639-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 09/23/2019] [Indexed: 11/08/2022] Open
Abstract
AbstractNanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.
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17
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Wu X, Li M, Ying Y, Long Y. The Effects of Tetramethylammonium Cation on Oligonucleotide Analysis with Aerolysin Nanopore. ChemElectroChem 2019. [DOI: 10.1002/celc.201901376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xue‐Yuan Wu
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Meng‐Yin Li
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi‐Lun Ying
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
| | - Yi‐Tao Long
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
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18
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Cihan A, Tokunaga TK, Birkholzer JT. Adsorption and Capillary Condensation-Induced Imbibition in Nanoporous Media. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9611-9621. [PMID: 31241970 DOI: 10.1021/acs.langmuir.9b00813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Multiphase flow phenomena in nanoporous media are encountered in many science and engineering applications. Shales, for example, possessing complex nanopore networks, have considerable importance as source rocks for unconventional oil and gas production and as low-permeability seals for geologic carbon sequestration or nuclear waste disposal. This study presents a theoretical investigation of the processes controlling adsorption, capillary condensation, and imbibition in such nanoporous media, with a particular focus on understanding the effects of fluid-fluid and fluid-pore wall interaction forces in the interconnected nanopore space. Building on a new theoretical framework, we developed a numerical model for the multiphase nanoporous flow and tested it against water vapor uptake measurements conducted on a shale core sample. The model, which is based on the density functional approach, explicitly includes the relevant interaction forces among fluids and solids while allowing for a continuum representation of the porous medium. The experimental data include gravimetrically measured mass changes in an initially dry core sample exposed to varying levels of relative humidity, starting with a low relative humidity (rh = 0.31) followed by a period of a higher relative humidity (rh = 0.81). During this process, water vapor uptake in the dry core is recorded as a function of time. Our model suggests that, under low rh conditions, the flow within the shale sample is controlled by adsorption- and diffusion-type processes. After increasing the rh to 0.81, the uptake of water vapor becomes more significant, and according to our model, this can be explained by capillary condensation followed by immiscible displacement in the core sample. It appears that strong fluid-pore wall attractive forces cause condensation near the inlet, which then induces water imbibition further into sample.
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Affiliation(s)
- Abdullah Cihan
- Energy Geosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Tetsu K Tokunaga
- Energy Geosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jens T Birkholzer
- Energy Geosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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19
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Wilson JS, Churchill-Angus AM, Davies SP, Sedelnikova SE, Tzokov SB, Rafferty JB, Bullough PA, Bisson C, Baker PJ. Identification and structural analysis of the tripartite α-pore forming toxin of Aeromonas hydrophila. Nat Commun 2019; 10:2900. [PMID: 31263098 PMCID: PMC6602965 DOI: 10.1038/s41467-019-10777-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
The alpha helical CytolysinA family of pore forming toxins (α-PFT) contains single, two, and three component members. Structures of the single component Eschericia coli ClyA and the two component Yersinia enterolytica YaxAB show both undergo conformational changes from soluble to pore forms, and oligomerization to produce the active pore. Here we identify tripartite α-PFTs in pathogenic Gram negative bacteria, including Aeromonas hydrophila (AhlABC). We show that the AhlABC toxin requires all three components for maximal cell lysis. We present structures of pore components which describe a bi-fold hinge mechanism for soluble to pore transition in AhlB and a contrasting tetrameric assembly employed by soluble AhlC to hide their hydrophobic membrane associated residues. We propose a model of pore assembly where the AhlC tetramer dissociates, binds a single membrane leaflet, recruits AhlB promoting soluble to pore transition, prior to AhlA binding to form the active hydrophilic lined pore. Pore forming toxins (PFTs) form the major group of virulence factors in many pathogenic bacteria. Here the authors identify tripartite α-helical PFTs in pathogenic Gram negative bacteria and structurally characterize AhlABC from Aeromonas hydrophila and propose a model for its pore assembly.
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Affiliation(s)
- Jason S Wilson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Alicia M Churchill-Angus
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Simon P Davies
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK.,School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana E Sedelnikova
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Svetomir B Tzokov
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Per A Bullough
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Claudine Bisson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK.,ISMB, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Patrick J Baker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK.
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20
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Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications. Int J Mol Sci 2019; 20:ijms20061437. [PMID: 30901910 PMCID: PMC6472214 DOI: 10.3390/ijms20061437] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022] Open
Abstract
In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.
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21
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Krishnan R S, Satheesan R, Puthumadathil N, Kumar KS, Jayasree P, Mahendran KR. Autonomously Assembled Synthetic Transmembrane Peptide Pore. J Am Chem Soc 2019; 141:2949-2959. [DOI: 10.1021/jacs.8b09973] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Smrithi Krishnan R
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Remya Satheesan
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Neethu Puthumadathil
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - K. Santhosh Kumar
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Poornendhu Jayasree
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Kozhinjampara R. Mahendran
- Membrane Biology Laboratory, Interdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
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22
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Kim HJ, Choi UJ, Kim H, Lee K, Park KB, Kim HM, Kwak DK, Chi SW, Lee JS, Kim KB. Translocation of DNA and protein through a sequentially polymerized polyurea nanopore. NANOSCALE 2019; 11:444-453. [PMID: 30398270 DOI: 10.1039/c8nr06229c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we investigated the translocation of biomolecules, such as DNA and protein, through a sequentially polymerized polyurea nanopore, with a thin (<10 nm) polymer membrane of uniform thickness. The polyurea membrane was synthesized by molecular layer deposition using p-phenylenediisocyanate (PDI) and p-phenylenediamine (PDA) as sequential precursors. The membrane exhibited a hydrophobic surface with a highly negative surface charge density (-51 mC m-2 at pH 8). It was particularly noted that the high surface charge density of the membrane resulted in a highly developed electro-osmotic flow which, in turn, strongly influenced the capture probability of biomolecules, depending on the balance between the electro-osmotic and electrophoretic forces. For instance, the capture frequency of negatively charged DNA was demonstrated to be quite low, since these two forces more or less cancelled each other, whereas that of positively charged MDM2 was much higher, since these two forces were additive. We also identified that the mean translocation time of MDM2 through the polyurea nanopore was 26.1 ± 3.7 μs while that of the SiN nanopore was 14.2 ± 2.0 μs, hence suggesting that the enhanced electrostatic interaction between positively charged MDM2 and the negatively charged pore surface affects the translocation speed.
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Affiliation(s)
- Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea.
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23
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Taniguchi M, Ohshiro T. Nanopore Device for Single-Molecule Sensing Method and Its Application. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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24
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Tan CS, Fleming AM, Ren H, Burrows CJ, White HS. γ-Hemolysin Nanopore Is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level. J Am Chem Soc 2018; 140:14224-14234. [PMID: 30269492 DOI: 10.1021/jacs.8b08153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.
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Affiliation(s)
- Cherie S Tan
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
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25
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Niitsu A, Heal JW, Fauland K, Thomson AR, Woolfson DN. Membrane-spanning α-helical barrels as tractable protein-design targets. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630153 DOI: 10.1098/rstb.2016.0213] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Ai Niitsu
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Jack W Heal
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Kerstin Fauland
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK .,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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26
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Willems K, Van Meervelt V, Wloka C, Maglia G. Single-molecule nanopore enzymology. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630164 DOI: 10.1098/rstb.2016.0230] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Kherim Willems
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Department of Life Sciences and Imaging, IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Veerle Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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27
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Li X, Zhai T, Gao P, Cheng H, Hou R, Lou X, Xia F. Role of outer surface probes for regulating ion gating of nanochannels. Nat Commun 2018; 9:40. [PMID: 29298982 PMCID: PMC5752670 DOI: 10.1038/s41467-017-02447-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 11/29/2017] [Indexed: 12/04/2022] Open
Abstract
Nanochannels with functional elements have shown promise for DNA sequencing, single-molecule sensing, and ion gating. Ionic current measurement is currently a benchmark, but is focused solely on the contribution from nanochannels' inner-wall functional elements (NIWFE); the attributes of functional elements at nanochannels' outer surface (NOSFE) are nearly ignored, and remain elusive. Here we show that the role of NOSFE and NIWFE for ion gating can be distinguished by constructing DNA architectures using dual-current readout. The established molecular switches have continuously tunable and reversible ion-gating ability. We find that NOSFE exhibits negligible ion-gating behavior, but it can produce a synergistic effect in alliance with NIWFE. Moreover, the high-efficiency gating systems display more noticeable synergistic effect than the low-efficiency ones. We also reveal that the probe amount of NOSFE and NIWFE is almost equally distributed in our biomimetic nanochannels, which is potentially a premise for the synergistic ion-gating phenomena.
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Affiliation(s)
- Xinchun Li
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
- Pharmaceutical Analysis Division, School of Pharmacy, Guangxi Medical University, 530021, Nanning, China
| | - Tianyou Zhai
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
| | - Pengcheng Gao
- Faculty of Materials Science and Chemistry, China University of Geosciences, 430074, Wuhan, China
| | - Hongli Cheng
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
| | - Ruizuo Hou
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
| | - Xiaoding Lou
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, 430074, Wuhan, China
| | - Fan Xia
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, 430074, Wuhan, China.
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28
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Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
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Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
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29
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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30
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Mahendran KR, Niitsu A, Kong L, Thomson AR, Sessions RB, Woolfson DN, Bayley H. A monodisperse transmembrane α-helical peptide barrel. Nat Chem 2016; 9:411-419. [PMID: 28430192 DOI: 10.1038/nchem.2647] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.
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Affiliation(s)
- Kozhinjampara R Mahendran
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
| | - Ai Niitsu
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Lingbing Kong
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
| | - Andrew R Thomson
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Derek N Woolfson
- School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK.,School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA UK
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31
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Franceschini L, Brouns T, Willems K, Carlon E, Maglia G. DNA Translocation through Nanopores at Physiological Ionic Strengths Requires Precise Nanoscale Engineering. ACS NANO 2016; 10:8394-402. [PMID: 27513592 PMCID: PMC5221729 DOI: 10.1021/acsnano.6b03159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Many important processes in biology involve the translocation of a biopolymer through a nanometer-scale pore. Moreover, the electrophoretic transport of DNA across nanopores is under intense investigation for single-molecule DNA sequencing and analysis. Here, we show that the precise patterning of the ClyA biological nanopore with positive charges is crucial to observe the electrophoretic translocation of DNA at physiological ionic strength. Surprisingly, the strongly electronegative 3.3 nm internal constriction of the nanopore did not require modifications. Further, DNA translocation could only be observed from the wide entry of the nanopore. Our results suggest that the engineered positive charges are important to align the DNA in order to overcome the entropic and electrostatic barriers for DNA translocation through the narrow constriction. Finally, the dependencies of nucleic acid translocations on the Debye length of the solution are consistent with a physical model where the capture of double-stranded DNA is diffusion-limited while the capture of single-stranded DNA is reaction-limited.
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32
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Ayub M, Bayley H. Engineered transmembrane pores. Curr Opin Chem Biol 2016; 34:117-126. [PMID: 27658267 DOI: 10.1016/j.cbpa.2016.08.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022]
Abstract
Today, hundreds of researchers are working on nanopores, making an impact in both basic science and biotechnology. Proteins remain the most versatile sources of nanopores, based on our ability to engineer them with sub-nanometer precision. Recent work aimed at the construction and discovery of novel pores has included unnatural amino acid mutagenesis and the application of selection techniques. The diversity of structures has now been increased through the development of helix-based pores as well as the better-known β barrels. New developments also include truncated pores, which pierce bilayers through lipid rearrangement, and hybrid pores, which do away with bilayers altogether. Pore dimers, which span two lipid bilayers, have been constructed and pores based on DNA nanostructures are gaining in importance. While nanopore DNA sequencing has received enthusiastic attention, protein pores have a wider range of potential applications, requiring specifications that will require engineering efforts to continue for years to come.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom.
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33
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Wloka C, Mutter NL, Soskine M, Maglia G. Alpha-Helical Fragaceatoxin C Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic Acid Analysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606742] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carsten Wloka
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Natalie Lisa Mutter
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Misha Soskine
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Giovanni Maglia
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
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34
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Wloka C, Mutter NL, Soskine M, Maglia G. Alpha-Helical Fragaceatoxin C Nanopore Engineered for Double-Stranded and Single-Stranded Nucleic Acid Analysis. Angew Chem Int Ed Engl 2016; 55:12494-8. [DOI: 10.1002/anie.201606742] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Carsten Wloka
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Natalie Lisa Mutter
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Misha Soskine
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
| | - Giovanni Maglia
- Chemical Biology I; Groningen Biomolecular Sciences and Biotechnology Institute (GBB); University of Groningen; 9747 AG Groningen The Netherlands
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35
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Zhou Z, Ji Z, Wang S, Haque F, Guo P. Oriented single directional insertion of nanochannel of bacteriophage SPP1 DNA packaging motor into lipid bilayer via polar hydrophobicity. Biomaterials 2016; 105:222-227. [PMID: 27529454 DOI: 10.1016/j.biomaterials.2016.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/23/2022]
Abstract
Insertion of biological nanopore into artificial membrane is of fundamental importance in nanotechnology. Many applications require control and knowledge of channel orientation. In this work, the insertion orientation of the bacteriophage SPP1 and phi29 DNA packaging motors into lipid membranes was investigated. Single molecule electrophysiological assays and Ni-NTA-nanogold binding assays revealed that both SPP1 and phi29 motor channels exhibited a one-way traffic property for TAT peptide translocation from N- to C-termini of the protein channels. SPP1 motor channels preferentially inserts into liposomes with their C-terminal wider region facing inward. Changing the hydrophobicity of the N- or C-termini of phi29 connector alters the insertion orientation, suggesting that the hydrophobicity and hydrophilicity of the termini of the protein channel governs the orientation of the insertion into lipid membrane. It is proposed that the specificity in motor channel orientation is a result of the hydrophilic/hydrophobic interaction at the air/water interface when the protein channels are incorporating into liposome membranes.
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Affiliation(s)
- Zhi Zhou
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Zhouxiang Ji
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Shaoying Wang
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Farzin Haque
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
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36
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Cao C, Ying YL, Hu ZL, Liao DF, Tian H, Long YT. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore. NATURE NANOTECHNOLOGY 2016; 11:713-8. [PMID: 27111839 DOI: 10.1038/nnano.2016.66] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 03/21/2016] [Indexed: 05/22/2023]
Abstract
Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Zheng-Li Hu
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Dong-Fang Liao
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - He Tian
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
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37
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Abstract
This tutorial review charts the development of man-made molecular machines; from solution-phase to transmembrane assemblies.
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Affiliation(s)
- Matthew A. Watson
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh
- UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh
- UK
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38
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Watson MA, Cockroft SL. An Autonomously Reciprocating Transmembrane Nanoactuator. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Matthew A. Watson
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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39
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Watson MA, Cockroft SL. An Autonomously Reciprocating Transmembrane Nanoactuator. Angew Chem Int Ed Engl 2015; 55:1345-9. [DOI: 10.1002/anie.201508845] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Matthew A. Watson
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry; University of Edinburgh; Joseph Black Building; David Brewster Road Edinburgh EH9 3FJ UK
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40
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Ornelas C. Brief Timelapse on Dendrimer Chemistry: Advances, Limitations, and Expectations. MACROMOL CHEM PHYS 2015. [DOI: 10.1002/macp.201500393] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Catia Ornelas
- Institute of Chemistry; University of Campinas - Unicamp; Campinas SP 13083-970 Brazil
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41
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Ho CW, Van Meervelt V, Tsai KC, De Temmerman PJ, Mast J, Maglia G. Engineering a nanopore with co-chaperonin function. SCIENCE ADVANCES 2015; 1:e1500905. [PMID: 26824063 PMCID: PMC4730846 DOI: 10.1126/sciadv.1500905] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
The emergence of an enzymatic function can reveal functional insights and allows the engineering of biological systems with enhanced properties. We engineered an alpha hemolysin nanopore to function as GroES, a protein that, in complex with GroEL, forms a two-stroke protein-folding nanomachine. The transmembrane co-chaperonin was prepared by recombination of GroES functional elements with the nanopore, suggesting that emergent functions in molecular machines can be added bottom-up by incorporating modular elements into preexisting protein scaffolds. The binding of a single-ring version of GroEL to individual GroES nanopores prompted large changes to the unitary nanopore current, most likely reflecting the allosteric transitions of the chaperonin apical domains. One of the GroEL-induced current levels showed fast fluctuations (<1 ms), a characteristic that might be instrumental for efficient substrate encapsulation or folding. In the presence of unfolded proteins, the pattern of current transitions changed, suggesting a possible mechanism in which the free energy of adenosine triphosphate binding and hydrolysis is expended only when substrate proteins are occupied.
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Affiliation(s)
- Ching-Wen Ho
- Department of Chemistry, University of Leuven, Leuven 3001, Belgium
| | | | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Pieter-Jan De Temmerman
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Jan Mast
- Electron Microscopy Unit, Veterinary and Agrochemical Research Centre (CODA-CERVA), Brussels 1180, Belgium
| | - Giovanni Maglia
- Groningen Biotechnology Institute, University of Groningen, Groningen 9747AG, Netherlands
- Corresponding author. E-mail:
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42
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Biesemans A, Soskine M, Maglia G. A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore. NANO LETTERS 2015; 15:6076-6081. [PMID: 26243210 PMCID: PMC4606981 DOI: 10.1021/acs.nanolett.5b02309] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rotaxanes, pseudorotaxanes, and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing, and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two protein stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<-50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (-100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.
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Affiliation(s)
- Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
- Corresponding author:
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43
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Zhang L, Wang X. Coarse-grained modeling of vesicle responses to active rotational nanoparticles. NANOSCALE 2015; 7:13458-13467. [PMID: 26140682 DOI: 10.1039/c5nr01652e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In recent years, magnetically-driven-rotating superparamagnetic nanoparticles have been emerging as a valuable component in designing targeted drug delivery carriers and cellular killers via membranes' physical rupture. The lack of an in-depth understanding of how to control the interaction of rotational nanoparticles (RNPs) with vesicles has hindered progress in the development of their relevant biomedical applications. Here we perform dissipative particle dynamics simulations to analyze the rotation frequencies, size, and coating patterns of the RNPs as they interact with the vesicle so as to provide novel designs of drug delivery applications. Results have revealed that the RNPs are capable of triggering local disturbance around the vesicle and therefore promoting the vesicle translocation toward the RNPs. By investigating the translocation time and driving forces required for RNPs to enter inside the vesicle at various rotation frequencies as well as the interaction energy between coated RNPs and the vesicle, we have tuned the coating pattern of the ligands on the surface of RNPs to open a specified channel in the vesicle for promoting drug delivery. Our findings can provide useful guidelines for the molecular design of patterned RNPs for controllable bio/inorganic interfaces and help establish qualitative rules for the organization and optimization of ligands on the surface of the desired drug delivery carriers.
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Affiliation(s)
- Liuyang Zhang
- College of Engineering and NanoSEC, University of Georgia, Athens, GA 30602, USA.
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44
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Liu N, Yang Z, Ou X, Wei B, Zhang J, Jia Y, Xia F. Nanopore-based analysis of biochemical species. Mikrochim Acta 2015; 183:955-963. [PMID: 27013767 PMCID: PMC4778144 DOI: 10.1007/s00604-015-1560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/30/2015] [Indexed: 12/11/2022]
Abstract
Biological nanochannels or nanopores play a crucial role in basic biochemical processes in cells. Artificial nanopores possessing dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels are of particular interest with respect to the design of biosensors with a sensitivity that can go down to the fM level and even to single molecule detection. Nanopore-based analysis (NPA) is currently a new research field with fascinating prospects. This review (with 118 refs.) summarizes the progress made in this field in the recent 10 years. Following an introduction into the fundamentals of NPA, we demonstrate its potential by describing selected methods for sensing (a) proteins such as streptavidin, certain antibodies, or thrombin via aptamers; (b) oligomers, larger nucleic acids, or micro-RNA; (c) small molecules, (d) ions such as K(I) which is vital to the maintenance of life, or Hg(II) which is dangerous to health. We summarize the results and discuss the merits and limitations of the various methods at last. Graphical abstractSchematic of a signal-off system and a signal-on system in nanopore analysis. The effective diameter of nanopores decreases when targets undergo certain interactions with receptors attached on the inner surface of the nanopore. Correspondingly, the current will drop on appearance of the analyte. This is referred to as a "signal-off" system. Conversely, it is called a "signal-on" system.
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Affiliation(s)
- Nannan Liu
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Zekun Yang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Xiaowen Ou
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Benmei Wei
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Juntao Zhang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Yongmei Jia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Fan Xia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
- />National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074 China
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45
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Ficici E, Andricioaei I, Howorka S. Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance. NANO LETTERS 2015; 15:4822-4828. [PMID: 26053678 DOI: 10.1021/acs.nanolett.5b01960] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hyperbranched dendrimers are nanocarriers for drugs, imaging agents, and catalysts. Their nanoscale confinement is of fundamental interest and occurs when dendrimers with bioactive payload block or pass biological nanochannels or when catalysts are entrapped in inorganic nanoporous support scaffolds. The molecular process of confinement and its effect on dendrimer conformations are, however, poorly understood. Here, we use single-molecule nanopore measurements and molecular dynamics simulations to establish an atomically detailed model of pore dendrimer interactions. We discover and explain that electrophoretic migration of polycationic PAMAM dendrimers into confined space is not dictated by the diameter of the branched molecules but by their size and generation-dependent compressibility. Differences in structural flexibility also rationalize the apparent anomaly that the experimental nanopore current read-out depends in nonlinear fashion on dendrimer size. Nanoscale confinement is inferred to reduce the protonation of the polycationic structures. Our model can likely be expanded to other dendrimers and be applied to improve the analysis of biophysical experiments, rationally design functional materials such as nanoporous filtration devices or nanoscale drug carriers that effectively pass biological pores.
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Affiliation(s)
- Emel Ficici
- †Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Ioan Andricioaei
- †Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Stefan Howorka
- ‡Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London WC1H0AJ, England, United Kingdom
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46
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Abstract
Cell-to-cell communications via the tunneling nanotubes or gap junction channels are vital for the development and maintenance of multicellular organisms. Instead of these intrinsic communication pathways, how to design artificial communication channels between cells remains a challenging but interesting problem. Here, we perform dissipative particle dynamics (DPD) simulations to analyze the interaction between rotational nanotubes (RNTs) and vesicles so as to provide a novel design mechanism for cell-to-cell communication. Simulation results have demonstrated that the RNTs are capable of generating local disturbance and promote vesicle translocation toward the RNTs. Through ligand pattern designing on the RNTs, we can find a suitable nanotube candidate with a specific ligand coating pattern for forming the RNT-vesicle network. The results also show that a RNT can act as a bridged channel between vesicles, which facilitates substance transfer. Our findings provide useful guidelines for the molecular design of patterned RNTs for creating a synthetic channel between cells.
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Affiliation(s)
- Liuyang Zhang
- College of Engineering and NanoSEC, University of Georgia, Athens, Georgia 30602, United States
| | - Xianqiao Wang
- College of Engineering and NanoSEC, University of Georgia, Athens, Georgia 30602, United States
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47
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Langecker M, Ivankin A, Carson S, Kinney SM, Simmel FC, Wanunu M. Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability. NANO LETTERS 2015; 15:783-90. [PMID: 25495735 PMCID: PMC4296928 DOI: 10.1021/nl504522n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/09/2014] [Indexed: 05/21/2023]
Abstract
Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.
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Affiliation(s)
- Martin Langecker
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Andrey Ivankin
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shannon
R. M. Kinney
- Department
of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, Massachusetts 01119, United States
| | - Friedrich C. Simmel
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- E-mail:
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- E-mail:
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48
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Van Meervelt V, Soskine M, Maglia G. Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore. ACS NANO 2014; 8:12826-35. [PMID: 25493908 PMCID: PMC4410316 DOI: 10.1021/nn506077e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we showed that folded proteins can be internalized inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalization of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores can be used to probe conformational heterogeneity in protein:DNA interactions.
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Affiliation(s)
| | - Misha Soskine
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
| | - Giovanni Maglia
- Department of Chemistry, KU Leuven, Leuven, B-3001, Belgium
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, the Netherlands
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49
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Affiliation(s)
- Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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50
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Qian W, Doi K, Uehara S, Morita K, Kawano S. Theoretical study of the transpore velocity control of single-stranded DNA. Int J Mol Sci 2014; 15:13817-32. [PMID: 25116683 PMCID: PMC4159826 DOI: 10.3390/ijms150813817] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/17/2022] Open
Abstract
The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.
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Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoshi Uehara
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kaito Morita
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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