1
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Mojtabavi M, Greive SJ, Antson AA, Wanunu M. High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized within a Solid-State Nanopore. J Am Chem Soc 2022; 144:22540-22548. [PMID: 36455212 DOI: 10.1021/jacs.2c08514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The application of nanopores as label-free, single-molecule biosensors for electrical or optical probing of structural features in biomolecules has been widely explored. While biological nanopores (membrane proteins and bacteriophage portal proteins) and solid-state nanopores (thin films and two-dimensional materials) have been extensively employed, the third class of nanopores known as hybrid nanopores, where an artificial membrane substitutes the organic support membrane of proteins, has been only sparsely studied due to challenges in implementation. G20c portal protein contains a natural DNA pore that is used by viruses for filling their capsid with viral genomic DNA. We have previously developed a lipid-free hybrid nanopore by "corking" the G20c portal protein into a SiNx nanopore. Herein, we demonstrate that through chemical functionalization of the synthetic nanopore, covalent linkage between the solid-state pore and the G20c portal protein considerably improves the hybrid pore stability, lifetime, and voltage resilience. Moreover, we demonstrate electric-field-driven and motor protein-mediated transport of DNA molecules through this hybrid nanopore. Our integrated protein/solid-state device can serve as a robust and durable framework for sensing and sequencing at high voltages, potentially providing higher resolution, higher signal-to-noise ratio, and higher throughput compared to the more conventional membrane-embedded protein platforms.
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Affiliation(s)
- Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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2
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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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3
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Si W, Zhu Z, Wu G, Zhang Y, Chen Y, Sha J. Encoding Manipulation of DNA-Nanoparticle Assembled Nanorobot Using Independently Charged Array Nanopores. SMALL METHODS 2022; 6:e2200318. [PMID: 35656741 DOI: 10.1002/smtd.202200318] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/05/2022] [Indexed: 06/15/2023]
Abstract
During the past decades, scientists have developed different kinds of nanorobots based on various driving principles to realize controlled manipulation of them for potential applications like medical diagnosis and directed cargo delivery. In order to design a nanorobot with advantages of simple operation and precise control that can enrich the family of intelligent nanorobots, an encoding manipulation method is proposed to control the movement of a DNA-nanoparticle assembled nanorobot by combing electrophoresis and electroosmosis effect in independently charged array nanopores. The nanorobot is composed of one nanoparticle and one or two ssDNAs. ssDNAs act as the legs of the nanorobot. The selective ion transport through charged nanopores can induce cooperation and competition between the electroosmosis and electrophoresis, which is the main power to activate the nanorobot. Thus by simply switching the applied electric field and surface charge density of each nanopore which is defined as the encoded nanopore according to a predetermined strategy, the well-controlled encoding manipulation including capturing, releasing, jumping, and crawling of the nanorobot is realized in this work. The study is expected to realize its value in many interesting applications like drug delivery, nanosurgery, and so on in the near future.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Zhendong Zhu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
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4
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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5
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Pontón I, Sánchez-García D. Preparation of porphyrin and phthalocyanine conjugates for biomedical applications. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621300068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The aim of this review is to offer a succinct overview of the main synthetic techniques used in the preparation of conjugates containing porphyrins, including chlorins and bacteriochlorins and phthalocyanines for biomedical applications and photodynamic therapy (PDT). To illustrate the conjugation techniques representative examples from the literature will be presented.
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Affiliation(s)
- Iris Pontón
- Grup d’Enginyeria de Materials (GEMAT), Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - David Sánchez-García
- Grup d’Enginyeria de Materials (GEMAT), Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
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6
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Rao VB, Fokine A, Fang Q. The remarkable viral portal vertex: structure and a plausible model for mechanism. Curr Opin Virol 2021; 51:65-73. [PMID: 34619513 DOI: 10.1016/j.coviro.2021.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 01/20/2023]
Abstract
Many icosahedral viruses including tailed bacteriophages and herpes viruses have a unique portal vertex where a dodecameric protein ring is associated with a fivefold capsid shell. While the peripheral regions of the portal ring are involved in capsid assembly, its central channel is used to transport DNA into and out of capsid during genome packaging and infection. Though the atomic structure of this highly conserved, turbine-shaped, portal is known for nearly two decades, its molecular mechanism remains a mystery. Recent high-resolution in situ structures reveal various conformational states of the portal and the asymmetric interactions between the 12-fold portal and the fivefold capsid. These lead to a valve-like mechanism for this symmetry-mismatched portal vertex that regulates DNA flow through the channel, a critical function for high fidelity assembly of an infectious virion.
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Affiliation(s)
- Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA.
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Qianglin Fang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
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7
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Qiao D, Joshi H, Zhu H, Wang F, Xu Y, Gao J, Huang F, Aksimentiev A, Feng J. Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport. J Am Chem Soc 2021; 143:15975-15983. [PMID: 34403582 DOI: 10.1021/jacs.1c04910] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Reproducing the structure and function of biological membrane channels, synthetic nanopores have been developed for applications in membrane filtration technologies and biomolecular sensing. Stable stand-alone synthetic nanopores have been created from a variety of materials, including peptides, nucleic acids, synthetic polymers, and solid-state membranes. In contrast to biological nanopores, however, furnishing such synthetic nanopores with an atomically defined shape, including deliberate placement of each and every chemical group, remains a major challenge. Here, we introduce a chemosynthetic macromolecule-extended pillararene macrocycle (EPM)-as a chemically defined transmembrane nanopore that exhibits selective transmembrane transport. Our ionic current measurements reveal stable insertion of individual EPM nanopores into a lipid bilayer membrane and remarkable cation type-selective transport, with up to a 21-fold selectivity for potassium over sodium ions. Taken together, direct chemical synthesis offers a path to de novo design of a new class of synthetic nanopores with custom transport functionality imprinted in their atomically defined chemical structure.
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Affiliation(s)
- Dan Qiao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana Illinois 61801, United States
| | - Huangtianzhi Zhu
- State Key Laboratory of Chemical Engineering, Key Laboratory of Excited-State Materials of Zhejiang Province, Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Fushi Wang
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yang Xu
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Jia Gao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering, Key Laboratory of Excited-State Materials of Zhejiang Province, Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana Illinois 61801, United States
| | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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8
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Chen Y, Zhu Z, Tian Y, Jiang L. Rational ion transport management mediated through membrane structures. EXPLORATION 2021; 1:20210101. [PMCID: PMC10190948 DOI: 10.1002/exp.20210101] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/13/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Yupeng Chen
- Key Laboratory of Bio‐Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry Beihang University Beijing P. R. China
| | - Zhongpeng Zhu
- Key Laboratory of Bio‐Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry Beihang University Beijing P. R. China
| | - Ye Tian
- CAS Key Laboratory of Bio‐Inspired Materials and Interfacial Science CAS Center for Excellence in Nanoscience Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing P. R. China
- University of Chinese Academy of Sciences Beijing P. R. China
| | - Lei Jiang
- Key Laboratory of Bio‐Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry Beihang University Beijing P. R. China
- CAS Key Laboratory of Bio‐Inspired Materials and Interfacial Science CAS Center for Excellence in Nanoscience Technical Institute of Physics and Chemistry, Chinese Academy of Sciences Beijing P. R. China
- University of Chinese Academy of Sciences Beijing P. R. China
- School of Future Technology University of Chinese Academy of Sciences Beijing P. R. China
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9
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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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10
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Vikraman D, Satheesan R, Kumar KS, Mahendran KR. Nanopore Passport Control for Substrate-Specific Translocation. ACS NANO 2020; 14:2285-2295. [PMID: 31976649 DOI: 10.1021/acsnano.9b09408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Membrane protein pores have demonstrated applications in nanobiotechnology and single-molecule chemistry for effective detection of biomolecules. Here, we define the molecular basis of carbohydrate polymers translocation through a substrate-specific bacterial nanopore, CymA, which has a 15-residue N terminus segment inside the pore, restricting its diameter. Using single-channel recordings, we determined the kinetics of cationic cyclic oligosaccharide binding and elucidated the translocation mechanism across the pore in real-time. The cationic cyclic hexasaccharide binds to the densely packed negatively charged residues at the extracellular side of the pore with high affinity, facilitating its entry into the pore driven by the applied voltage. Further, the dissociation rate constant increased with increasing voltages, indicating unidirectional translocation toward the pore exit. Specifically, a larger cationic cyclic octasaccharide rapidly blocked the pore more effectively, resulting in the complete closure of the pore with increasing voltage, implying only strong binding. Further, we show that uncharged oligosaccharides exclusively bind to the extracellular side of the pore and the electroosmotic flow most likely drives their translocation. We propose that CymA favors selective translocation of cyclic hexasaccharide and linear maltooligosaccharides due to an asymmetrical charge pattern and the N terminus that regulates the substrate transport. We suggest that this substrate-specific nanopore with sophisticated geometry will be useful for complex biopolymer characterization.
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Affiliation(s)
- Devika Vikraman
- 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
- Manipal Academy of Higher Education , Manipal , Karnataka , 576104 , India
| | - K Santhosh Kumar
- 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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11
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Ji Z, Jordan M, Jayasinghe L, Guo P. Insertion of channel of phi29 DNA packaging motor into polymer membrane for high-throughput sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 25:102170. [PMID: 32035271 DOI: 10.1016/j.nano.2020.102170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/25/2019] [Accepted: 01/29/2020] [Indexed: 11/19/2022]
Abstract
The connector channel of bacteriophage phi29 DNA packaging motor has been inserted into the lipid bilayer membrane and has shown potential for the sensing of DNA, RNA, chemicals, peptides, and antibodies. Properties such as high solubility and large channel size have made phi29 channel an advantageous system for those applications; however, previously studied lipid membranes have short lifetimes, and they are frangible and unstable under voltages higher than 200 mV. Thus, the application of this lipid membrane platform for clinical applications is challenging. Here we report the insertion of the connector into the stable polymer membrane in MinION flow cell that contains 2048 wells for high-throughput sensing by the liposome-polymer fusion process. The successful insertion of phi29 connector was confirmed by a unique gating phenomenon. Peptide translocation through the inserted phi29 connector was also observed, revealing the potential of applying phi29 connector for high-throughput peptide sensing.
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Affiliation(s)
- Zhouxiang Ji
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Michael Jordan
- Oxford Nanopore Technologies Limited, Oxford Science Park, UK
| | | | - Peixuan Guo
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA; College of Medicine, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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12
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Wilson J, Sarthak K, Si W, Gao L, Aksimentiev A. Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model. ACS Sens 2019; 4:634-644. [PMID: 30821441 DOI: 10.1021/acssensors.8b01375] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach-the steric exclusion model (SEM) of nanopore conductance-that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.
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Affiliation(s)
| | | | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, 210096, China
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13
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Si W, Zhang Y, Sha J, Chen Y. Mechanisms of pressure-induced water infiltration process through graphene nanopores. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1559310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, People’s Republic of China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, People’s Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, People’s Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing, People’s Republic of China
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14
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Sha J, Si W, Xu B, Zhang S, Li K, Lin K, Shi H, Chen Y. Identification of Spherical and Nonspherical Proteins by a Solid-State Nanopore. Anal Chem 2018; 90:13826-13831. [DOI: 10.1021/acs.analchem.8b04136] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Bing Xu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Shuai Zhang
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kun Li
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kabin Lin
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Hongjiao Shi
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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15
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Cressiot B, Greive SJ, Mojtabavi M, Antson AA, Wanunu M. Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors. Nat Commun 2018; 9:4652. [PMID: 30405123 PMCID: PMC6220183 DOI: 10.1038/s41467-018-07116-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopore-based sensors are advancing the sensitivity and selectivity of single-molecule detection in molecular medicine and biotechnology. Current electrical sensing devices are based on either membrane protein pores supported in planar lipid bilayers or solid-state (SS) pores fabricated in thin metallic membranes. While both types of nanosensors have been used in a variety of applications, each has inherent disadvantages that limit its use. Hybrid nanopores, consisting of a protein pore supported within a SS membrane, combine the robust nature of SS membranes with the precise and simple engineering of protein nanopores. We demonstrate here a novel lipid-free hybrid nanopore comprising a natural DNA pore from a thermostable virus, electrokinetically inserted into a larger nanopore supported in a silicon nitride membrane. The hybrid pore is stable and easy to fabricate, and, most importantly, exhibits low peripheral leakage allowing sensing and discrimination among different types of biomolecules.
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Affiliation(s)
- Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.,LAMBE, Université d'Evry Val d'Essonne, Université de Cergy Pontoise, CNRS, CEA, Université Paris-Saclay, Evry, F-91025, France
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA.
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16
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Prevelige PE, Cortines JR. Phage assembly and the special role of the portal protein. Curr Opin Virol 2018; 31:66-73. [PMID: 30274853 DOI: 10.1016/j.coviro.2018.09.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/16/2018] [Accepted: 09/21/2018] [Indexed: 12/18/2022]
Abstract
Virus infections are ultimately dependent on a successful viral genome delivery to the host cell. The bacteriophage family Caudovirales evolved specialized machinery that fulfills this function: the portal proteins complex. The complexes are arranged as dodecameric rings and are a structural part of capsids incorporated at a five-fold vertex. They are involved in crucial aspects of viral replication, such as virion assembly, DNA packaging and DNA delivery. This review focuses on the organization and the mechanism through which these portal complexes achieve viral genome delivery and their similarities to other viral portal complexes.
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Affiliation(s)
- Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, 35294, United States
| | - Juliana R Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Brazil.
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17
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Mamad-Hemouch H, Bacri L, Huin C, Przybylski C, Thiébot B, Patriarche G, Jarroux N, Pelta J. Versatile cyclodextrin nanotube synthesis with functional anchors for efficient ion channel formation: design, characterization and ion conductance. NANOSCALE 2018; 10:15303-15316. [PMID: 30069556 DOI: 10.1039/c8nr02623h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biomimetic ion channels with different materials have been extensively designed to study the dynamics in a confined medium. These channels allow the development of several applications, such as ultra-fast sequencing and biomarker detection. When considering their synthesis, the use of cheap, non-cytotoxic and readily available materials is an increasing priority. Cyclodextrins, in supramolecular architectures, are widely utilized for pharmaceutical and biotechnological applications. Recent work has shown that short nanotubes (NTs) based on alpha-cyclodextrin (α-CD) assemble transient ion channels into membranes without cytotoxicity. In this study, we probe the influence of new cyclodextrin NT structural parameters and chemical modifications on channel formation, stability and electrical conductance. We report the successful synthesis of β- and γ-cyclodextrin nanotubes (β-CDNTs and γ-CDNTs), as evidenced by mass-spectrometry and high-resolution transmission electron microscopy. CDNTs were characterized by their length, diameter and number of CDs. Two hydrophobic groups, silylated or vinylated, were attached along the γ-CDNTs, improving the insertion time into the membrane. All NTs synthesized form spontaneous biomimetic ion channels. The hydrophobic NTs exhibit higher stability in membranes. Electrophysiological measurements show that ion transport is the main contribution of NT conductance and that the ion energy penalty for the entry into these NTs is similar to that of biological channels.
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Affiliation(s)
- Hajar Mamad-Hemouch
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.
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18
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Ji Z, Kang X, Wang S, Guo P. Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference. Biomaterials 2018; 182:227-233. [PMID: 30138785 DOI: 10.1016/j.biomaterials.2018.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/17/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022]
Abstract
Detection, differentiation, mapping, and sequencing of proteins are important in proteomics for the assessment of cell development such as protein methylation or phosphorylation as well as the diagnosis of diseases including metabolic disorder, mental illness, immunological ailments, and malignant cancers. Nanopore technology has demonstrated the potential for the sequencing or sensing of DNA, RNA, chemicals, or other macromolecules. Due to the diversity of protein in shape, structure and charge and the composition versatility of 20 amino acids, the sequencing of proteins remains challenging. Herein, we report the application of the channel of bacteriophage T7 DNA packaging motor for the differentiation of an assortment of peptides of a single amino acid difference. Explicit fingerprints or signatures were obtained based on current blockage and dwell time of individual peptide. Data from the clear mapping of small proteins after protease digestion suggests the potential of using T7 motor channel for proteomics including protein sequencing.
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Affiliation(s)
- Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xinqi Kang
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Shaoying Wang
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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Abstract
Many icosahedral viruses use a specialized portal vertex for genome encapsidation in the viral capsid (or head). This structure then controls release of the viral genetic information to the host cell at the beginning of infection. In tailed bacteriophages, the portal system is connected to a tail device that delivers their genome to the bacterial cytoplasm. The head-to-tail interface is a multiprotein complex that locks the viral DNA inside the phage capsid correctly positioned for egress and that controls its ejection when the viral particle interacts with the host cell receptor. Here we review the molecular mechanisms how this interface is assembled and how it carries out those two critical steps in the life cycle of tailed phages.
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Affiliation(s)
- Paulo Tavares
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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