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Qin S, Nap RJ, Huang K, Szleifer I. Influence of Membrane Permittivity on Charge Regulation of Weak Polyelectrolytes End-Tethered in Nanopores. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01391] [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]
Affiliation(s)
- Shiyi Qin
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Rikkert J. Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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López ML, Queralt-Martín M, Alcaraz A. Stochastic pumping of ions based on colored noise in bacterial channels under acidic stress. NANOSCALE 2016; 8:13422-8. [PMID: 27349445 DOI: 10.1039/c6nr02638a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fluctuation-driven ion transport can be obtained in bacterial channels with the aid of different types of colored noise including the biologically relevant Lorentzian one. Using the electrochemical rectification of the channel current as a ratchet mechanism we observe transport of ions up to their concentration gradient under conditions similar to that met in vivo, namely moderate pH gradients and asymmetrically charged lipid membranes. We find that depending on the direction of the concentration gradient the channel can pump either cations or anions from the diluted side to the concentrated one. We discuss the possible relevance of this phenomenon for the pH homeostasis of bacterial cells.
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Affiliation(s)
- M Lidón López
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071, Castellón, Spain.
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Liu L, Li C, Ma J, Wu Y, Ni Z, Chen Y. Theoretical and experimental studies on ionic currents in nanopore-based biosensors. IET Nanobiotechnol 2014; 8:247-56. [PMID: 25429504 DOI: 10.1049/iet-nbt.2013.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Novel generation of analytical technology based on nanopores has provided possibilities to fabricate nanofluidic devices for low-cost DNA sequencing or rapid biosensing. In this paper, a simplified model was suggested to describe DNA molecule's translocation through a nanopore, and the internal potential, ion concentration, ionic flowing speed and ionic current in nanopores with different sizes were theoretically calculated and discussed on the basis of Poisson-Boltzmann equation, Navier-Stokes equation and Nernst-Planck equation by considering several important parameters, such as the applied voltage, the thickness and the electric potential distributions in nanopores. In this way, the basic ionic currents, the modulated ionic currents and the current drops induced by translocation were obtained, and the size effects of the nanopores were carefully compared and discussed based on the calculated results and experimental data, which indicated that nanopores with a size of 10 nm or so are more advantageous to achieve high quality ionic current signals in DNA sensing.
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Affiliation(s)
- Lei Liu
- Suzhou Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Suzhou Research Institute of Southeast University, Suzhou 215123, People's Republic of China.
| | - Chu Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Jian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Yingdong Wu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, Jiangsu 211189, People's Republic of China
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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Liu L, Wang B, Sha J, Yang Y, Hou Y, Ni Z, Chen Y. Voltage-driven translocation behaviors of IgG molecule through nanopore arrays. NANOSCALE RESEARCH LETTERS 2013; 8:229. [PMID: 23676116 PMCID: PMC3664219 DOI: 10.1186/1556-276x-8-229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 01/12/2013] [Indexed: 06/01/2023]
Abstract
Nanopore-based biosensing has attracted more and more interests in the past years, which is also regarded as an emerging field with major impact on bio-analysis and fundamental understanding of nanoscale interactions down to single-molecule level. In this work, the voltage-driven translocation properties of goat antibody to human immunoglobulin G (IgG) are investigated using nanopore arrays in polycarbonate membranes. Obviously, the background ionic currents are modulated by IgG molecules for their physical place-holding effect. However, the detected ionic currents do 'not' continuously decrease as conceived; the currents first decrease, then increase, and finally stabilize with increasing IgG concentration. To understand this phenomenon, a simplified model is suggested, and the calculated results contribute to the understanding of the abnormal phenomenon in the actual ionic current changing tendency.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Bing Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yue Yang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yaozong Hou
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
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Rode AB, Endoh T, Tateishi-Karimata H, Takahashi S, Sugimoto N. Real-time monitoring of DNA hybridization kinetics on living cell surfaces. Chem Commun (Camb) 2013; 49:8444-6. [DOI: 10.1039/c3cc42990c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Stoloff DH, Wanunu M. Recent trends in nanopores for biotechnology. Curr Opin Biotechnol 2012; 24:699-704. [PMID: 23266100 DOI: 10.1016/j.copbio.2012.11.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Nanopore technology employs a nanoscale hole in an insulating membrane to stochastically sense with high throughput individual biomolecules in solution. The generality of the nanopore detection principle and the ease of single-molecule detection suggest many potential applications of nanopores in biotechnology. Recent progress has been made with nanopore fabrication and sophistication, as well as with applications in DNA/protein mapping, biomolecular structure analysis, protein detection, and DNA sequencing. In addition, concepts for DNA sequencing devices have been suggested, and computational efforts have been made. The state of the nanopore field is maturing and given the right type of nanopore and operating conditions, nearly every application could revolutionize medicine in terms of speed, cost, and quality. In this review, we summarize progress in nanopores for biotechnological applications over the past 2-3 years.
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Affiliation(s)
- Daniel H Stoloff
- Department of Physics, Northeastern University, Boston, MA, United States
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