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Salehirozveh M, Kure Larsen AK, Stojmenovic M, Thei F, Dong M. In-situ PLL-g-PEG Functionalized Nanopore for Enhancing Protein Characterization. Chem Asian J 2023; 18:e202300515. [PMID: 37497831 DOI: 10.1002/asia.202300515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Indexed: 07/28/2023]
Abstract
Single-molecule nanopore detection technology has revolutionized proteomics research by enabling highly sensitive and label-free detection of individual proteins. Herein, we designed a small, portable, and leak-free flowcell made of PMMA for nanopore experiments. In addition, we developed an in situ functionalizing PLL-g-PEG approach to produce non-sticky nanopores for measuring the volume of diseases-relevant biomarker, such as the Alpha-1 antitrypsin (AAT) protein. The in situ functionalization method allows continuous monitoring, ensuring adequate functionalization, which can be directly used for translocation experiments. The functionalized nanopores exhibit improved characteristics, including an increased nanopore lifetime and enhanced translocation events of the AAT proteins. Furthermore, we demonstrated the reduction in the translocation event's dwell time, along with an increase in current blockade amplitudes and translocation numbers under different voltage stimuli. The study also successfully measures the single AAT protein volume (253 nm3 ), which closely aligns with the previously reported hydrodynamic volume. The real-time in situ PLL-g-PEG functionalizing method and the developed nanopore flowcell hold great promise for various nanopores applications involving non-sticky single-molecule characterization.
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Affiliation(s)
- Mostafa Salehirozveh
- Department Of Physics And Astronomy, University of Bologna, Bologna, Italy
- Elements srl, Cesena, Italy
| | - Anne-Kathrine Kure Larsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Sino-Danish Center for Education and Research, Aarhus, Denmark
- University of the Chinese Academy of Sciences, Beijing, China
| | | | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Biology - Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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2
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Svirelis J, Adali Z, Emilsson G, Medin J, Andersson J, Vattikunta R, Hulander M, Järlebark J, Kolman K, Olsson O, Sakiyama Y, Lim RYH, Dahlin A. Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates. Nat Commun 2023; 14:5131. [PMID: 37612271 PMCID: PMC10447545 DOI: 10.1038/s41467-023-40889-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zeynep Adali
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Radhika Vattikunta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Krzysztof Kolman
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Oliver Olsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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3
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Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
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Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
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4
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Qin J, Ziemann E, Bar-Zeev E, Bone SE, Liang Y, Mauter MS, Herzberg M, Bernstein R. Microporous Polyethersulfone Membranes Grafted with Zwitterionic Polymer Brushes Showing Microfiltration Permeance and Ultrafiltration Bacteriophage Removal. ACS APPLIED MATERIALS & INTERFACES 2023; 15:18343-18353. [PMID: 37010122 DOI: 10.1021/acsami.3c01495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Virus removal from water using microfiltration (MF) membranes is of great interest but remains challenging owing to the membranes' mean pore sizes typically being significantly larger than most viruses. We present microporous membranes grafted with polyzwitterionic brushes (N-dimethylammonium betaine) that combine bacteriophage removal in the range of ultrafiltration (UF) membranes with the permeance of MF membranes. Brush structures were grafted in two steps: free-radical polymerization followed by atom transfer radical polymerization (ATRP). Attenuated total reflection Fourier transform infrared (ATR-FTIR) and X-ray photoelectron (XPS) verified that grafting occurred at both sides of the membranes and that the grafting increased with increasing the zwitterion monomer concentration. The log reduction values (LRVs) of the pristine membrane increased from less than 0.5 LRV for T4 (∼100 nm) and NT1 (∼50 nm) bacteriophages to up to 4.5 LRV for the T4 and 3.1 LRV for the NT1 for the brush-grafted membranes with a permeance of about 1000 LMH/bar. The high permeance was attributed to a high-water fraction in the ultra-hydrophilic brush structure. The high measured LRVs of the brush-grafted membranes were attributed to enhanced bacteriophages exclusion from the membrane surface and entrapment of the ones that penetrated the pores due to the membranes' smaller mean pore-size and cross-section porosity than those of the pristine membrane, as seen by scanning electron microscopy (SEM) and measured using liquid-liquid porometry. Micro X-ray fluorescence (μ-XRF) spectrometry and nanoscale secondary ion mass spectrometry showed that 100 nm Si-coated gold nanospheres accumulated on the surface of the pristine membrane but not on the brush-coated membrane and that the nanospheres that penetrated the membranes were entrapped in the brush-grafted membrane but passed the pristine one. These results corroborate the LRVs obtained during filtration experiments and support the inference that the increased removal was due to a combined exclusion mechanism and entrapment. Overall, these microporous brush-grafted membranes show potential for use in advanced water treatment.
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Affiliation(s)
- Ji Qin
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research of the Ben-Gurion University of the Negev, Campus Sde Boker, Midreshet 84990, Israel
| | - Eric Ziemann
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research of the Ben-Gurion University of the Negev, Campus Sde Boker, Midreshet 84990, Israel
| | - Edo Bar-Zeev
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research of the Ben-Gurion University of the Negev, Campus Sde Boker, Midreshet 84990, Israel
| | - Sharon E Bone
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yuanzhe Liang
- Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Meagan S Mauter
- Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Moshe Herzberg
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research of the Ben-Gurion University of the Negev, Campus Sde Boker, Midreshet 84990, Israel
| | - Roy Bernstein
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research of the Ben-Gurion University of the Negev, Campus Sde Boker, Midreshet 84990, Israel
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5
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Andersson J, Svirelis J, Medin J, Järlebark J, Hailes R, Dahlin A. Pore performance: artificial nanoscale constructs that mimic the biomolecular transport of the nuclear pore complex. NANOSCALE ADVANCES 2022; 4:4925-4937. [PMID: 36504753 PMCID: PMC9680827 DOI: 10.1039/d2na00389a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/12/2022] [Indexed: 06/17/2023]
Abstract
The nuclear pore complex is a nanoscale assembly that achieves shuttle-cargo transport of biomolecules: a certain cargo molecule can only pass the barrier if it is attached to a shuttle molecule. In this review we summarize the most important efforts aiming to reproduce this feature in artificial settings. This can be achieved by solid state nanopores that have been functionalized with the most important proteins found in the biological system. Alternatively, the nanopores are chemically modified with synthetic polymers. However, only a few studies have demonstrated a shuttle-cargo transport mechanism and due to cargo leakage, the selectivity is not comparable to that of the biological system. Other recent approaches are based on DNA origami, though biomolecule transport has not yet been studied with these. The highest selectivity has been achieved with macroscopic gels, but they are yet to be scaled down to nano-dimensions. It is concluded that although several interesting studies exist, we are still far from achieving selective and efficient artificial shuttle-cargo transport of biomolecules. Besides being of fundamental interest, such a system could be potentially useful in bioanalytical devices.
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Affiliation(s)
- John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Rebekah Hailes
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
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6
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Hong JK, Ruhoff AM, Mathur K, Neto C, Waterhouse A. Mechanisms for Reduced Fibrin Clot Formation on Liquid-Infused Surfaces. Adv Healthc Mater 2022; 11:e2201360. [PMID: 36040004 DOI: 10.1002/adhm.202201360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/09/2022] [Indexed: 01/28/2023]
Abstract
Biomedical devices are prone to blood clot formation (thrombosis), and liquid-infused surfaces (LIS) are effective in reducing the thrombotic response. However, the mechanisms that underpin this performance, and in particular the role of the lubricant, are not well understood. In this work, it is investigated whether the mechanism of LIS action is related to i) inhibition of factor XII (FXII) activation and the contact pathway; ii) reduced fibrin density of clots formed on surfaces; iii) increased mobility of proteins or cells on the surface due to the interfacial flow of the lubricant. The chosen LIS is covalently tethered, nanostructured layers of perfluorocarbons, infused with thin films of medical-grade perfluorodecalin (tethered-liquid perfluorocarbon), prepared with chemical vapor deposition previously optimized to retain lubricant under flow. Results show that in the absence of external flow, interfacial mobility is inherently higher at the liquid-blood interface, making it a key contributor to the low thrombogenicity of LIS, as FXII activity and fibrin density are equivalent at the interface. The findings of this study advance the understanding of the anti-thrombotic behavior of LIS-coated biomedical devices for future coating design. More broadly, enhanced interfacial mobility may be an important, underexplored mechanism for the anti-fouling behavior of surface coatings.
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Affiliation(s)
- Jun Ki Hong
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Alexander M Ruhoff
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kavya Mathur
- Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.,School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chiara Neto
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anna Waterhouse
- School of Medical Science, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Heart Research Institute, The University of Sydney, Newtown, NSW 2042, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
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7
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Chen G, Dormidontova E. PEO-Grafted Gold Nanopore: Grafting Density, Chain Length, and Curvature Effects. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guang Chen
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Elena Dormidontova
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
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8
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Mollahosseini A, Abdelrasoul A. Novel Insights in Hemodialysis: Most Recent Theories on the Membrane Hemocompatibility Improvement. BIOMEDICAL ENGINEERING ADVANCES 2022. [DOI: 10.1016/j.bea.2022.100034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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9
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Svirelis J, Andersson J, Stradner A, Dahlin A. Accurate Correction of the "Bulk Response" in Surface Plasmon Resonance Sensing Provides New Insights on Interactions Involving Lysozyme and Poly(ethylene glycol). ACS Sens 2022; 7:1175-1182. [PMID: 35298135 PMCID: PMC9040059 DOI: 10.1021/acssensors.2c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Surface plasmon resonance
is a very well-established surface sensitive
technique for label-free analysis of biomolecular interactions, generating
thousands of publications each year. An inconvenient effect that complicates
interpretation of SPR results is the “bulk response”
from molecules in solution, which generate signals without really
binding to the surface. Here we present a physical model for determining
the bulk response contribution and verify its accuracy. Our method
does not require a reference channel or a separate surface region.
We show that proper subtraction of the bulk response reveals an interaction
between poly(ethylene glycol) brushes and the protein lysozyme at
physiological conditions. Importantly, we also show that the bulk
response correction method implemented in commercial instruments is
not generally accurate. Using our method, the equilibrium affinity
between polymer and protein is determined to be KD = 200 μM. One reason for the weak affinity is
that the interaction is relatively short-lived (1/koff < 30 s). Furthermore, we show that the bulk response
correction also reveals the dynamics of self-interactions between
lysozyme molecules on surfaces. Besides providing new insights on
important biomolecular interactions, our method can be widely applied
to improve the accuracy of SPR data generated by instruments worldwide.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Anna Stradner
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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10
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Peters DT, Reifs A, Alonso-Caballero A, Madkour A, Waller H, Kenny B, Perez-Jimenez R, Lakey JH. Unraveling the molecular determinants of the anti-phagocytic protein cloak of plague bacteria. PLoS Pathog 2022; 18:e1010447. [PMID: 35358289 PMCID: PMC9004762 DOI: 10.1371/journal.ppat.1010447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 04/12/2022] [Accepted: 03/16/2022] [Indexed: 12/03/2022] Open
Abstract
The pathogenic bacterium Yersina pestis is protected from macrophage engulfment by a capsule like antigen, F1, formed of long polymers of the monomer protein, Caf1. However, despite the importance of this pathogen, the mechanism of protection was not understood. Here we demonstrate how F1 protects the bacteria from phagocytosis. First, we show that Escherichia coli expressing F1 showed greatly reduced adherence to macrophages. Furthermore, the few cells that did adhere remained on the macrophage surface and were not engulfed. We then inserted, by mutation, an “RGDS” integrin binding motif into Caf1. This did not change the number of cells adhering to macrophages but increased the fraction of adherent cells that were engulfed. Therefore, F1 protects in two separate ways, reducing cell adhesion, possibly by acting as a polymer brush, and hiding innate receptor binding sites needed for engulfment. F1 is very robust and we show that E. coli expressing weakened mutant polymers are engulfed like the RGDS mutant. This suggests that innate attachment sites on the native cell surface are exposed if F1 is weakened. Single-molecule force spectroscopy (SMFS) experiments revealed that wild-type F1 displays a very high mechanical stability of 400 pN. However, the mechanical resistance of the destabilised mutants, that were fully engulfed, was only 20% weaker. By only marginally exceeding the mechanical force applied to the Caf1 polymer during phagocytosis it may be that the exceptional tensile strength evolved to resist the forces applied at this stage of engulfment. Macrophages, a type of white blood cell, form an important element of our immune defence. They interrogate other cells’ surfaces for molecular clues and ingest those presenting a threat in a process known as phagocytosis. Not surprisingly, pathogenic bacteria have developed ways to evade this fate. The plague bacterium, Yersinia pestis, produces the long polymeric F1 coat protein which enables it to avoid ingestion, but the mechanism was unclear. We show that equipping Escherichia coli cells with an F1 coat protected them from phagocytosis by two separate mechanisms, reducing contact with the macrophage surface and hiding the signals that tell the macrophages they are targets. F1 is also a very stable protein polymer and using single molecule force spectroscopy we showed it also has a very high resistance to pulling forces. Surprisingly, mutations which reduced this by only 20% caused adherent bacteria to be fully ingested, indicating that cells are subject to significant forces prior to recognition and ingestion. Thus, F1 has evolved three notable properties (i) physical; creation of a hydrated polymer brush to inhibit surface interactions, (ii) chemical; absence of molecular recognition clues needed for engulfment and (iii) mechanical; strength that maintains the camouflage layer during surface stretching.
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Affiliation(s)
- Daniel T. Peters
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Azzeldin Madkour
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen Waller
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Brendan Kenny
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Raul Perez-Jimenez
- CIC nanoGUNE BRTA, San Sebastian, Spain
- Ikerbasque Foundation for Science, Bilbao, Spain
| | - Jeremy H. Lakey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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11
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Kapinos LE, Lim RYH. Multivalent Interactions with Intrinsically Disordered Proteins Probed by Surface Plasmon Resonance. Methods Mol Biol 2022; 2502:311-328. [PMID: 35412248 DOI: 10.1007/978-1-0716-2337-4_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multivalent interactions underpin associations between intrinsically disordered proteins (IDPs) and their binding partners. This is a subject of considerable interest and governs how nuclear transport receptors (NTRs) orchestrate the nucleocytoplasmic transport (NCT) of signal-specific cargoes through nuclear pore complexes (NPCs) in eukaryotic cells. Specifically, IDPs termed phenylalanine-glycine nucleoporins (FG Nups) exert multivalent interactions with NTRs to facilitate their transport selectivity and speed through the NPC. Here, we document the use of surface plasmon resonance (SPR) to quantify the affinity and kinetics of NTR-FG Nup binding as a function of FG Nup surface density. Moreover, we describe an in situ method that measures conformational height changes that occur in a FG Nup layer following NTR-binding. Protocols by which the as-obtained SPR results are treated with respect to mass transport limitations are further described. Overall, the SPR methodology described here can be applied to studying multivalent interactions and the role of avidity in diverse biological and biointerfacial systems.
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Affiliation(s)
- Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland.
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12
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Hoogenboom BW, Hough LE, Lemke EA, Lim RYH, Onck PR, Zilman A. Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment. PHYSICS REPORTS 2021; 921:1-53. [PMID: 35892075 PMCID: PMC9306291 DOI: 10.1016/j.physrep.2021.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.
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Affiliation(s)
- Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado, Boulder CO 80309, United States of America
| | - Edward A. Lemke
- Biocenter Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Anton Zilman
- Department of Physics and Institute for Biomedical Engineering (IBME), University of Toronto, Toronto, ON M5S 1A7, Canada
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13
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Reynaud L, Bouchet-Spinelli A, Janot JM, Buhot A, Balme S, Raillon C. Discrimination of α-Thrombin and γ-Thrombin Using Aptamer-Functionalized Nanopore Sensing. Anal Chem 2021; 93:7889-7897. [PMID: 34038092 DOI: 10.1021/acs.analchem.1c00461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein detection and identification at the single-molecule level are major challenges in many biotechnological fields. Solid-state nanopores have raised attention as label-free biosensors with high sensitivity. Here, we use solid-state nanopore sensing to discriminate two closely related proteins, α-thrombin and γ-thrombin. We show that aptamer functionalization improves protein discrimination thanks to a significant difference in the relative current blockade amplitude. To enhance discrimination, we postprocessed the signals using machine learning and training algorithms and we were able to reach an accuracy of 98.8% using seven features and ensemble methods.
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Affiliation(s)
- Lucile Reynaud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | | | - Jean-Marc Janot
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | - Sébastien Balme
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Camille Raillon
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
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14
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Andersson J, Ferrand-Drake del Castillo G, Bilotto P, Höök F, Valtiner M, Dahlin A. Control of Polymer Brush Morphology, Rheology, and Protein Repulsion by Hydrogen Bond Complexation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4943-4952. [PMID: 33851532 PMCID: PMC8154870 DOI: 10.1021/acs.langmuir.1c00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Polymer brushes are widely used to alter the properties of interfaces. In particular, poly(ethylene glycol) (PEG) and similar polymers can make surfaces inert toward biomolecular adsorption. Neutral hydrophilic brushes are normally considered to have static properties at a given temperature. As an example, PEG is not responsive to pH or ionic strength. Here we show that, by simply introducing a polymeric acid such as poly(methacrylic acid) (PMAA), the highly hydrated brush barrier can change its properties entirely. This is caused by multivalent hydrogen bonds in an extremely pH-sensitive process. Remarkably, it is sufficient to reduce the pH to 5 for complexation to occur at the interface, which is two units higher than in the corresponding bulk systems. Below this critical pH, PMAA starts to bind to PEG in large amounts (comparable to the PEG amount), causing the brush to gradually compact and dehydrate. The brush also undergoes major rheology changes, from viscoelastic to rigid. Furthermore, the protein repelling ability of PEG is lost after reaching a threshold in the amount of PMAA bound. The changes in brush properties are tunable and become more pronounced when more PMAA is bound. The initial brush state is fully recovered when releasing PMAA by returning to physiological pH. Our findings are relevant for many applications involving functional interfaces, such as capture-release of biomolecules.
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Affiliation(s)
- John Andersson
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
| | | | - Pierluigi Bilotto
- Institute
of Applied Physics, Group of Applied Interface Physics, Vienna University of Technology, 1040 Vienna, Austria
| | - Fredrik Höök
- Department
of Physics, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Markus Valtiner
- Institute
of Applied Physics, Group of Applied Interface Physics, Vienna University of Technology, 1040 Vienna, Austria
| | - Andreas Dahlin
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Gothenburg, Sweden
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15
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Yong H, Molcrette B, Sperling M, Montel F, Sommer JU. Regulating the Translocation of DNA through Poly( N-isopropylacrylamide)-Decorated Switchable Nanopores by Cononsolvency Effect. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huaisong Yong
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Bastien Molcrette
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Marcel Sperling
- Fraunhofer-Institut für Angewandte Polymerforschung, Potsdam-Golm 14476, Germany
| | - Fabien Montel
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Institute for Theoretical Physics, Technische Universität Dresden, Dresden 01069, Germany
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16
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Pastorino C, Müller M. Liquid and Droplet Transport in Brush-Coated Cylindrical Nanochannels: Brush-Assisted Droplet Formation. J Phys Chem B 2021; 125:442-449. [PMID: 33400523 DOI: 10.1021/acs.jpcb.0c09189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study, by coarse-grained molecular dynamics simulations, equilibrium and flow properties of a liquid in cylindrical nanochannels, coated with polymer brushes. The parameters of the interaction potential model confer a chemical incompatibility between brush monomers and liquid particles. First, we study cylindrical channels whose radii are larger than the brush height and a continuous column of liquid forms at the center of the channel. These results are contrasted to the limiting case in which the radius of the cylinder is comparable to the brush height. In this second case, the grafted polymers interact across the channel and "close" it. We observe a train of droplets as the stable liquid morphology. The droplet size is comparable to the cylinder radius. By applying a constant body force onto the liquid, we induce a Poiseuille-like flow and investigate the morphology and flow rate as a function of driving force. Upon increasing the driving force, we encounter a nonequilibrium transition from a closed channel with slowly moving droplets to a flowing liquid thread at the center. The switching between these two states is reversible.
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Affiliation(s)
- C Pastorino
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av.Gral. Paz 1499, B1650 San Martín, Pcia. de Buenos Aires, Argentina.,Instituto de Nanociencia y Nanotecnología CONICET-CNEA, B1650 Buenos Aires, Argentina
| | - M Müller
- Institut für Theoretische Physik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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17
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Li S, Zeng S, Wen C, Barbe L, Tenje M, Zhang Z, Hjort K, Zhang SL. Dynamics of DNA Clogging in Hafnium Oxide Nanopores. J Phys Chem B 2020; 124:11573-11583. [PMID: 33315405 PMCID: PMC7770817 DOI: 10.1021/acs.jpcb.0c07756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Interfacing
solid-state nanopores with biological systems has been
exploited as a versatile analytical platform for analysis of individual
biomolecules. Although clogging of solid-state nanopores due to nonspecific
interactions between analytes and pore walls poses a persistent challenge
in attaining the anticipated sensing efficacy, insufficient studies
focus on elucidating the clogging dynamics. Herein, we investigate
the DNA clogging behavior by passing double-stranded (ds) DNA molecules
of different lengths through hafnium oxide(HfO2)-coated
silicon (Si) nanopore arrays, at different bias voltages and electrolyte
pH values. Employing stable and photoluminescent-free HfO2/Si nanopore arrays permits a parallelized visualization of DNA clogging
with confocal fluorescence microscopy. We find that the probability
of pore clogging increases with both DNA length and bias voltage.
Two types of clogging are discerned: persistent and temporary. In
the time-resolved analysis, temporary clogging events exhibit a shorter
lifetime at higher bias voltage. Furthermore, we show that the surface
charge density has a prominent effect on the clogging probability
because of electrostatic attraction between the dsDNA and the HfO2 pore walls. An analytical model based on examining the energy
landscape along the DNA translocation trajectory is developed to qualitatively
evaluate the DNA–pore interaction. Both experimental and theoretical
results indicate that the occurrence of clogging is strongly dependent
on the configuration of translocating DNA molecules and the electrostatic
interaction between DNA and charged pore surface. These findings provide
a detailed account of the DNA clogging phenomenon and are of practical
interest for DNA sensing based on solid-state nanopores.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Laurent Barbe
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Maria Tenje
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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18
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Reynaud L, Bouchet-Spinelli A, Raillon C, Buhot A. Sensing with Nanopores and Aptamers: A Way Forward. SENSORS 2020; 20:s20164495. [PMID: 32796729 PMCID: PMC7472324 DOI: 10.3390/s20164495] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
In the 90s, the development of a novel single molecule technique based on nanopore sensing emerged. Preliminary improvements were based on the molecular or biological engineering of protein nanopores along with the use of nanotechnologies developed in the context of microelectronics. Since the last decade, the convergence between those two worlds has allowed for biomimetic approaches. In this respect, the combination of nanopores with aptamers, single-stranded oligonucleotides specifically selected towards molecular or cellular targets from an in vitro method, gained a lot of interest with potential applications for the single molecule detection and recognition in various domains like health, environment or security. The recent developments performed by combining nanopores and aptamers are highlighted in this review and some perspectives are drawn.
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19
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Ferhan AR, Yoon BK, Jeon WY, Cho NJ. Biologically interfaced nanoplasmonic sensors. NANOSCALE ADVANCES 2020; 2:3103-3114. [PMID: 36134263 PMCID: PMC9418064 DOI: 10.1039/d0na00279h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/26/2020] [Indexed: 05/30/2023]
Abstract
Understanding biointerfacial processes is crucial in various fields across fundamental and applied biology, but performing quantitative studies via conventional characterization techniques remains challenging due to instrumentation as well as analytical complexities and limitations. In order to accelerate translational research and address current challenges in healthcare and medicine, there is an outstanding need to develop surface-sensitive technologies with advanced measurement capabilities. Along this line, nanoplasmonic sensing has emerged as a powerful tool to quantitatively study biointerfacial processes owing to its high spatial resolution at the nanoscale. Consequently, the development of robust biological interfacing strategies becomes imperative to maximize its characterization potential. This review will highlight and discuss the critical role of biological interfacing within the context of constructing nanoplasmonic sensing platforms for biointerfacial science applications. Apart from paving the way for the development of highly surface-sensitive characterization tools that will spur fundamental biological interaction studies and improve the overall understanding of biological processes, the basic principles behind biointerfacing strategies presented in this review are also applicable to other fields that involve an interface between an inorganic material and a biological system.
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Affiliation(s)
- Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
- School of Chemical Engineering, Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Won-Yong Jeon
- School of Chemical Engineering, Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University 50 Nanyang Avenue 639798 Singapore
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20
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Bayat H, Raoufi M, Zamrik I, Schönherr H. Poly(diethylene glycol methylether methacrylate) Brush-Functionalized Anodic Alumina Nanopores: Curvature-Dependent Polymerization Kinetics and Nanopore Filling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2663-2672. [PMID: 32073275 DOI: 10.1021/acs.langmuir.9b03700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report on the synthesis and characterization of poly(diethylene glycol methylether methacrylate) (PDEGMA) brushes by surface-initiated atom transfer radical polymerization inside ordered cylindrical nanopores of anodic aluminum oxide with different pore radii between 20 and 185 nm. In particular, the dependence of polymerization kinetics and the degree of pore filling on the interfacial curvature were analyzed. On the basis of field emission scanning electron microscopy data and thermal gravimetric analysis (TGA), it was concluded that the polymerization rate was faster at the pore orifice compared to the pore interior and also as compared to the analogous reaction carried out on flat aluminum oxide substrates. The apparent steady-state polymerization rate near the orifice increased with decreasing pore size. Likewise, the overall apparent polymerization rate estimated from TGA data indicated stronger confinement for pores with increased curvature as well as increased mass transport limitations due to the blockage of the pore orifice. Only for pores with a diameter to length ratio of ∼1, PDEGMA brushes were concluded to grow uniformly with constant thickness. However, because of mass transport limitations in longer pores, incomplete pore filling was observed, which leads presumably to a PDEGMA gradient brush. This study contributes to a better understanding of polymer brush-functionalized nanopores and the impact of confinement, in which the control of polymer brush thickness together with grafting density along the nanopores is key for applications of PDEGMA brushes confined inside nanopores.
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Affiliation(s)
- Haider Bayat
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Mohammad Raoufi
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Imad Zamrik
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Holger Schönherr
- Physical Chemistry I & Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, School of Science and Technology, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
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21
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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22
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Zeng S, Wen C, Solomon P, Zhang SL, Zhang Z. Rectification of protein translocation in truncated pyramidal nanopores. NATURE NANOTECHNOLOGY 2019; 14:1056-1062. [PMID: 31591525 DOI: 10.1038/s41565-019-0549-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/28/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore technology presents an emerging single-molecule-based analytical tool for the separation and analysis of nanoparticles. Different approaches have been pursued to attain the anticipated detection performance. Here, we report the rectification behaviour of protein translocation through silicon-based truncated pyramidal nanopores. When the size of translocating proteins is comparable to the smallest physical constriction of the nanopore, the frequency of translocation events observed is lower for proteins that travel from the larger to the small opening of the nanopore than for those that travel in the reverse direction. When the proteins are appreciably smaller than the nanopore, an opposite rectification in the frequency of translocation events is evident. The maximum rectification factor achieved is around ten. Numerical simulations reveal the formation of an electro-osmotic vortex in such asymmetric nanopores. The vortex-protein interaction is found to play a decisive role in rectifying the translocation in terms of polarity and amplitude. The reported phenomenon can be potentially exploitable for the discrimination of various nanoparticles.
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Affiliation(s)
- Shuangshuang Zeng
- Division of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden
| | - Chenyu Wen
- Division of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden
| | - Paul Solomon
- IBM T.J. Watson Research Center, Yorktown Heights, NY, USA
| | - Shi-Li Zhang
- Division of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden
| | - Zhen Zhang
- Division of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden.
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23
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Wu T, Lankshear ER, Downard AJ. Simultaneous Electro‐Click and Electrochemically Mediated Polymerization Reactions for One‐Pot Grafting from a Controlled Density of Anchor Sites. ChemElectroChem 2019. [DOI: 10.1002/celc.201901395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ting Wu
- School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Ethan R. Lankshear
- School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Alison J. Downard
- School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
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24
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Malekian B, Schoch RL, Robson T, Ferrand-Drake Del Castillo G, Xiong K, Emilsson G, Kapinos LE, Lim RYH, Dahlin A. Detecting Selective Protein Binding Inside Plasmonic Nanopores: Toward a Mimic of the Nuclear Pore Complex. Front Chem 2018; 6:637. [PMID: 30619840 PMCID: PMC6308133 DOI: 10.3389/fchem.2018.00637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022] Open
Abstract
Biosensors based on plasmonic nanostructures offer label-free and real-time monitoring of biomolecular interactions. However, so do many other surface sensitive techniques with equal or better resolution in terms of surface coverage. Yet, plasmonic nanostructures offer unique possibilities to study effects associated with nanoscale geometry. In this work we use plasmonic nanopores with double gold films and detect binding of proteins inside them. By thiol and trietoxysilane chemistry, receptors are selectively positioned on the silicon nitride interior walls. Larger (~150 nm) nanopores are used detect binding of averaged sized proteins (~60 kg/mol) with high signal to noise (>100). Further, we fabricate pores that approach the size of the nuclear pore complex (diameter down to 50 nm) and graft disordered phenylalanine-glycine nucleoporin domains to the walls, followed by titration of karyopherinβ1 transport receptors. The interactions are shown to occur with similar affinity as determined by conventional surface plasmon resonance on planar surfaces. Our work illustrates another unique application of plasmonic nanostructures, namely the possibility to mimic the geometry of a biological nanomachine with integrated optical sensing capabilities.
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Affiliation(s)
- Bita Malekian
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Rafael L Schoch
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Timothy Robson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Kunli Xiong
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
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25
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Zilman A. Aggregation, Phase Separation and Spatial Morphologies of the Assemblies of FG Nucleoporins. J Mol Biol 2018; 430:4730-4740. [DOI: 10.1016/j.jmb.2018.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/17/2022]
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26
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Boyaciyan D, Braun L, Löhmann O, Silvi L, Schneck E, von Klitzing R. Gold nanoparticle distribution in polyelectrolyte brushes loaded at different pH conditions. J Chem Phys 2018; 149:163322. [DOI: 10.1063/1.5035554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Dikran Boyaciyan
- Soft Matter at Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt,
Germany
| | - Larissa Braun
- Soft Matter at Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt,
Germany
| | - Oliver Löhmann
- Soft Matter at Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt,
Germany
| | - Luca Silvi
- Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin,
Germany
| | - Emanuel Schneck
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476 Potsdam,
Germany
| | - Regine von Klitzing
- Soft Matter at Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, 64287 Darmstadt,
Germany
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27
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Emilsson G, Sakiyama Y, Malekian B, Xiong K, Adali-Kaya Z, Lim RYH, Dahlin AB. Gating Protein Transport in Solid State Nanopores by Single Molecule Recognition. ACS CENTRAL SCIENCE 2018; 4:1007-1014. [PMID: 30159397 PMCID: PMC6107858 DOI: 10.1021/acscentsci.8b00268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 05/30/2023]
Abstract
Control of molecular translocation through nanoscale apertures is of great interest for DNA sequencing, biomolecular filters, and new platforms for single molecule analysis. However, methods for controlling the permeability of nanopores are very limited. Here, we show how nanopores functionalized with poly(ethylene glycol) brushes, which fully prevent protein translocation, can be reversibly gated to an "open" state by binding of single IgG antibodies that disrupt the macromolecular barrier. On the basis of surface plasmon resonance data we propose a two-state model describing the antibody-polymer interaction kinetics. Reversibly (weakly) bound antibodies decrease the protein exclusion height while irreversibly (strongly) bound antibodies do not. Our results are further supported by fluorescence readout from pore arrays and high-speed atomic force microscopy on single pores. This type of dynamic barrier control on the nanoscale provides new possibilities for biomolecular separation and analysis.
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Affiliation(s)
- Gustav Emilsson
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Göteborg, Sweden
| | - Yusuke Sakiyama
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, 4056 Basel, Switzerland
| | - Bita Malekian
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Göteborg, Sweden
| | - Kunli Xiong
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Göteborg, Sweden
| | - Zeynep Adali-Kaya
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Göteborg, Sweden
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, 4056 Basel, Switzerland
| | - Andreas B. Dahlin
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, 41296 Göteborg, Sweden
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