1
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Martínez-Miguel M, Kyvik AR, M Ernst L, Martínez-Moreno A, Cano-Garrido O, Garcia-Fruitós E, Vazquez E, Ventosa N, Guasch J, Veciana J, Villaverde A, Ratera I. Stable anchoring of bacteria-based protein nanoparticles for surface enhanced cell guidance. J Mater Chem B 2020; 8:5080-5088. [PMID: 32400840 DOI: 10.1039/d0tb00702a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In tissue engineering, biological, physical, and chemical inputs have to be combined to properly mimic cellular environments and successfully build artificial tissues which can be designed to fulfill different biomedical needs such as the shortage of organ donors or the development of in vitro disease models for drug testing. Inclusion body-like protein nanoparticles (pNPs) can simultaneously provide such physical and biochemical stimuli to cells when attached to surfaces. However, this attachment has only been made by physisorption. To provide a stable anchoring, a covalent binding of lactic acid bacteria (LAB) produced pNPs, which lack the innate pyrogenic impurities of Gram-negative bacteria like Escherichia coli, is presented. The reported micropatterns feature a robust nanoscale topography with an unprecedented mechanical stability. In addition, they are denser and more capable of influencing cell morphology and orientation. The increased stability and the absence of pyrogenic impurities represent a step forward towards the translation of this material to a clinical setting.
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Affiliation(s)
- Marc Martínez-Miguel
- Department of Molecular Nanoscience and Organic Materials, Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra 08193, Spain.
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2
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Dirscherl C, Springer S. Protein micropatterns printed on glass: Novel tools for protein-ligand binding assays in live cells. Eng Life Sci 2017; 18:124-131. [PMID: 32624894 DOI: 10.1002/elsc.201700010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 08/10/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022] Open
Abstract
Micrometer-sized patterns of proteins on glass or silica surfaces are in widespread use as protein arrays for probing with ligands or recombinant proteins. More recently, they have been used to capture the surface proteins of mammalian cells seeded onto them, and to arrange these surface proteins into pattern structures. Binding of small molecule ligands or of other proteins, transmembrane or intracellular, to these captured surface proteins can then be quantified. However, reproducible production of protein micropatterns on surfaces can be technically difficult. In this review, we outline the wide potential and the current practical uses of printed protein micropatterns in a historical overview, and we detail some potential pitfalls and difficulties from our own experience, as well as ways to circumvent them.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry Jacobs University Bremen Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry Jacobs University Bremen Germany
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3
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Dirscherl C, Palankar R, Delcea M, Kolesnikova TA, Springer S. Specific Capture of Peptide-Receptive Major Histocompatibility Complex Class I Molecules by Antibody Micropatterns Allows for a Novel Peptide-Binding Assay in Live Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602974. [PMID: 28151581 DOI: 10.1002/smll.201602974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Binding assays with fluorescently labeled ligands and recombinant receptor proteins are commonly performed in 2D arrays. But many cell surface receptors only function in their native membrane environment and/or in a specific conformation, such as they appear on the surface of live cells. Thus, receptors on live cells should be used for ligand binding assays. Here, it is shown that antibodies preprinted on a glass surface can be used to specifically array a peptide receptor of the immune system, i.e., the major histocompatibility complex class I molecule H-2Kb , into a defined pattern on the surface of live cells. Monoclonal antibodies make it feasible to capture a distinct subpopulation of H-2Kb and hold it at the cell surface. This patterned receptor enables a novel peptide-binding assay, in which the specific binding of a fluorescently labeled index peptide is visualized by microscopy. Measurements of ligand binding to captured cell surface receptors in defined confirmations apply to many problems in cell biology and thus represent a promising tool in the field of biosensors.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Raghavendra Palankar
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Nanostructure Group, ZIK HIKE, University of Greifswald, Fleischmannstraße 42-44, 17489, Greifswald, Germany
| | - Tatiana A Kolesnikova
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
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4
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Abstract
Chemists and biologists have long recognized small molecule probes as powerful tools for functional genomics and proteomics studies. The possibility of specifically attaching chemical probes to individual proteins with spatial and temporal resolution has greatly improved our ability to visualize and characterize proteins in their native environment. The continued development of novel molecular probes for protein labeling is, therefore, of fundamental importance to gain new insights into biological processes in living cells and organisms. Several excellent approaches for the site-specific labeling of fusion proteins with chemical probes exist. Herein I discuss the design and generation of chemical probes for the SNAP-tag and CLIP-tag systems. The first part of this chapter is dedicated to reviewing the principles of the SNAP-tag technology, followed by a section dedicated to the development of chemical probes for unique applications, such as super-resolution imaging, protein trafficking and recycling, protein-protein interactions, and biomolecular sensing. The last part of the chapter contains experimental protocols and technical notes for the synthesis of selected SNAP-tag substrates and labeling of SNAP-tag fusion proteins in vitro and in living cells.
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Affiliation(s)
- Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA,
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5
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Microfluidic antibody arrays for simultaneous cell separation and stimulus. Anal Bioanal Chem 2014; 406:7867-73. [PMID: 25354890 DOI: 10.1007/s00216-014-8244-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/29/2014] [Accepted: 10/06/2014] [Indexed: 01/09/2023]
Abstract
A microfluidic chip containing stamped antibody arrays was developed for simultaneous cell separation and drug testing. Poly(dimethyl siloxane) (PDMS) stamping was used to deposit antibodies in a microfluidic channel, forming discrete cell-capture regions on the surface. Cell mixtures were then introduced, resulting in the separation of cells when specific antibodies were used. Anti-CD19 antibody regions resulted in 94 % capture purity for CD19+ Ramos cells. An antibody that captures multiple cell types, for example anti-CD71, can also be used to capture several cell types simultaneously. Cells could also be loaded onto the arrays with spatial control using laminar streams. Both Ramos B cells and HuT 78 T cells were isolated in the chip and exposed to staurosporine in the same channel. Both cell lines had similar responses to the drug, with 2-10 % of cells remaining viable after 20 h of drug treatment, depending on cell type. The chip can also be used to analyze the efficacy of antibody therapy against cancer cells. Anti-CD95 was deposited on the surface and used for simultaneous cell capture and apoptosis induction via the extrinsic pathway. Cells captured on anti-CD95 surfaces had significant viability loss (15 % viability after 24 h) when compared with a control anti-CD71 antibody (81 % viability after 24 h). This chip can be used for a variety of cell separation and/or drug testing studies, enabling researchers to isolate cells and test them against different anti-cancer compounds and to follow cell response using fluorescence or other readout methods.
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6
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Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology. J Membr Biol 2014; 247:815-26. [DOI: 10.1007/s00232-014-9663-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
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7
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Yu Q, Wang Q, Li B, Lin Q, Duan Y. Technological Development of Antibody Immobilization for Optical Immunoassays: Progress and Prospects. Crit Rev Anal Chem 2014. [DOI: 10.1080/10408347.2014.881249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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8
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Della Pia EA, Holm JV, Lloret N, Le Bon C, Popot JL, Zoonens M, Nygård J, Martinez KL. A step closer to membrane protein multiplexed nanoarrays using biotin-doped polypyrrole. ACS NANO 2014; 8:1844-53. [PMID: 24476392 PMCID: PMC4004317 DOI: 10.1021/nn406252h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/29/2014] [Indexed: 05/23/2023]
Abstract
Whether for fundamental biological research or for diagnostic and drug discovery applications, protein micro- and nanoarrays are attractive technologies because of their low sample consumption, high-throughput, and multiplexing capabilities. However, the arraying platforms developed so far are still not able to handle membrane proteins, and specific methods to selectively immobilize these hydrophobic and fragile molecules are needed to understand their function and structural complexity. Here we integrate two technologies, electropolymerization and amphipols, to demonstrate the electrically addressable functionalization of micro- and nanosurfaces with membrane proteins. Gold surfaces are selectively modified by electrogeneration of a polymeric film in the presence of biotin, where avidin conjugates can then be selectively immobilized. The method is successfully applied to the preparation of protein-multiplexed arrays by sequential electropolymerization and biomolecular functionalization steps. The surface density of the proteins bound to the electrodes can be easily tuned by adjusting the amount of biotin deposited during electropolymerization. Amphipols are specially designed amphipathic polymers that provide a straightforward method to stabilize and add functionalities to membrane proteins. Exploiting the strong affinity of biotin for streptavidin, we anchor distinct membrane proteins onto different electrodes via a biotin-tagged amphipol. Antibody-recognition events demonstrate that the proteins are stably immobilized and that the electrodeposition of polypyrrole films bearing biotin units is compatible with the protein-binding activity. Since polypyrrole films show good conductivity properties, the platform described here is particularly well suited to prepare electronically transduced bionanosensors.
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Affiliation(s)
- Eduardo Antonio Della Pia
- Bio-Nanotechnology Laboratory, Department of Neuroscience and Pharmacology & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jeppe V. Holm
- Niels Bohr Institute, Center for Quantum Devices & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
| | - Noemie Lloret
- Bio-Nanotechnology Laboratory, Department of Neuroscience and Pharmacology & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Christel Le Bon
- Institut de Biologie Physico-Chimique, UMR 7099, CNRS/Université Paris-7, 13 Rue Pierre et Marie Curie, F-75005 Paris, France
| | - Jean-Luc Popot
- Institut de Biologie Physico-Chimique, UMR 7099, CNRS/Université Paris-7, 13 Rue Pierre et Marie Curie, F-75005 Paris, France
| | - Manuela Zoonens
- Institut de Biologie Physico-Chimique, UMR 7099, CNRS/Université Paris-7, 13 Rue Pierre et Marie Curie, F-75005 Paris, France
| | - Jesper Nygård
- Niels Bohr Institute, Center for Quantum Devices & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
| | - Karen Laurence Martinez
- Bio-Nanotechnology Laboratory, Department of Neuroscience and Pharmacology & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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9
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Sateriale A, Roy NH, Huston CD. SNAP-tag technology optimized for use in Entamoeba histolytica. PLoS One 2013; 8:e83997. [PMID: 24391864 PMCID: PMC3877135 DOI: 10.1371/journal.pone.0083997] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/08/2013] [Indexed: 01/11/2023] Open
Abstract
Entamoeba histolytica is a protozoan parasite responsible for invasive intestinal and extraintestinal amebiasis. The pathology of amebiasis is still poorly understood, which can be largely attributed to lack of molecular tools. Here we present the optimization of SNAP-tag technology via codon optimization specific for E. histolytica. The resultant SNAP protein is highly expressed in amebic trophozoites, and shows proper localization when tagged with an endoplasmic reticulum retention signal. We further demonstrate the capabilities of this system using super resolution microscopy, done for the first time in E. histolytica.
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Affiliation(s)
- Adam Sateriale
- University of Vermont Cellular, Molecular, and Biomedical Sciences Program, Burlington, Vermont, United States of America
- University of Vermont Department of Medicine, Burlington, Vermont, United States of America
| | - Nathan H. Roy
- University of Vermont Cellular, Molecular, and Biomedical Sciences Program, Burlington, Vermont, United States of America
- University of Vermont Microbiology and Molecular Genetics, Burlington, Vermont, United States of America
| | - Christopher D. Huston
- University of Vermont Cellular, Molecular, and Biomedical Sciences Program, Burlington, Vermont, United States of America
- University of Vermont Microbiology and Molecular Genetics, Burlington, Vermont, United States of America
- University of Vermont Department of Medicine, Burlington, Vermont, United States of America
- * E-mail:
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10
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Rostgaard KR, Frederiksen RS, Liu YCC, Berthing T, Madsen MH, Holm J, Nygård J, Martinez KL. Vertical nanowire arrays as a versatile platform for protein detection and analysis. NANOSCALE 2013; 5:10226-35. [PMID: 24062006 DOI: 10.1039/c3nr03113f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein microarrays are valuable tools for protein assays. Reducing spot sizes from micro- to nano-scale facilitates miniaturization of platforms and consequently decreased material consumption, but faces inherent challenges in the reduction of fluorescent signals and compatibility with complex solutions. Here we show that vertical arrays of nanowires (NWs) can overcome several bottlenecks of using nanoarrays for extraction and analysis of proteins. The high aspect ratio of the NWs results in a large surface area available for protein immobilization and renders passivation of the surface between the NWs unnecessary. Fluorescence detection of proteins allows quantitative measurements and spatial resolution, enabling us to track individual NWs through several analytical steps, thereby allowing multiplexed detection of different proteins immobilized on different regions of the NW array. We use NW arrays for on-chip extraction, detection and functional analysis of proteins on a nano-scale platform that holds great promise for performing protein analysis on minute amounts of material. The demonstration made here on highly ordered arrays of indium arsenide (InAs) NWs is generic and can be extended to many high aspect ratio nanostructures.
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Affiliation(s)
- Katrine R Rostgaard
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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11
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Tran TNN, Cui J, Hartman MR, Peng S, Funabashi H, Duan F, Yang D, March JC, Lis JT, Cui H, Luo D. A universal DNA-based protein detection system. J Am Chem Soc 2013; 135:14008-11. [PMID: 23978265 DOI: 10.1021/ja405872g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein immune detection requires secondary antibodies which must be carefully selected in order to avoid interspecies cross-reactivity, and is therefore restricted by the limited availability of primary/secondary antibody pairs. Here we present a versatile DNA-based protein detection system using a universal adapter to interface between IgG antibodies and DNA-modified reporter molecules. As a demonstration of this capability, we successfully used DNA nano-barcodes, quantum dots, and horseradish peroxidase enzyme to detect multiple proteins using our DNA-based labeling system. Our system not only eliminates secondary antibodies but also serves as a novel method platform for protein detection with modularity, high capacity, and multiplexed capability.
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Affiliation(s)
- Thua N N Tran
- Department of Biological & Environmental Engineering, ∥Department of Molecular Biology and Genetics, and ⊥Kavli Institute at Cornell for Nanoscale Science, Cornell University , Ithaca, New York 14853, United States
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12
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Wu SC, Wong SL. Structure-guided design of an engineered streptavidin with reusability to purify streptavidin-binding peptide tagged proteins or biotinylated proteins. PLoS One 2013; 8:e69530. [PMID: 23874971 PMCID: PMC3712923 DOI: 10.1371/journal.pone.0069530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/13/2013] [Indexed: 12/13/2022] Open
Abstract
Development of a high-affinity streptavidin-binding peptide (SBP) tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin and SBP with streptavidin were explored. Loop3-4 which serves as a mobile lid for the biotin binding pocket in streptavidin is in the closed state with biotin binding. In contrast, this loop is in the open state with SBP binding. Replacement of glycine-48 with a bulkier residue (threonine) in this loop selectively reduces the biotin binding affinity (Kd) from 4 × 10(-14) M to 4.45 × 10(-10) M without affecting the SBP binding affinity. Introduction of a second mutation (S27A) to the first mutein (G48T) results in the development of a novel engineered streptavidin SAVSBPM18 which could be recombinantly produced in the functional form from Bacillus subtilis via secretion. To form an intact binding pocket for tight binding of SBP, two diagonally oriented subunits in a tetrameric streptavidin are required. It is vital for SAVSBPM18 to be stably in the tetrameric state in solution. This was confirmed using an HPLC/Laser light scattering system. SAVSBPM18 retains high binding affinity to SBP but has reversible biotin binding capability. The SAVSBPM18 matrix can be applied to affinity purify SBP-tagged proteins or biotinylated molecules to homogeneity with high recovery in a reusable manner. A mild washing step is sufficient to regenerate the matrix which can be reused for multiple rounds. Other applications including development of automated protein purification systems, lab-on-a-chip micro-devices, reusable biosensors, bioreactors and microarrays, and strippable detection agents for various blots are possible.
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Affiliation(s)
- Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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13
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Sapsford KE, Algar WR, Berti L, Gemmill KB, Casey BJ, Oh E, Stewart MH, Medintz IL. Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology. Chem Rev 2013; 113:1904-2074. [PMID: 23432378 DOI: 10.1021/cr300143v] [Citation(s) in RCA: 818] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Department of Chemistry and Materials Science, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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14
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Wasserberg D, Uhlenheuer DA, Neirynck P, Cabanas-Danés J, Schenkel JH, Ravoo BJ, An Q, Huskens J, Milroy LG, Brunsveld L, Jonkheijm P. Immobilization of Ferrocene-Modified SNAP-Fusion Proteins. Int J Mol Sci 2013; 14:4066-80. [PMID: 23429193 PMCID: PMC3588085 DOI: 10.3390/ijms14024066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 12/16/2022] Open
Abstract
The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties.
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Affiliation(s)
- Dorothee Wasserberg
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Dana A. Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Pauline Neirynck
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Jordi Cabanas-Danés
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jan Hendrik Schenkel
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Bart Jan Ravoo
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Qi An
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jurriaan Huskens
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
| | - Pascal Jonkheijm
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
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15
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Micropatterning of biomolecules on a glass substrate in fused silica microchannels by using photolabile linker-based surface activation. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0856-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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16
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Braddick LM, Garland PJ, Praeger MF, Butement J, Friedrich D, Morgan DJ, Melvin T. Uniform aligned bioconjugation of biomolecule motifs for integration within microfabricated microfluidic devices. Anal Biochem 2012; 424:195-205. [DOI: 10.1016/j.ab.2012.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/07/2012] [Accepted: 02/16/2012] [Indexed: 11/26/2022]
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17
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Uhlenheuer DA, Wasserberg D, Haase C, Nguyen HD, Schenkel JH, Huskens J, Ravoo BJ, Jonkheijm P, Brunsveld L. Directed Supramolecular Surface Assembly of SNAP-tag Fusion Proteins. Chemistry 2012; 18:6788-94. [DOI: 10.1002/chem.201200238] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Indexed: 02/04/2023]
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18
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Kwok CW, Strähle U, Zhao Y, Scharnweber T, Weigel S, Welle A. Selective immobilization of Sonic hedgehog on benzylguanine terminated patterned self-assembled monolayers. Biomaterials 2011; 32:6719-28. [DOI: 10.1016/j.biomaterials.2011.05.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 05/24/2011] [Indexed: 11/16/2022]
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19
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Kaltenbach M, Stein V, Hollfelder F. SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution. Chembiochem 2011; 12:2208-16. [PMID: 21780273 DOI: 10.1002/cbic.201100240] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Indexed: 01/25/2023]
Abstract
Display systems connect a protein with the DNA encoding it. Such systems (e.g., phage or ribosome display) have found widespread application in the directed evolution of protein binders and constitute a key element of the biotechnological toolkit. In this proof-of-concept study we describe the construction of a system that allows the display of multiple copies of a protein of interest in order to take advantage of avidity effects during affinity panning. To this end, dendrimer-like DNA is used as a scaffold with docking points that can join the coding DNA with multiple protein copies. Each DNA construct is compartmentalised in water-in-oil emulsion droplets. The corresponding protein is expressed, in vitro, inside the droplets as a SNAP-tag fusion. The covalent bond between DNA and the SNAP-tag is created by reaction with dendrimer-bound benzylguanine (BG). The ability to form dendrimer-like DNA straightforwardly from oligonucleotides bearing BG allowed the comparison of a series of templates differing in size, valency and position of BG. In model selections the most efficient constructs show recoveries of up to 0.86 % and up to 400-fold enrichments. The comparison of mono- and multivalent constructs suggests that the avidity effect enhances enrichment by up to fivefold and recovery by up to 25-fold. Our data establish a multivalent format for SNAP-display based on dendrimer-like DNA as the first in vitro display system with defined tailor-made valencies and explore a new application for DNA nanostructures. These data suggest that multivalent SNAP dendrimers have the potential to facilitate the selection of protein binders especially during early rounds of directed evolution, allowing a larger diversity of candidate binders to be recovered.
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Affiliation(s)
- Miriam Kaltenbach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
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Bhuyan M, Katayev E, Stadlbauer S, Nonaka H, Ojida A, Hamachi I, König B. Rigid Luminescent Bis-Zinc(II)-Bis-Cyclen Complexes for the Detection of Phosphate Anions and Non-Covalent Protein Labeling in Aqueous Solution. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100103] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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21
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Liu YCC, Rieben N, Iversen L, Sørensen BS, Park J, Nygård J, Martinez KL. Specific and reversible immobilization of histidine-tagged proteins on functionalized silicon nanowires. NANOTECHNOLOGY 2010; 21:245105. [PMID: 20498527 DOI: 10.1088/0957-4484/21/24/245105] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Silicon nanowire (Si NW)-based field effect transistors (FETs) have shown great potential as biosensors (bioFETs) for ultra-sensitive and label-free detection of biomolecular interactions. Their sensitivity depends not only on the device properties, but also on the function of the biological recognition motif attached to the Si NWs. In this study, we show that SiNWs can be chemically functionalized with Ni:NTA motifs, suitable for the specific immobilization of proteins via a short polyhistidine tag (His-tag) at close proximity to the SiNW surface. We demonstrate that the proteins preserve their function upon immobilization onto SiNWs. Importantly, the protein immobilization on the Si NWs is shown to be reversible after addition of EDTA or imidazole, thus allowing the regeneration of the bioFET when needed, such as in the case of proteins having a limited lifetime. We anticipate that our methodology may find a generic use for the development of bioFETs exploiting functional protein assays because of its high compatibility to various types of NWs and proteins.
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Affiliation(s)
- Yi-Chi C Liu
- Bio-Nanotechnology Laboratory, Department of Neuroscience and Pharmacology & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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22
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Engin S, Trouillet V, Franz CM, Welle A, Bruns M, Wedlich D. Benzylguanine thiol self-assembled monolayers for the immobilization of SNAP-tag proteins on microcontact-printed surface structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6097-6101. [PMID: 20369837 DOI: 10.1021/la904829y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The site-selective, oriented, covalent immobilization of proteins on surfaces is an important issue in the establishment of microarrays, biosensors, biocatalysts, and cell assays. Here we describe the preparation of self-assembled monolayers consisting of benzylguanine thiols (BGT) to which SNAP-tag fusion proteins can be covalently linked. The SNAP-tag, a modified O(6)-alkylguanine-DNA alkyltransferase (AGT), reacts with the headgroup of BGT and becomes covalently bound upon the release of guanine. Bacterially produced recombinant His-tag-SNAP-tag-GFP was used to demonstrate the site-specific immobilization on BGT surface patterns created by microcontact printing (microCP). With this versatile method, any SNAP-tag protein can be coupled to a surface.
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Affiliation(s)
- Sinem Engin
- Center for Functional Nanostructures, Karlsruhe Institute for Technology, Kaiserstrasse 12, D-76131 Karlsruhe, Germany
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Iversen L, Younes-Metzler O, Martinez KL, Stamou D. Chemically specific laser-induced patterning of alkanethiol SAMs: characterization by SEM and AFM. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:12819-24. [PMID: 19624108 DOI: 10.1021/la901872g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Self-assembled monolayers (SAMs) are widely used to modify the interfacial properties of solid surfaces in either a homogeneous or a patterned manner. One of the many techniques developed for patterning SAMs involves heating the surface with a focused laser beam. Localized heating can result in pattern formation through either the ablation of both the solid substrate and the SAM (chemically nonspecific patterning) or, at lower temperatures, the selective breaking of the chemical bonds between the SAM and the substrate (chemically specific patterning). The latter method is termed chemically specific laser-induced patterning and is demonstrated for alkanethiol monolayers on gold (Au). In this report, the interplay between alkanethiol desorption and nanoscale Au ablation is studied using atomic force microscopy to image both the topographical and the chemical features of laser patterned areas. Frequently the two processes occur simultaneously but with different spatial extents, as predicted theoretically, due to their different threshold temperatures. By tuning the exposure conditions (laser power and irradiation time), parameters are established where local heating causes alkanethiol desorption without any Au ablation, thus, allowing chemically specific desorption and patterning of alkanethiol SAMs. This allows chemical patterns to be created without changes in the surface topography. Using scanning electron microscopy, a linear dependence of pattern size on irradiation time is demonstrated for circular features 0.5-1 microm in diameter.
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Affiliation(s)
- Lars Iversen
- BioNanotechnology Laboratory, Department of Neuroscience and Pharmacology, Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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Affinity capturing for targeting proteins into micro and nanostructures. Anal Bioanal Chem 2009; 393:1563-70. [DOI: 10.1007/s00216-008-2595-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
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