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Bilal M, Asgher M, Cheng H, Yan Y, Iqbal HMN. Multi-point enzyme immobilization, surface chemistry, and novel platforms: a paradigm shift in biocatalyst design. Crit Rev Biotechnol 2019; 39:202-219. [PMID: 30394121 DOI: 10.1080/07388551.2018.1531822] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Engineering enzymes with improved catalytic properties in non-natural environments have been concerned with their diverse industrial and biotechnological applications. Immobilization represents a promising but straightforward route, and immobilized biocatalysts often display higher activities and stabilities compared to free enzymes. Owing to their unique physicochemical characteristics, including the high-specific surface area, exceptional chemical, electrical, and mechanical properties, efficient enzyme loading, and multivalent functionalization, nano-based materials are postulated as suitable carriers for biomolecules or enzyme immobilization. Enzymes immobilized on nanomaterial-based supports are more robust, stable, and recoverable than their pristine counterparts, and are even used for continuous catalytic processes. Furthermore, the unique intrinsic properties of nanomaterials, particularly nanoparticles, also confer the immobilized enzymes to be used for their broader applications. Herein, an effort has been made to present novel potentialities of multi-point enzyme immobilization in the current biotechnological sector. Various nano-based platforms for enzyme/biomolecule immobilization are discussed in the second part of the review. In summary, recent developments in the use of nanomaterials as new carriers to construct robust nano-biocatalytic systems are reviewed, and future trends are pointed out in this article.
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Affiliation(s)
- Muhammad Bilal
- a School of Life Science and Food Engineering , Huaiyin Institute of Technology , Huaian , China
| | - Muhammad Asgher
- b Department of Biochemistry , University of Agriculture Faisalabad , Faisalabad , Pakistan
| | - Hairong Cheng
- c State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai , China
| | - Yunjun Yan
- d Key Lab of Molecular Biophysics of Ministry of Education , College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan , China
| | - Hafiz M N Iqbal
- e Tecnologico de Monterrey, School of Engineering and Sciences , Campus Monterrey , Monterrey , Mexico
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Karav S, Cohen JL, Barile D, de Moura Bell JMLN. Recent advances in immobilization strategies for glycosidases. Biotechnol Prog 2016; 33:104-112. [PMID: 27718339 DOI: 10.1002/btpr.2385] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/31/2016] [Indexed: 11/11/2022]
Abstract
Glycans play important biological roles in cell-to-cell interactions, protection against pathogens, as well as in proper protein folding and stability, and are thus interesting targets for scientists. Although their mechanisms of action have been widely investigated and hypothesized, their biological functions are not well understood due to the lack of deglycosylation methods for large-scale isolation of these compounds. Isolation of glycans in their native state is crucial for the investigation of their biological functions. However, current enzymatic and chemical deglycosylation techniques require harsh pretreatment and reaction conditions (high temperature and use of detergents) that hinder the isolation of native glycan structures. Indeed, the recent isolation of new endoglycosidases that are able to cleave a wider variety of linkages and efficiently hydrolyze native proteins has opened up the opportunity to elucidate the biological roles of a higher variety of glycans in their native state. As an example, our research group recently isolated a novel Endo-β-N-acetylglucosaminidase from Bifidobacterium longum subsp. infantis ATCC 15697 (EndoBI-1) that cleaves N-N'-diacetyl chitobiose moieties found in the N-linked glycan (N-glycan) core of high mannose, hybrid, and complex N-glycans. This enzyme is also active on native proteins, which enables native glycan isolation, a key advantage when evaluating their biological activities. Efficient, stable, and economically viable enzymatic release of N-glycans requires the selection of appropriate immobilization strategies. In this review, we discuss the state-of-the-art of various immobilization techniques (physical adsorption, covalent binding, aggregation, and entrapment) for glycosidases, as well as their potential substrates and matrices. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:104-112, 2017.
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Affiliation(s)
- Sercan Karav
- Department of Molecular Biology and Genetics, Canakkale 18 Mart University, Canakkale, Turkey
| | - Joshua L Cohen
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA, 95616
| | - Daniela Barile
- Department of Food Science and Technology, University of California, One Shields Avenue, Davis, CA, 95616.,Foods for Health Institute, University of California, One Shields Avenue, Davis, CA, 95616
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Liu Y, Yu J. Oriented immobilization of proteins on solid supports for use in biosensors and biochips: a review. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1623-4] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zanetti M, Maniglio D, Fasoli C, Pola M, Borga E, Corradi C, Dalla Serra M, Iannotta S, Motta A, Toccoli T. A New Cells-Compatible Microfluidic Device for Single Channel Recordings. ELECTROANAL 2014. [DOI: 10.1002/elan.201400152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Jeong GM, Seong H, Kim YS, Im SG, Jeong KJ. Site-specific immobilization of proteins on non-conventional substrates via solvent-free initiated chemical vapour deposition (iCVD) process. Polym Chem 2014. [DOI: 10.1039/c4py00167b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ma X, Zhang QY. Protein Microarrays for Quantitative Detection of PAI-1 in Serum. Chin J Cancer Res 2012; 24:220-5. [PMID: 23358703 PMCID: PMC3555280 DOI: 10.1007/s11670-012-0220-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 01/18/2012] [Indexed: 10/28/2022] Open
Abstract
OBJECTIVE Plasminogen activator inhibitor-1 (PAI-1), one crucial component of the plasminogen activator system, is a major player in the pathogenesis of many vascular diseases as well as in cancer. High levels of PAI-1 in breast cancer tissue are associated with poor prognosis. The aim of this study is to evaluate rigorously the potential of serum PAI-1 concentration functioning as a general screening test in diagnostic or prognostic assays. METHODS A protein-microarray-based sandwich fluorescence immunoassay (FIA) was developed to detect PAI-1 in serum. Several conditions of this microarray-based FIA were optimized to establish an efficacious method. Serum specimens of 84 healthy women and 285 women with breast cancer were analyzed using the optimized FIA microarray. RESULTS The median serum PAI-1 level of breast cancer patients was higher than that of healthy women (109.7 ng/ml vs. 63.4 ng/ml). Analysis of covariance revealed that PAI-1 levels of the two groups were significantly different (P<0.001) when controlling for an age effect on PAI-1 levels. However, PAI-1 values in TNM stage I-IV patients respectively were not significantly different from each other. CONCLUSION This microarray-based sandwich FIA holds potential for quantitative analysis of tumor markers such as PAI-1.
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Affiliation(s)
- Xu Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Clinical Laboratory, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Prouse MB, Campbell MM. The interaction between MYB proteins and their target DNA binding sites. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:67-77. [DOI: 10.1016/j.bbagrm.2011.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/17/2011] [Accepted: 10/18/2011] [Indexed: 02/02/2023]
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Abstract
Protein microarray or protein chip is an important tool in proteomics. However, duplicating the success of the DNA chip for the protein chip has been difficult. This account discusses a key issue in protein microarray development, i.e., surface chemistry. Ideally, the surface chemistry for protein microarray fabrication should satisfy the following criteria: the surface resists nonspecific adsorption; functional groups for the facile immobilization of protein molecules of interest are readily available; bonding between a protein molecule and a solid surface is balanced to provide sufficient stability but minimal disturbance on the delicate three-dimensional structure of the protein; linking chemistry allows the control of protein orientation; the local chemical environment favors the immobilized protein molecules to retain their native conformation; and finally, the specificity of linking chemistry is so high that no pre-purification of proteins is required. Strategies to achieve such an ideal situation are discussed, with successful examples from our laboratories illustrated. Finally, the need of surface technology for membrane protein microarray fabrication is addressed.
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Affiliation(s)
- ATHENA GUO
- MicroSurfaces, Inc., 4001 Stinson Blvd, Suite 430, Minneapolis, MN 55421, USA
| | - XIAOYANG ZHU
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Tsougeni K, Tserepi A, Constantoudis V, Gogolides E, Petrou PS, Kakabakos SE. Plasma nanotextured PMMA surfaces for protein arrays: increased protein binding and enhanced detection sensitivity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:13883-13891. [PMID: 20666412 DOI: 10.1021/la101957w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Poly(methyl methacrylate) (PMMA) substrates were nanotextured through treatment in oxygen plasma to create substrates with increased surface area for protein microarray applications. Conditions of plasma treatment were found for maximum uniform protein adsorption on these nanotextured PMMA surfaces. Similar results were obtained using both a high-density plasma (HDP) and a low-density reactive ion etcher (RIE), suggesting independence from the plasma reactor type. The protein binding was evaluated by studying the adsorption of two model proteins, namely, biotinylated bovine serum albumin (b-BSA) and rabbit gamma-globulins (RgG). The immobilization of these proteins onto the surfaces was quantitatively determined through reaction with fluorescently labeled binding molecules. It was found that the adsorption of both proteins was increased up to 6-fold with plasma treatment compared to untreated surfaces and up to 4-fold compared to epoxy-coated glass slides. The sensitivity of detection was improved by 2 orders of magnitude. Moreover, highly homogeneous protein spots were created on optimized plasma-nanotextured surfaces through deposition with an automated microarray spotter, revealing the potential of plasma-nanotextured surfaces as protein microarray substrates.
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Affiliation(s)
- K Tsougeni
- Institute of Microelectronics, NCSR Demokritos, P.O. Box 60228, Aghia Paraskevi, Attiki, 153 10 Greece
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El Khoury G, Laurenceau E, Chevolot Y, Mérieux Y, Desbos A, Fabien N, Rigal D, Souteyrand E, Cloarec JP. Development of miniaturized immunoassay: Influence of surface chemistry and comparison with enzyme-linked immunosorbent assay and Western blot. Anal Biochem 2010; 400:10-8. [DOI: 10.1016/j.ab.2010.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 01/06/2010] [Accepted: 01/10/2010] [Indexed: 10/19/2022]
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Zangar RC, Varnum SM, Bollinger N. Studying Cellular Processes and Detecting Disease with Protein Microarrays. Drug Metab Rev 2008; 37:473-87. [PMID: 16257831 DOI: 10.1080/03602530500205309] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Protein microarrays are a rapidly developing analytic tool with diverse applications in biomedical research. These applications include profiling of disease markers or autoimmune responses, understanding molecular pathways, protein modifications, and protein activities. One factor that is driving this expanding usage is the wide variety of experimental formats that protein microarrays can take. In this review, we provide a short, conceptual overview of the different approaches for protein microarray. We then examine some of the most significant applications of these microarrays to date, with an emphasis on how global protein analyses can be used to facilitate biomedical research.
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Affiliation(s)
- Richard C Zangar
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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Quantification of the activity of biomolecules in microarrays obtained by direct laser transfer. Biomed Microdevices 2008; 10:719-25. [DOI: 10.1007/s10544-008-9183-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bi X, Hartono D, Yang KL. Controlling orientations of immobilized oligopeptides using N-terminal cysteine labels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:5238-5240. [PMID: 18399669 DOI: 10.1021/la800458s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This letter reports a strategy of using N-terminal cysteine labels for controlling the immobilization of oligopeptides on aldehyde-terminated surfaces through the formation of stable thiazolidine rings. We also study the effect of cysteine position (either N-terminal or C-terminal) and lysine residue on the immobilization of oligopeptides. On the basis of our ellipsometry and quartz crystal microbalance (QCM) results, we conclude that the proposed immobilization strategy is highly site-specific. It works only when cysteine is in the N-terminal position, and the formation of thiazolidine is much faster than the formation of imines between lysine residues and aldehydes, even in the presence of a reducing agent such as NaBH(3)CN. By labeling an oligopeptide CSNKTRIDEANNKATKML with an N-terminal cysteine, we immobilize this oligopeptide on an aldehyde-terminated surface and investigate the enzymatic activity of trypsin acting on the oligopeptide. It is found that trypsin is able to cleave the immobilized oligopeptide having a single anchoring point at the N-terminal cysteine. No cleavage is observed when the oligopeptide is immobilized through multiple anchoring points at lysine residues.
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Affiliation(s)
- Xinyan Bi
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576
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El Khoury G, Laurenceau E, Dugas V, Chevolot Y, Mérieux Y, Duclos MC, Souteyrand E, Rigal D, Wallach J, Cloarec JP. Acid deprotection of covalently immobilized peptide probes on glass slides for peptide microarrays. ACTA ACUST UNITED AC 2007; 2007:2242-6. [PMID: 18002437 DOI: 10.1109/iembs.2007.4352771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein microarray technology has shown great advancements in the field of biomedical research and diagnosis, it allows to study and understand protein activities and protein - ligand interactions (e.g. detection of antigen-autoantibody interaction in autoimmune diseases. Autoantibodies are frequently targeted against antigens of the cell nucleus (double and single stranded DNA, histones, and nuclear antigens). The biological activities of proteins (e.g. enzymes, antibodies...) are controlled by peptides sequences of the active site. Consequently, we were interested in the investigation of peptide microarrays in order to further implement in situ peptide synthesis, in particular, deprotection reaction on glass supported peptides. In this work, a protected and biotinylated synthetic peptide was covalently immobilized onto amino functionalized glass surface by activation of its the C-terminus; this allows to orientate the peptide onto the surface. The peptide contains a fragment of the C-terminal end of the human histone H3 protein. The immobilized peptide was then deprotected by using concentrated trifluoroacetic acid solution. After the deprotection, surface stability and peptide grafting density were evaluated by indirect labelling of the immobilized peptide using Cy3 streptavidin conjugates. We also studied biological interaction of IgG polyclonal anti-histone H3 antibody with the immobilized peptide epitope to insure the efficiency of the acid deprotection. The specificity of the antibody interaction with the protected versus non protected peptides. This approach may be applied to in situ synthetic and prototected peptides, in order to elaborate a micro-immunoassay prototype for measurement of peptide-protein interactions on high density microarrays, and detection of antibodies in biological fluids such as serum.
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Olle EW, Deogracias MP, Messamore JE, McClintock SD, Barron AG, Anderson TD, Johnson KJ. Screening of serum samples from Wegener's granulomatosis patients using antibody microarrays. Proteomics Clin Appl 2007; 1:1212-20. [PMID: 21136620 DOI: 10.1002/prca.200600906] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Indexed: 02/02/2023]
Abstract
Wegener's Granulomatosis (WG) is an idiopathic granulomatosis autoimmune vasculitis that primarily affects small vessels and is associated with glomerulonephritis and pulmonary granulomatous vasculitis. Anti-neutrophil cytoplasmic auto-antibodies (cANCA) against proteinase-3 are used to identify WG, but ANCA titers are not present in some patients with the localized disease. The objective of this study was to develop an antibody array to help identify protein expression patterns in serum from patients with WG as compared to normals. The arrays were tested for limits of detection, background, and cross reactivity using standard proteins. The arrays were hybridized with either normal patient serum (n = 30) or with serum samples from a population of WG patients (n = 26) that were age and sex matched. Data analysis and curve fitting of the standard dilution series calculated r(2) values and determined a sensitivity of <50 pg/mL for the majority of proteins. A total of 24 proteins were assessed. Several statistically significant increases (p<0.05) were seen in the expression of: angiotensin converting enzyme-I, IFN-γ, IL-8, s-ICAM-1 and s-VCAM in WG patients as compared to controls. Utilizing the antibody microarray technology has led to the identification of potential biomarkers of vascular injury in the serum of WG patients.
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Affiliation(s)
- Eric W Olle
- University of Michigan, Department of Pathology, Ann Arbor, MI, USA; Safety Sciences, Pfizer Global Research & Development, Ann Arbor, MI, USA
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Jung ST, Jeong KJ, Iverson BL, Georgiou G. Binding and enrichment ofEscherichia coli spheroplasts expressing inner membrane tethered scFv antibodies on surface immobilized antigens. Biotechnol Bioeng 2007; 98:39-47. [PMID: 17657772 DOI: 10.1002/bit.21405] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Anchored periplasmic expression (APEx) is a new method for the isolation of high affinity ligand-binding proteins from large combinatorial libraries (Harvey et al., 2004, Proc Natl Acad Sci USA 101(25): 9193-9198). In APEx, proteins are expressed as fusions to a membrane anchor that tethers them onto the periplasmic side of the Escherichia coli inner membrane. Conversion of the cells into spheroplasts and incubation with soluble fluorescently conjugated ligands results in the specific labeling of cells expressing ligand-binding proteins and their subsequent isolation by flow cytometry. Here we show that scFv antibody fragments expressed in the APEx format allow the binding of spheroplasts to immobilized ligands. ScFv antibodies specific for the cardiac glycoside digoxin or for the protective antigen (PA) of Bacillus anthracis as a negative control were expressed in E. coli as fusions to either N-terminal or C-terminal membrane anchoring domains. Only the C-terminally anchored fusions resulted in specific recognition and binding of spheroplasts onto TentaGel beads with immobilized antigen. Following three rounds of flow cytometric screening, spheroplasts expressing anti-digoxin scFvs were enriched 950-fold from a large excess (1,000 x) of spheroplasts expressing anti-PA antibodies. These results indicate that the APEx technology may be employed for the screening of libraries based on binding to insoluble antigens possibly including antigens on cell surfaces.
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Affiliation(s)
- Sang Taek Jung
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
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Mohamadi MR, Mahmoudian L, Kaji N, Tokeshi M, Baba Y. Dynamic coating using methylcellulose and polysorbate 20 for nondenaturing electrophoresis of proteins on plastic microchips. Electrophoresis 2007; 28:830-6. [PMID: 17274100 DOI: 10.1002/elps.200600373] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A dynamic coating using methylcellulose (MC) and a nonionic detergent (polysorbate 20) was developed, which controlled protein adsorption onto the surface of microchannels on a microchip made of poly(methyl methacrylate) (PMMA). Optimum concentration of polysorbate 20 in combination with the range of MC concentrations controlled the protein adsorption onto the microchannel surface, and increased the solubility of the protein samples while facilitating the injection of high concentrations of MC solutions into the microchannels. Higher concentrations of nonionic detergent increased the EOF mobility as opposed to the electrophoretic mobility and caused the electrophoresis to fail. Nondenaturing microchip electrophoresis of protein samples with molecular masses ranging from 20 to 100 kDa were completed in 100 s. Also, successful separation of a BSA sample and its complex with anti-BSA mAb ( 220 kDa) was achieved on a PMMA microchip. The separation exhibited high reproducibility in both migration time (RSD = 1%) and peak area (RSD = 10-15%).
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Affiliation(s)
- Mohamad Reza Mohamadi
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan.
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Abstract
In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein immobilization, in order to fully realize the potential of protein biochips. In fact, protein immobilization is the key to the success of microarray technology. Proteins need to be immobilized onto surfaces with high density in order to allow the usage of small amount of sample solution. Nonspecific protein adsorption needs to be avoided or at least minimized in order to improve detection performances. Moreover, full retention of protein conformation and activity is a challenging task to be accomplished. Although a large number of review papers on protein biochips have been published in recent years, few have focused on protein immobilization technology. In this review, current protein immobilization strategies, including physical, covalent, and bioaffinity immobilization for the fabrication of protein biochips, are described. Particular consideration has been given to oriented immobilization, also referred to as site-specific immobilization, which is believed will improve homogeneous surface covering and accessibility of the active site.
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Affiliation(s)
- Federica Rusmini
- Department of Polymer Chemistry and Biomaterials (PBM), Institute for Biomedical Technology (BMTI), Faculty of Science and Technology, University of Twente, Enschede, 7500 AE, The Netherlands
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Palmer RE, Leung C. Immobilisation of proteins by atomic clusters on surfaces. Trends Biotechnol 2007; 25:48-55. [PMID: 17173994 DOI: 10.1016/j.tibtech.2006.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Accepted: 12/06/2006] [Indexed: 12/20/2022]
Abstract
In this Opinion article, we describe a nanotechnology-based approach to immobilize and orient proteins onto surfaces using atomic clusters prepared by physical methods. This is relevant to future protein biochips where dilute arrays of protein binding sites, each designed to immobilize no more than one protein molecule, would be ideal. In the case of a surface consisting of size-selected atomic gold clusters, proteins containing free cysteine residues can chemisorb directly to the bare cluster surface, thus effecting oriented immobilisation. The selection of atomic gold clusters in the size range 1-100 atoms (<3nm in diameter) is intended to ensure that, typically, only one protein can bind directly to the cluster surface. These nanoclusters of a smaller size scale than that of the protein present minimal contact between the gold and the protein, and hence imply a reduced risk of protein denaturing compared with gold films or extended surfaces.
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Affiliation(s)
- Richard E Palmer
- Nanoscale Physics Research Laboratory, School of Physics and Astronomy, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Song S, Li B, Wang L, Wu H, Hu J, Li M, Fan C. A cancer protein microarray platform using antibody fragments and its clinical applications. MOLECULAR BIOSYSTEMS 2006; 3:151-8. [PMID: 17245494 DOI: 10.1039/b608973a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antibody microarrays have shown great potential for measurement of either a spectrum of target proteins in proteomics or disease-associated antigens in molecular diagnostics. Despite its importance, the applications of antibody microarrays are still limited by a variety of fundamental problems. Among them, cross-reactivity significantly limits the multiplexing ability in parallel sandwich immunoassays. As a result, it is very important to design new capture probes in order to incorporate a universal label into the assay configuration. In this report, an antibody fragments (F(ab')2) microarray platform for serum tumor markers was developed. Each antigen was detected at different concentrations to assemble its calibration curve, and combinations of different markers were tested to examine the specificity of simultaneous detection based on the F(ab')2 microarrays. Diagnostics of serum samples with this cancer antibody microarray platform and immunoradiometric assays (IRMA) were also performed. Wide range calibration curves (0-1280 U mL(-1)) were obtained for each tumor marker. Comparative studies demonstrated that such F(ab')2 microarrays exhibited both moderately improved sensitivity and better specificity than full-sized monoclonal antibody microarrays. It is also demonstrated that this microarray platform is quantitative, highly specific and reasonably sensitive. More importantly, clinical applications of our F(ab')2 microarray platform for upwards of 100 patient serum samples clearly show its potential in cancer diagnostics.
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Affiliation(s)
- Shiping Song
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
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Charles PT, Velez F, Soto CM, Goldman ER, Martin BD, Ray RI, Taitt CR. A galactose polyacrylate-based hydrogel scaffold for the detection of cholera toxin and staphylococcal enterotoxin B in a sandwich immunoassay format. Anal Chim Acta 2006; 578:2-10. [PMID: 17723688 DOI: 10.1016/j.aca.2006.04.083] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/19/2006] [Accepted: 04/22/2006] [Indexed: 11/29/2022]
Abstract
A galactoside-based polyacrylate hydrogel was used as a scaffold to immobilize antibodies for the development of a sandwich immunoassay to detect cholera toxin (CT) and staphylococcal enterotoxin B (SEB). The hydrogel possesses large pores and simulates a solution-like environment allowing easy penetration of large biomolecules. Highly crosslinked hydrogels containing pendant amine or carboxyl functionalities were polymerized through a free-radical polymerization process. Covalent crosslinking of the antibodies on hydrogel films was accomplished using a homobifunctional crosslinker or carbodiimide chemistry. Utilizing the two different crosslinking methodologies, our results demonstrated the effectiveness of repetitive additions of crosslinker reactant into a single location on the gel surface. This approach in fact increased the amount of immobilized antibody. Patterned arrays of the immobilized antibodies for sandwich immunoassay development were achieved using a PDMS template containing micro-channels. This template provided a suitable means for applying reagents in multiple cycles. Fluorescence and three-dimensional (3D) imaging by confocal microscopy and laser scanning confocal microscopy of Cy3-labeled anti-CT and/or Cy3-anti-SEB tracer molecules provided qualitative and quantitative measurements on the efficiency of protein immobilization, detection sensitivity and signal-to-noise ratios. As a result of using the galactose polyacrylate-base hydrogel as a platform for immunoassay development, we have successfully been able to achieve low limits of detection for SEB and cholera toxins (1.0 ng mL(-1)). Repetitive additions (>3 cycles) of the crosslinker and antibody have also shown a dramatic increase in the immobilization of antibody resulting in improved immunoassay sensitivity. Fluorescence signal-to-noise ratios using the hydrogel-based immunoassays have been observed as high a 40:1.
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Affiliation(s)
- Paul T Charles
- U.S. Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC 20375, USA.
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Tinazli A, Tang J, Valiokas R, Picuric S, Lata S, Piehler J, Liedberg B, Tampé R. High-affinity chelator thiols for switchable and oriented immobilization of histidine-tagged proteins: a generic platform for protein chip technologies. Chemistry 2006; 11:5249-59. [PMID: 15991207 DOI: 10.1002/chem.200500154] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein micro-/nanoarrays are becoming increasingly important in systematic approaches for the exploration of protein-protein interactions and dynamic protein networks, so there is a high demand for specific, generic, stable, uniform, and locally addressable protein immobilization on solid supports. Here we present multivalent metal-chelating thiols that are suitable for stable binding of histidine-tagged proteins on biocompatible self-assembled monolayers (SAMs). The architectures and physicochemical properties of these SAMs have been probed by various surface-sensitive techniques such as contact angle goniometry, ellipsometry, and infrared reflection-absorption spectroscopy. The specific molecular organization of proteins and protein complexes was demonstrated by surface plasmon resonance, confocal laser scanning, and atomic force microscopy. In contrast to the mono-NTA/His6 tag interaction, which has major drawbacks because of its low affinity and fast dissociation, drastically improved stability of protein binding by these multivalent chelator surfaces was observed. The immobilized histidine-tagged proteins are uniformly oriented and retain their function. At the same time, proteins can be removed from the chip surface under mild conditions (switchability). This new platform for switchable and oriented immobilization should assist proteome-wide wide analyses of protein-protein interactions as well as structural and single-molecule studies.
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Affiliation(s)
- Ali Tinazli
- Institute of Biochemistry, Biocenter, Johann Wolfgang Goethe-University, Marie-Curie-Strasse 9, 60439 Frankfurt, Germany
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24
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Dai J, Bao Z, Sun L, Hong SU, Baker GL, Bruening ML. High-capacity binding of proteins by poly(acrylic acid) brushes and their derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4274-81. [PMID: 16618175 DOI: 10.1021/la0600550] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Polymeric coatings with high protein-binding capacities are important for increasing the output of affinity-based protein purification and decreasing the detection limits of antibody microarrays. This report describes the use of thick poly(acrylic acid) (PAA) brushes to immobilize as much as 80 monolayers of protein. The brushes were prepared using a recently developed procedure that allows polymerization of 100-nm-thick poly(tert-butyl acrylate) films from a surface in just 5 min along with hydrolysis of these films to PAA in 15 min. Covalent binding of bovine serum albumin (BSA) to PAA brushes that were activated using standard coupling agents, however, resulted in immobilization of less than two monolayers of BSA because of competitive hydrolysis of the esters in the activated film. In contrast, derivatization of PAA with nitrilotriacetate (NTA)-Cu2+ complexes yielded films capable of binding many monolayers of protein via metal-ion affinity interactions. For example, derivatization of 55-nm-thick PAA films with NTA-Cu2+ allowed immobilization of about 15 monolayers (5.8 microg/cm2 or 58 nm) of BSA. The binding capacity was even higher for myoglobin (7.7 microg/cm2) and anti-IgG (9.6 microg/cm2). Remarkably, electrostatic adsorption of lysozyme in 55-nm-thick, underivatized PAA resulted in as much as 80 monolayers (16.2 microg/cm2 or 162 nm) of adsorbed protein. Polymer synthesis, derivatization, and swelling, as well as BSA immobilization kinetics and thermodynamics were characterized using reflectance FT-IR spectroscopy, ellipsometry, and protein assays.
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Affiliation(s)
- Jinhua Dai
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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25
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Schäferling M, Nagl S. Optical technologies for the read out and quality control of DNA and protein microarrays. Anal Bioanal Chem 2006; 385:500-17. [PMID: 16609845 DOI: 10.1007/s00216-006-0317-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 11/02/2005] [Accepted: 01/13/2006] [Indexed: 10/24/2022]
Abstract
Microarray formats have become an important tool for parallel (or multiplexed) monitoring of biomolecular interactions. Surface-immobilized probes like oligonucleotides, cDNA, proteins, or antibodies can be used for the screening of their complementary targets, covering different applications like gene or protein expression profiling, analysis of point mutations, or immunodiagnostics. Numerous reviews have appeared on this topic in recent years, documenting the intriguing progress of these miniaturized assay formats. Most of them highlight all aspects of microarray preparation, surface chemistry, and patterning, and try to give a systematic survey of the different kinds of applications of this new technique. This review places the emphasis on optical technologies for microarray analysis. As the fluorescent read out of microarrays is dominating the field, this topic will be the focus of the review. Basic principles of labeling and signal amplification techniques will be introduced. Recent developments in total internal reflection fluorescence, resonance energy transfer assays, and time-resolved imaging are addressed, as well as non-fluorescent imaging methods. Finally, some label-free detection modes are discussed, such as surface plasmon microscopy or ellipsometry, since these are particularly interesting for microarray development and quality control purposes.
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Affiliation(s)
- Michael Schäferling
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany.
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26
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Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. ACTA ACUST UNITED AC 2006; 23:77-88. [PMID: 16527536 DOI: 10.1016/j.bioeng.2006.02.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 02/01/2006] [Accepted: 02/01/2006] [Indexed: 10/24/2022]
Abstract
Microarrays of proteins and peptides make it possible the screening of thousands of binding events in a parallel and high throughput fashion; therefore they are emerging as a powerful tool for proteomics and clinical assays. The complex nature of Proteome, the wide dynamic range of protein concentration in real samples and the critical role of immobilized protein orientation must be taken into account to maximize the utility of protein microarrays. Immobilization strategy and designing of an ideal local chemical environment on the solid surface are both essential for the success of a protein microarray experiment. This review article will focus on protein and peptide arrays highlighting their technical challenges and presenting new directions by means of a set of selected recent applications.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM) - C.N.R., Via Mario Bianco, 9, 20131 Milano, Italy.
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27
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Zhou X, Zhou J. Protein microarrays on hybrid polymeric thin films prepared by self-assembly of polyelectrolytes for multiple-protein immunoassays. Proteomics 2006; 6:1415-26. [PMID: 16404721 DOI: 10.1002/pmic.200500138] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report here the development and characterization of protein microarrays fabricated on nanoengineered 3-D polyelectrolyte thin films (PET) deposited on glass slide by consecutive adsorption of polyelectrolytes via self-assembly technique. Antibodies or antigens were immobilized in the PET-coated glass slides by electrostatic adsorption and entrapment of porous structure of the 3-D polymer film and thus establishing a platform for parallel analysis. Both antigen and antibody microarrays were fabricated on the PET-coated slides, and direct and indirect immunoassays on protein microarrays for multiple-analyte detection were demonstrated. Microarrays produced on these PET-coated slides have consistent spot morphology and provide performance features needed for proteomic analysis. The protein microarrays on the PET films provide LOD as low as 6 pg/mL and dynamic ranges up to three orders of magnitude, which are wider than the protein microarrays fabricated on aldehyde and poly-L-lysine functionalized slides. The PET films constructed by self-assembly technique in aqueous solution is green chemistry based, cost-effective method to generate 3-D thin film coatings on glass surface, and the coated slide is well suited for immobilizing many types of biological molecules so that a wide variety of microarray formats can be developed on this type of slide.
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Affiliation(s)
- Xichun Zhou
- Genomics Group, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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28
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Zubtsov DA, Ivanov SM, Rubina AY, Dementieva EI, Chechetkin VR, Zasedatelev AS. Effect of mixing on reaction–diffusion kinetics for protein hydrogel-based microchips. J Biotechnol 2006; 122:16-27. [PMID: 16182399 DOI: 10.1016/j.jbiotec.2005.08.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Revised: 07/11/2005] [Accepted: 08/04/2005] [Indexed: 11/19/2022]
Abstract
Protein hydrogel-based microchips are being developed for high-throughput evaluation of the concentrations and activities of various proteins. To shorten the time of analysis, the reaction-diffusion kinetics on gel microchips should be accelerated. Here we present the results of the experimental and theoretical analysis of the reaction-diffusion kinetics enforced by mixing with peristaltic pump. The experiments were carried out on gel-based protein microchips with immobilized antibodies under the conditions utilized for on-chip immunoassay. The dependence of fluorescence signals at saturation and corresponding saturation times on the concentrations of immobilized antibodies and antigen in solution proved to be in good agreement with theoretical predictions. It is shown that the enhancement of transport with peristaltic pump results in more than five-fold acceleration of binding kinetics. Our results suggest useful criteria for the optimal conditions for assays on gel microchips to balance high sensitivity and rapid fluorescence saturation kinetics.
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Affiliation(s)
- D A Zubtsov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, Russia
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29
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Tamaru SI, Kiyonaka S, Hamachi I. Three Distinct Read-Out Modes for Enzyme Activity Can Operate in a Semi-Wet Supramolecular Hydrogel. Chemistry 2005; 11:7294-304. [PMID: 16196071 DOI: 10.1002/chem.200500666] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Assays of hydrolytic enzyme activity, such as of glycosidases and phosphatase, as well as several proteases, using a semi-wet supramolecular hydrogel array composed of a glycosylated amino acetate are described. It has been demonstrated that the microcavity formed by gel fibrils is suitable to immobilize native enzymes without denaturation under semi-wet conditions, and thus the nanofiber has been rationally used as a sensing domain to monitor enzymatic reactions. By using a fluorogenic substrate, reducing the size of the hydrogel can significantly improve the problem of suppressed diffusion within the gel matrix thus making the hydrogel a promising semi-wet matrix for evaluating enzyme activity. Confocal laser scanning microscopy observations have shown that an environmentally sensitive fluorescent probe accumulates in the hydrophobic domain of the gel fiber and emits fluorescence more strongly upon hydrolytic cleavage of the substrate peptides. Not only a simple environmentally sensitive probe but also a FRET (fluorescence resonance energy transfer)-type read-out mode can be devised to analyze the enzymatic hydrolysis-triggered redistribution of the probe between the nanospace and the nanofiber to accomplish a more clearly distinguished enzyme assay. Thus, it is clear that three distinct read-out modes, that is, 1) fluorogenic substrates, 2) substrates bearing an environmentally sensitive probe, or 3) a substrate exhibiting FRET, can operate under the semi-wet hydrogel conditions used in these investigations. In addition, owing to the unique properties of the present supramolecular hydrogel in semi-wet conditions, that is, its phase-segregation properties and dynamics, the supramolecular substrate/enzyme array has successfully been used for high-throughput screening of single and multiple enzymes based on their activity, lysate analysis, and quantitative evaluation of inhibitor potency and selectivity.
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Affiliation(s)
- Shun-Ichi Tamaru
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Kyoto-daigaku Katsura, 615-8510, Japan
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30
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Olle EW, Messamore J, Deogracias MP, McClintock SD, Anderson TD, Johnson KJ. Comparison of antibody array substrates and the use of glycerol to normalize spot morphology. Exp Mol Pathol 2005; 79:206-9. [PMID: 16246325 DOI: 10.1016/j.yexmp.2005.09.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2005] [Accepted: 09/07/2005] [Indexed: 10/25/2022]
Abstract
Antibody microarrays are a high-throughput proteomic technology used to examine the expression of multiple proteins in complex solutions. Antibody microarrays can be manufactured on a variety of commercially available activated glass or coated slides. The goal of this study was to compare Hydrogeltrade mark, nitrocellulose, aldehyde-silane and epoxy-silane slides to determine the amount of antibody bound. The optimal substrate was defined as one that bound the greatest amount of antibody with minimal background. Our studies found that epoxy-silane enhanced surface (ES) slides gave the greatest degree of binding along with a minimal background. However, larger antibody microarrays showed variability in spot size, high intra-spot coefficient of variation and drying artifacts. Increasing the amount of glycerol in the spotting buffer caused a dose-dependent improvement in overall spot morphology. Glycerol was tested on 128 different antibodies and showed decreased: mean spot diameter, intra-spot coefficient of variation and drying artifacts. These studies revealed that the optimal slide substrate was epoxy-silane ES microarray slides. Furthermore, glycerol could normalize spot size, decrease intra-spot coefficient of variability, decrease drying artifacts and increase antibody-spotting density.
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Affiliation(s)
- Eric W Olle
- Pfizer Global Research and Development, Safety Sciences, Ann Arbor, MI 48105, USA
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31
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Dai J, Baker GL, Bruening ML. Use of Porous Membranes Modified with Polyelectrolyte Multilayers as Substrates for Protein Arrays with Low Nonspecific Adsorption. Anal Chem 2005; 78:135-40. [PMID: 16383320 DOI: 10.1021/ac0513966] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coating of substrates with polyelectrolyte multilayers terminated with poly(acrylic acid) (PAA) followed by activation of the free -COOH groups of PAA provides a surface that readily reacts with amine groups to allow covalent immobilization of antibodies. The use of this procedure to prepare arrays of antibodies in porous alumina supports facilitates construction of a flow-through system for analysis of fluorescently labeled antigens. Detection limits in the analysis of Cy5-labeled IgG are 0.02 ng/mL because of the high surface area of the alumina membrane, and the minimal diameter of the substrate pores results in binding limited by kinetics, not mass transport. Moreover, PAA-terminated films resist nonspecific protein adsorption, so blocking of antibody arrays with bovine serum albumin is not necessary. These microarrays are capable of effective analysis in 10% fetal bovine serum.
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Affiliation(s)
- Jinhua Dai
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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32
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Dyukova VI, Dementieva EI, Zubtsov DA, Galanina OE, Bovin NV, Rubina AY. Hydrogel glycan microarrays. Anal Biochem 2005; 347:94-105. [PMID: 16236238 DOI: 10.1016/j.ab.2005.09.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 09/11/2005] [Indexed: 11/29/2022]
Abstract
The technology of hydrogel microchips manufacturing, which was developed previously for covalent immobilization of DNA and proteins, was applied for the preparation of glycochips and combined glyco/protein chips. Microchips consist of hydrogel drops separated with hydrophobic surface. Spacered amino-saccharides and polyacrylamide glycoconjugates were used for immobilization. Gel elements were approximately 1 nl in volume (150 microm in diameter and 25 microm in height), and the amount of covalently immobilized saccharide in the glycoarray was 0.4-1.7 pmol per gel element. Hydrogel glycan microchips were used for quantitative assay of antibodies against blood group antigens and assay of lectins with fluorescent detection. In all cases, only specific interaction with chip-immobilized saccharides was observed, whereas the background signal was very low. The detection limit of on-chip assays was comparable to that of the standard 96-well plate assays. Mixing of reaction solution allowed us to decrease the duration of the assays significantly: 2-3 h for incubation and development steps and 10 min for washing. A method for determination of association constants for binding of compounds with chip-immobilized ligands from the kinetics of their binding is proposed. Combined microchips containing different types of biomolecules can be designed and used for simultaneous detection of different compounds.
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Affiliation(s)
- V I Dyukova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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33
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Chiari M, Cretich M, Corti A, Damin F, Pirri G, Longhi R. Peptide microarrays for the characterization of antigenic regions of human chromogranin A. Proteomics 2005; 5:3600-3. [PMID: 16097033 DOI: 10.1002/pmic.200401216] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microarraying peptides is a powerful proteomics technique for studying molecular recognition events. Since peptides have small molecular mass, they are not easily accessible when adsorbed onto solid supports. Moreover, peptides can lack a well-defined three-dimensional structure, and therefore a correct orientation is essential to promote the interaction with their target. In this work, we investigated the suitability as a peptide array substrate of a glass slide coated with a copolymer of N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and [3-(methacryloyl-oxy)propyl]trimethoxysilyl. This polymeric surface was used as substrate for peptides in the characterization of linear antigenic sites of human chromogranin A, a useful tissue and serum marker for neuroendocrine tumors and a precursor of many biologically active peptides. The microarray support provided sufficient accessibility of the ligand, with no need for a spacer, as the polymer chains prevent interaction of immobilized peptides with substrate. In addition, the polymeric surface constitutes an aqueous micro-environment in which linear epitopes are freely exposed despite peptide random orientation. The results reported in this article are in accordance with those obtained in conventional ELISA assays using biotinylated and non-biotinylated peptides.
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Affiliation(s)
- Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, Milan, Italy
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34
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Sauer S, Lange BMH, Gobom J, Nyarsik L, Seitz H, Lehrach H. Miniaturization in functional genomics and proteomics. Nat Rev Genet 2005; 6:465-76. [PMID: 15931170 DOI: 10.1038/nrg1618] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future.
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Affiliation(s)
- Sascha Sauer
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 73, D-14195 Berlin, Germany.
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35
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Yamaguchi S, Yoshimura I, Kohira T, Tamaru SI, Hamachi I. Cooperation between Artificial Receptors and Supramolecular Hydrogels for Sensing and Discriminating Phosphate Derivatives. J Am Chem Soc 2005; 127:11835-41. [PMID: 16104762 DOI: 10.1021/ja052838y] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study has successfully demonstrated that the cooperative action of artificial receptors with semi-wet supramolecular hydrogels may produce a unique and efficient molecular recognition device not only for the simple sensing of phosphate derivatives, but also for discriminating among phosphate derivatives. We directly observed by confocal laser scanning microscopy that fluorescent artificial receptors can dynamically change the location between the aqueous cavity and the hydrophobic fibers upon guest-binding under semi-wet conditions provided by the supramolecular hydrogel. On the basis of such a guest-dependent dynamic redistribution of the receptor molecules, a sophisticated means for molecular recognition of phosphate derivatives can be rationally designed in the hydrogel matrix. That is, the elaborate utilization of the hydrophobic fibrous domains, as well as the water-rich hydrophilic cavities, enables us to establish three distinct signal transduction modes for phosphate sensing: the use of (i) a photoinduced electron transfer type of chemosensor, (ii) an environmentally sensitive probe, and (iii) an artificial receptor displaying a fluorescence resonance energy transfer type of fluorescent signal change. Thus, one can selectively sense and discriminate the various phosphate derivatives, such as phosphate, phospho-tyrosine, phenyl phosphate, and adenosine triphosphate, using a fluorescence wavelength shift and a seesaw type of ratiometric fluorescence change, as well as a simple fluorescence intensity change. It is also shown that an array of the miniaturized hydrogel is promising for the rapid and high-throughput sensing of these phosphate derivatives.
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Affiliation(s)
- Satoshi Yamaguchi
- PRESTO (Synthesis and Control, Japan Science and Technology), Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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36
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Taitt CR, Anderson GP, Ligler FS. Evanescent wave fluorescence biosensors. Biosens Bioelectron 2005; 20:2470-87. [PMID: 15854820 DOI: 10.1016/j.bios.2004.10.026] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 10/24/2004] [Accepted: 10/28/2004] [Indexed: 10/26/2022]
Abstract
Since discovery and first use in the mid-1970s, evanescent wave fluorescence biosensors have developed into a diverse range of instruments, each designed to meet a particular detection need. In this review, we provide a brief synopsis of what evanescent wave fluorescence biosensors are, how they work, and how they are used. In addition, we have summarized the important patents that have impacted the evolution from laboratory curiosities to fully automated commercial products. Finally, we address the critical issues that evanescent wave fluorescence biosensors will face in the coming years.
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Affiliation(s)
- Chris Rowe Taitt
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, DC 20375-5348, USA
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37
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Rubina AY, Dyukova VI, Dementieva EI, Stomakhin AA, Nesmeyanov VA, Grishin EV, Zasedatelev AS. Quantitative immunoassay of biotoxins on hydrogel-based protein microchips. Anal Biochem 2005; 340:317-29. [PMID: 15840505 DOI: 10.1016/j.ab.2005.01.042] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Indexed: 11/23/2022]
Abstract
Three-dimensional gel-based microchips with immobilized proteins were used for quantitative immunoassay of a series of plant (ricin and viscumin) and bacterial (staphylococcal enterotoxin B, tetanus and diphtheria toxins, and lethal factor of anthrax) toxins. It was shown that different types of immunoassays (direct, competitive, and sandwich type) could be carried out on gel microchips. As shown by confocal microscope studies, antigen-antibody interactions involving the formation of tertiary antibody-antigen-antibody complex occur in the whole volume of microchip gel elements. Sandwich assay on microchips with immobilized antibodies provided the highest sensitivity of detection (0.1 ng/ml for ricin). Antibodies labeled with fluorescent dyes, horseradish peroxidase conjugates, or biotinylated antibodies with subsequent treatment with labeled avidin were used as developing antibodies. The results of immunoassays were recorded using fluorescence, chemiluminescence, or matrix-assisted laser desorption ionization mass spectrometry directly from microchip gel elements. Gel microchips with immobilized capture antibodies were used to analyze the sample simultaneously for the presence of all six biotoxins with the same sensitivity as that for any single toxin.
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Affiliation(s)
- A Yu Rubina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 ul. Vavilova, 119991 Moscow, Russia.
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38
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Ko IK, Kato K, Iwata H. Antibody microarray for correlating cell phenotype with surface marker. Biomaterials 2005; 26:687-96. [PMID: 15282147 DOI: 10.1016/j.biomaterials.2004.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 03/13/2004] [Indexed: 10/26/2022]
Abstract
To correlate cell surface markers with the cell phenotype, an antibody microarray prepared by covalently immobilizing antibodies onto a cellulose membrane and subsequent immunocytochemical staining were employed. The direct binding assay of a lymphoblastic leukemia cell line on the microarray showed that the immobilized antibody served to capture cells expressing the specific antigen. The density of bound cells increased linearly with an increasing content of antigen-expressing cells in suspension. The method was further applied to the analysis of surface antigens expressed on neural stem cells. A binding assay was performed with neural cells obtained from the neurosphere culture of the rat fetal striatum on a microarray spotted with eight kinds of antibodies and four different proteins, followed by immunocytochemical staining of cells bound to the microarray using antibodies to the intracellular markers of immature (nestin and vimentin) and mature (beta-tubulin III and glial fibrillary acidic protein) neural cells. As a result, the phenotype of bound cells could be correlated to surface antigen expression, which illustrated the potential of the solid-phase cytometry developed here for the identification of surface markers.
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MESH Headings
- Animals
- Antibodies/immunology
- Antibody Specificity
- Antigen-Antibody Reactions
- Antigens, CD/analysis
- Antigens, CD/immunology
- Antigens, Surface/analysis
- Antigens, Surface/immunology
- B-Lymphocytes/immunology
- Burkitt Lymphoma/pathology
- Cell Differentiation
- Cell Line, Tumor/immunology
- Cells, Cultured/immunology
- Cellulose
- Corpus Striatum/cytology
- Corpus Striatum/embryology
- Corpus Striatum/immunology
- Feasibility Studies
- Fluorescent Antibody Technique, Indirect
- Glial Fibrillary Acidic Protein/analysis
- Glial Fibrillary Acidic Protein/immunology
- Humans
- Immunophenotyping/methods
- Intermediate Filament Proteins/analysis
- Intermediate Filament Proteins/immunology
- Membranes, Artificial
- Microarray Analysis
- Microscopy, Fluorescence
- Nerve Tissue Proteins/analysis
- Nerve Tissue Proteins/immunology
- Nestin
- Neurons/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Rats
- Rats, Inbred F344
- Stem Cells/immunology
- T-Lymphocytes/immunology
- Tubulin/analysis
- Tubulin/immunology
- Vimentin/analysis
- Vimentin/immunology
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Affiliation(s)
- In Kap Ko
- Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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39
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Pişkin E, Garipcan B. Biochips: focusing on surfaces and surface modification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2005; 553:149-66. [PMID: 15503454 DOI: 10.1007/978-0-306-48584-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Erhan Pişkin
- Hacettepe University-Center of Bioengineering and Bioengineering Division, and TUBITAK: Center of Excellence-BIYOMUH, Beytepe, Ankara, Turkey
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40
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Cretich M, Pirri G, Damin F, Solinas I, Chiari M. A new polymeric coating for protein microarrays. Anal Biochem 2005; 332:67-74. [PMID: 15301950 DOI: 10.1016/j.ab.2004.05.041] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Indexed: 11/29/2022]
Abstract
Despite the increasing interest in arraying proteins in a high-density format, several technical issues still impede the development of protein microarray technology. One of the major problems is the availability of substrates that are able to bind native proteins with high density. In this study, we investigated the suitability of a novel surface as a support for protein microarrays. A polymeric glass coating is obtained by physical adsorption of a N,N-dimethylacrylamide (DMA), N,N-acryloyloxysuccinimide (NAS), and [3-(methacryloyl-oxy)propyl]trimethoxysilyl (MAPS) copolymer. The coating procedure provides a fast and inexpensive method of producing hydrophilic functional surfaces. The slide performance was investigated in a protein-protein interaction experiment and in the assessment of rheumatoid factor (RF) in human serum samples. The results demonstrate that the ligands immobilized on the polymeric surface maintain an active conformation and are easily accessible, providing a detection limit of 54amol/spot. Moreover, in the RF assay, after hybridization with the sera, the slides have a low background, leading to a detection limit of 900amol/spot.
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Affiliation(s)
- Marina Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), C.N.R., Via Mario Bianco 9, 20131 Milano, Italy.
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Abstract
We compare the catalytic activities of enzymes immobilized on silicon surfaces with and without orientation. While oriented sulfotransferases selectively immobilized on an otherwise zero-background surface via 6xHis tags faithfully reflect activities of solution phase enzymes, those with random orientation on the surface do not. This finding demonstrates that controlling the orientation of immobilized protein molecules and designing an ideal local chemical environment on the solid surface are both essential if protein microarrays are to be used as quantitative tools in biomedical research.
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Affiliation(s)
- Taewoon Cha
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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KRETSINGER ROBERTH. Proteins and the Flow of Information in Cellular Function. Mol Imaging 2005. [DOI: 10.1016/b978-019517720-6.50010-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Pathak S, Singh AK, McElhanon JR, Dentinger PM. Dendrimer-activated surfaces for high density and high activity protein chip applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:6075-6079. [PMID: 15248684 DOI: 10.1021/la036271f] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Highly functional Si and glass surfaces for protein immobilization have been prepared by a facile activation of native surface silanol groups. Poly(propyleneimine) dendrimers of generations 1-5 were immobilized onto the surface using a facile room-temperature coupling procedure that involved activation of native silanol groups of glass using 1,1'-carbonyldiimidazole under anhydrous conditions. The dendrimer-coated surfaces were used to immobilize proteins and were characterized with respect to surface loading and activity. A number of different chemical, physical, and biochemical techniques including contact angle measurement, ellipsometry, and fluorescence microscopy were used to characterize the resulting surfaces. Increasing the dendrimer generation past G-3 led to increased surface amine content, immobilized protein concentration, and the activity of immobilized alkaline phosphatase (used as a test system). Very high activity of the immobilized proteins in the case of higher generation (G-4 and G-5) dendrimers led us to conclude that such an approach has true potential for creating highly functional surfaces for protein chip applications.
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Affiliation(s)
- Srikant Pathak
- Materials Chemistry, Sandia National Laboratories, MS 9403, 7011 East Avenue, Livermore, California 94550, USA.
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