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Aparna GM, Tetala KKR. Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays. Biomolecules 2023; 13:biom13040602. [PMID: 37189350 DOI: 10.3390/biom13040602] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023] Open
Abstract
Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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DNA -based hydrogels for high-performance optical biosensing application. Talanta 2022; 244:123427. [DOI: 10.1016/j.talanta.2022.123427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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3
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Akbari F, Foroutan M. The effect of two layers of graphene with a striped pattern on wettability parameters of the biodroplets. ADSORPTION 2020. [DOI: 10.1007/s10450-020-00211-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Díaz-Betancor Z, Bañuls MJ, Maquieira Á. Photoclick chemistry to create dextran-based nucleic acid microarrays. Anal Bioanal Chem 2019; 411:6745-6754. [PMID: 31482291 DOI: 10.1007/s00216-019-02050-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
Abstract
In the literature, there are reports of the utilization of various hydrogels to create generic platforms for protein microarray applications. Here, a novel strategy was developed to obtain high-performance microarrays. In it, a dextran hydrogel is used to covalently immobilize oligonucleotides and proteins. This method employs aqueous solutions of dextran methacrylate (Dx-MA), which is a biocompatible photopolymerizable monomer. Capture probes are immobilized inside the hydrogel via a light-induced thiol-acrylate coupling reaction at the same time as the dextran polymer is formed. Hydrogel microarrays based on this technique were prepared on different surfaces, such as a Blu-ray Disk and polycarbonate or alkene-functionalized glass slides, and these systems showed high probe-loading capabilities and good biorecognition yields. This methodology presents advantages such as a low cost, a short analysis time, a low limit of detection, and multiplexing capabilities, among others. Confocal fluorescence microscopy analysis demonstrated that in these hydrogel-based microarrays, receptor immobilization and the biorecognition event occurred within the hydrogel and not merely on the surface.
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Affiliation(s)
- Zeneida Díaz-Betancor
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - María-José Bañuls
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain. .,Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Ángel Maquieira
- IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
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5
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A review on phenolic wastewater remediation using homogeneous and heterogeneous enzymatic processes: Current status and potential challenges. Sep Purif Technol 2019. [DOI: 10.1016/j.seppur.2019.03.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Vries RD, Andrade CAS, Bakuzis AF, Mandal SM, Franco OL. Next-generation nanoantibacterial tools developed from peptides. Nanomedicine (Lond) 2016; 10:1643-61. [PMID: 26008197 DOI: 10.2217/nnm.15.9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteria resistant against various antimicrobial compounds have emerged in many countries, and the age of resistance has just started. Among the more promising novel antimicrobial compounds on which current research is focusing are the antimicrobial peptides (AMPs). These are often less susceptible to bacterial resistance since multiple modifications in the cellular membranes, cell wall and metabolism are required to reduce their effectiveness. Most likely, the use of pure AMPs will be insufficient for controlling pathogenic bacteria, and innovative approaches are required to employ AMPs in new antibiotic treatments. Therefore, here we review novel bionanotechnological approaches, including nanofibers, nanoparticles and magnetic particles for effectively using AMPs in fighting infectious diseases.
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Affiliation(s)
- Renko de Vries
- 2Department of Biomedical Engineering, University Medical Center Groningen, University of Groningen, PO Box 196, 9700 AD Groningen, The Netherlands
| | - Cesar A S Andrade
- 3Departamento de Bioquímica e Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco, 50670-901 Recife, PE, Brazil
| | - Andris F Bakuzis
- 4Instituto de Física, Universidade Federal de Goiás, 74001-970, Goiânia, GO, Brazil
| | - Santi M Mandal
- 5Anti-Infective Research Lab, Department of Microbiology, Vidyasagar University, Midnapore 721102, West Bengal, Índia
| | - Octavio L Franco
- 6Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160, Brazil.,7S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
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7
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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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8
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Li Z, Zhao B, Wang D, Wen Y, Liu G, Dong H, Song S, Fan C. DNA nanostructure-based universal microarray platform for high-efficiency multiplex bioanalysis in biofluids. ACS APPLIED MATERIALS & INTERFACES 2014; 6:17944-53. [PMID: 25299733 DOI: 10.1021/am5047735] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microarrays of biomolecules have greatly promoted the development of the fields of genomics, proteomics, and clinical assays because of their remarkably parallel and high-throughput assay capability. Immobilization strategies for biomolecules on a solid support surface play a crucial role in the fabrication of high-performance biological microarrays. In this study, rationally designed DNA tetrahedra carrying three amino groups and one single-stranded DNA extension were synthesized by the self-assembly of four oligonucleotides, followed by high-performance liquid chromatography purification. We fabricated DNA tetrahedron-based microarrays by covalently coupling the DNA tetrahedron onto glass substrates. After their biorecognition capability was evaluated, DNA tetrahedron microarrays were utilized for the analysis of different types of bioactive molecules. The gap hybridization strategy, the sandwich configuration, and the engineering aptamer strategy were employed for the assay of miRNA biomarkers, protein cancer biomarkers, and small molecules, respectively. The arrays showed good capability to anchor capture biomolecules for improving biorecognition. Addressable and high-throughput analysis with improved sensitivity and specificity had been achieved. The limit of detection for let-7a miRNA, prostate specific antigen, and cocaine were 10 fM, 40 pg/mL, and 100 nM, respectively. More importantly, we demonstrated that the microarray platform worked well with clinical serum samples and showed good relativity with conventional chemical luminescent immunoassay. We have developed a novel approach for the fabrication of DNA tetrahedron-based microarrays and a universal DNA tetrahedron-based microarray platform for the detection of different types of bioactive molecules. The microarray platform shows great potential for clinical diagnosis.
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Affiliation(s)
- Zhenhua Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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9
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Development of a high density hemagglutinin protein microarray to determine the breadth of influenza antibody responses. Biotechniques 2014; 54:345-8. [PMID: 23750544 DOI: 10.2144/000114041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/13/2013] [Indexed: 11/23/2022] Open
Abstract
We have developed an influenza hemagglutinin protein microarray to assess humoral recognition of diverse influenza strains induced by vaccination and infection. Each array consists of controls and 127 hemagglutinin antigens from 60 viruses, spotted in replicates to generate a single array of 1296 spots. Six arrays are configured on a single slide, which in the following analysis was probed simultaneously with 2 isotype-specific fluorescent secondary antibodies yielding over 15,000 data points per slide. Here we report the use of this system to evaluate mouse, ferret, and human sera. The array allows simultaneous examination of the magnitude of antibody responses, the isotype of such antibodies, and the breadth of influenza strain recognition. We are advancing this technology as a platform for rapid, simple, high-throughput assessment of homologous and heterologous antibody responses to influenza disease and vaccination.
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Lee JR, Magee DM, Gaster RS, LaBaer J, Wang SX. Emerging protein array technologies for proteomics. Expert Rev Proteomics 2013; 10:65-75. [PMID: 23414360 DOI: 10.1586/epr.12.67] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Numerous efforts have been made to understand fundamental biology of diseases based on gene expression. However, the relationship between gene expression and onset of disease often remains obscure. The great advances in protein microarrays allow us to investigate this unclear question through protein profiles, which are regarded as more reliable than gene expressions to serve as the harbinger of disease onset or as the biomarker of disease treatment monitoring. The authors review two relatively new platforms of protein arrays, along with an introduction to the common basis of protein array technologies. Immobilization of proteins on the surface of arrays and neutralizing reactive areas after the immobilization are key practical issues in the field of protein array. One of the emerging protein array technologies is the magneto-nanosensor array, where giant magnetoresistive sensors are used to quantitatively measure the analytes of interest, which are labeled with magnetic nanoparticles. Similar to giant magnetoresistive sensors, several different ways of utilizing magnetic properties for biomolecular detection have been developed and are reviewed here. Another emerging protein array technology is nucleic acid programmable protein arrays, which have thousands of protein features directly expressed by nucleic acids on the array surface. The authors anticipate that these two emerging protein array platforms can be combined to produce synergistic benefits and open new applications in proteomics and clinical diagnostics.
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Affiliation(s)
- Jung-Rok Lee
- Department of Mechanical Engineering, Stanford University, 476 Lomita Mall, Room 208, Stanford, CA 94305, USA
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Scheicher SR, Kainz B, Köstler S, Reitinger N, Steiner N, Ditlbacher H, Leitner A, Pum D, Sleytr UB, Ribitsch V. 2D crystalline protein layers as immobilization matrices for the development of DNA microarrays. Biosens Bioelectron 2013; 40:32-7. [DOI: 10.1016/j.bios.2012.05.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/11/2012] [Accepted: 05/29/2012] [Indexed: 01/12/2023]
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12
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Ivanov IE, Morrison AE, Cobb JE, Fahey CA, Camesano TA. Creating antibacterial surfaces with the peptide chrysophsin-1. ACS APPLIED MATERIALS & INTERFACES 2012; 4:5891-5897. [PMID: 23043421 DOI: 10.1021/am301530a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immobilization of antimicrobial peptides (AMPs) holds potential for creating surfaces with bactericidal properties. In order to successfully incorporate AMPs into desired materials, increased fundamental understanding of the relationship between AMP immobilization and the efficacy of bound peptides as antibacterial agents is required. In this study, we characterize the relationship between surface binding of the AMP and subsequent ability of the peptide to kill bacteria. Surface immobilization of the AMP chrysophsin-1 (CHY1) via a flexible linker is studied in real-time, using a quartz crystal microbalance with dissipation monitoring (QCM-D). Depending on whether the AMP is physically adsorbed to the surface or attached covalently via a zero-length or flexible cross-linker, changes could be observed in AMP orientation, surface density, flexibility, and activity against bacteria. Covalent surface binding of CHY1 led to the formation of solvated monolayers of vertically positioned peptide molecules, while the physical adsorption of CHY1 led to the deposition of rigid monolayers of horizontally positioned peptide molecules on the sensor surface. Covalently bound peptides were not removed by extensive washing and did not leach from the surface. Zero-length immobilization of the peptide decreased its ability to kill E. coli to 34% ± 7% of added bacteria, while binding via a flexible linker resulted in 82% ± 11% of bacteria being killed by the AMP.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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Schertzer MJ, Ahamed MJ, Ben-Mrad R, Lea P, Sullivan PE. Characterizing the surface quality and droplet interface shape for microarray plates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:9961-9966. [PMID: 22671939 DOI: 10.1021/la302091t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The variation in the surface quality of microarray plates was examined by measuring the contact angles of 480 droplets on five microarray plates. It was found that the measured contact angle did not accurately predict the droplet shape for moderate Bond numbers (~0.5 ≤ N(B) ≤ 5). By defining an apparent contact angle using the ratio of the contact radius to the height, the variance in the predicted interface shape decreased by greater than a factor of 3 for both local and globally averaged characteristics. The error in the predicted droplet height was also reduced by 3 orders of magnitude.
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Affiliation(s)
- M J Schertzer
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
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14
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Deng X, Eyster TW, Elkasabi Y, Lahann J. Bio-Orthogonal Polymer Coatings for Co-Presentation of Biomolecules. Macromol Rapid Commun 2012; 33:640-5. [DOI: 10.1002/marc.201100819] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/19/2011] [Indexed: 11/11/2022]
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15
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Mok AK, Kedzierski NA, Chung PN, Lukeman PS. Positional photocleavage control of DNA-based nanoswitches. Chem Commun (Camb) 2011; 47:4905-7. [DOI: 10.1039/c1cc10292c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Onaizi SA, Leong SS. Tethering antimicrobial peptides: Current status and potential challenges. Biotechnol Adv 2011; 29:67-74. [DOI: 10.1016/j.biotechadv.2010.08.012] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/12/2010] [Accepted: 08/22/2010] [Indexed: 12/14/2022]
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17
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Byeon JY, Limpoco FT, Bailey RC. Efficient bioconjugation of protein capture agents to biosensor surfaces using aniline-catalyzed hydrazone ligation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:15430-5. [PMID: 20809595 PMCID: PMC2947609 DOI: 10.1021/la1021824] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Aniline-catalyzed hydrazone ligation between surface-immobilized hydrazines and aldehyde-modified antibodies is shown to be an efficient method for attaching protein capture agents to model oxide-coated biosensor substrates. Silicon photonic microring resonators are used to directly evaluate the efficiency of this surface bioconjugate reaction at various pHs and in the presence or absence of aniline as a nucleophilic catalyst. It is found that aniline significantly increases the net antibody loading for surfaces functionalized over a pH range from 4.5 to 7.4, allowing derivatization of substrates with reduced incubation time and sample consumption. This increase in antibody loading directly results in more sensitive antigen detection when functionalized microrings are employed in a label-free immunoassay. Furthermore, these experiments also reveal an interesting pH-dependent noncovalent binding trend that plays an important role in dictating the amount of antibody attached onto the substrate, highlighting the competing contributions of the bioconjugate reaction rate and the dynamic interactions that control opportunities for a solution-phase biomolecule to react with a substrate-bound reagent.
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Affiliation(s)
- Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - F. T. Limpoco
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
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Neumann T, Bonham AJ, Dame G, Berchtold B, Brandstetter T, Rühe J. Temperature and Time-Resolved Total Internal Reflectance Fluorescence Analysis of Reusable DNA Hydrogel Chips. Anal Chem 2010; 82:6124-31. [DOI: 10.1021/ac1008578] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thorsten Neumann
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Andrew J. Bonham
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Gregory Dame
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Bernd Berchtold
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Thomas Brandstetter
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
| | - Jürgen Rühe
- University of Freiburg – IMTEK, Department of Microsystems Engineering, Laboratory for Chemistry and Physics of Interfaces, Georges-Koehler-Allee 103, D-79110 Freiburg, Germany, University of California Santa Barbara, Department of Chemistry and Biochemistry, Santa Barbara, California 93106, and University of California, Berkeley Bioengineering Department, 306 Stanley Hall, Berkeley, California 94720-1762
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Wark AW, Lee J, Kim S, Faisal SN, Lee HJ. Bioaffinity detection of pathogens on surfaces. J IND ENG CHEM 2010; 16:169-177. [PMID: 32288511 PMCID: PMC7129010 DOI: 10.1016/j.jiec.2010.01.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 12/04/2009] [Indexed: 01/12/2023]
Abstract
The demand for improved technologies capable of rapidly detecting pathogens with high sensitivity and selectivity in complex environments continues to be a significant challenge that helps drive the development of new analytical techniques. Surface-based detection platforms are particularly attractive as multiple bioaffinity interactions between different targets and corresponding probe molecules can be monitored simultaneously in a single measurement. Furthermore, the possibilities for developing new signal transduction mechanisms alongside novel signal amplification strategies are much more varied. In this article, we describe some of the latest advances in the use of surface bioaffinity detection of pathogens. Three major sections will be discussed: (i) a brief overview on the choice of probe molecules such as antibodies, proteins and aptamers specific to pathogens and surface attachment chemistries to immobilize those probes onto various substrates, (ii) highlighting examples among the current generation of surface biosensors, and (iii) exploring emerging technologies that are highly promising and likely to form the basis of the next generation of pathogenic sensors.
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Affiliation(s)
- Alastair W. Wark
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
| | - Jaeyoung Lee
- Electrochemical Reaction and Technology Laboratory, Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea
| | - Suhee Kim
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
| | - Shaikh Nayeem Faisal
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
| | - Hye Jin Lee
- Department of Chemistry, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea
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Grunwald I, Groth E, Wirth I, Schumacher J, Maiwald M, Zoellmer V, Busse M. Surface biofunctionalization and production of miniaturized sensor structures using aerosol printing technologies. Biofabrication 2010; 2:014106. [DOI: 10.1088/1758-5082/2/1/014106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sethi D, Gandhi RP, Kuma P, Gupta KC. Chemical strategies for immobilization of oligonucleotides. Biotechnol J 2010; 4:1513-29. [PMID: 19844919 DOI: 10.1002/biot.200900162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
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Pastré D, Hamon L, Sorel I, Le Cam E, Curmi PA, Piétrement O. Specific DNA-protein interactions on mica investigated by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:2618-2623. [PMID: 19791748 DOI: 10.1021/la902727b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA processing by site-specific proteins on surface remains a challenging issue for nanobioscience applications and, in particular, for high-resolution imaging by atomic force microscopy (AFM). To obtain high-resolution conditions, mica, an atomically flat and negatively charged surface, is generally used. However, even though many specific DNA/protein interactions have already been observed by AFM, little is known about DNA accessibility to specific enzymes on mica. Here we measured the accessibility of adsorbed DNA to restriction endonucleases (EcoRI and EcoRV) using AFM. By increasing the concentration of divalent or multivalent salts, DNA adsorption on mica switches from weak to strong binding. Interestingly, while the accessibility of strongly bound DNA was inhibited, loosely adsorbed DNA was efficiently cleaved on mica. This result opens new perspective to study DNA/protein interaction by AFM or to modify specifically DNA on surface.
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Affiliation(s)
- David Pastré
- Laboratoire Structure et Activité des Biomolécules Normales et Pathologiques, INSERM/UEVE U829, Université d'Evry val d'Essonne, Evry F-91025, France.
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Schüler T, Kretschmer R, Jessing S, Urban M, Fritzsche W, Möller R, Popp J. A disposable and cost efficient microfluidic device for the rapid chip-based electrical detection of DNA. Biosens Bioelectron 2009; 25:15-21. [DOI: 10.1016/j.bios.2009.05.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/19/2009] [Accepted: 05/21/2009] [Indexed: 10/20/2022]
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UV cross-linking of unmodified DNA on glass surfaces. Anal Bioanal Chem 2009; 395:1097-105. [DOI: 10.1007/s00216-009-3045-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/22/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
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25
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Yang H, Fung SY, Pritzker M, Chen P. Ionic-complementary peptide matrix for enzyme immobilization and biomolecular sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:7773-7777. [PMID: 19594172 DOI: 10.1021/la901456k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A novel electrochemical biosensing platform is described using biocompatible, self-assembled ionic-complementary peptide nanofibers. The compatibility of a graphite electrode modified by these peptide nanofibers with enzymes is demonstrated using a model enzyme glucose oxidase (GOx). A glucose biosensor has been successfully fabricated by incorporating this enzyme into the modified electrode. From measurement of its electrode response and sensitivity, this nanofiber-modified electrode shows promise as an enzyme-based biosensor. The findings presented here demonstrate excellent potential of the use of ionic-complementary peptides to modify electrode surfaces for biomolecular sensing and diagnostics.
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Affiliation(s)
- Hong Yang
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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26
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Honciuc A, Baptiste DJ, Schwartz DK. Hydrophobic interaction microscopy: mapping the solid/ liquid interface using amphiphilic probe molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:4339-4342. [PMID: 19253960 DOI: 10.1021/la9004246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The adsorption, interfacial mobility, and desorption of amphiphilic molecules are extremely sensitive to the chemical properties of the interface at which they adsorb; we demonstrate here that this sensitivity can be used to map subtle spatial variations of surface hydrophobicity. We have used total internal reflection fluorescence microscopy to observe the dynamic behavior of individual fluorescently labeled fatty acid molecules at the interface between water and a hydrophobically modified fused silica surface. Patterned surfaces were prepared by photodegradation of trimethylsilane-modified surfaces using a contact photomask; the degree of hydrophobic contrast was varied by controlling the dose of ultraviolet radiation. Cumulative images of single-molecule fluorescence, integrated over various exposure times, exhibited structural features consistent with the photopattern, and the fluorescence contrast was systematically related to the hydrophobic contrast. Lateral force microscopy was also used to characterize the patterned surfaces and provided qualitative images when the hydrophobic contrast was relatively high. However, the fluorescent probes provided more sensitive, reproducible, and reliable images of the lateral hydrophobic variations.
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Affiliation(s)
- Andrei Honciuc
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
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27
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Harper JC, Polsky R, Wheeler DR, Lopez DM, Arango DC, Brozik SM. A multifunctional thin film Au electrode surface formed by consecutive electrochemical reduction of aryl diazonium salts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3282-3288. [PMID: 19437729 DOI: 10.1021/la803215z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A multifunctional thin film surface capable of immobilizing two diverse molecules on a single gold electrode was prepared by consecutive electrodeposition of nitrophenyl and phenylboronic acid pinacol ester (PBA-PE) diazonium salts. Activation of the stacked film toward binding platinum nanoparticles (PtNPs) and yeast cells occurred via chemical deprotection of the pinacol ester followed by electroreduction of nitro to amino groups. FTIR spectral analysis was used to study and verify film composition at each stage of preparation. The affect of electrodeposition protocol over the thickness of the nitrophenyl and PBA-PE layers was explored and had a profound impact on the film properties. Thicker nitrophenyl films led to diminished PBA-PE diazonium reduction currents during assembly and decreased phenylboronic acid (PBA) layer thickness while allowing for higher PtNP loading and catalytic currents from PtNP-mediated peroxide reduction. Multilayer PBA films could be formed over the nitrophenyl film; however, only submonlayer PBA films permitted access to the underlying layer. The sequence of functional group activation toward binding was also shown to be significant, as perchlorate used to remove pinacol ester also converted aminophenyl groups accessible to the solution to nitrophenyl groups, preventing electrostatic PtNP binding. Finally, SEM images show PtNPs immobilized in close proximity (nanometers) to captured yeast cells on the PBA-aminophenyl-Au film. Such multibinding functionality films that maintain conductivity for subsequent electrochemical measurements hold promise for the development of electrochemical and/or optical platforms for fundamental cell studies, genomic and proteomic analysis, and biosensing.
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Affiliation(s)
- Jason C Harper
- Biosensors & Nanomaterials, Sandia National Laboratories, PO Box 5800, MS-0892, Albuquerque, New Mexico 87185, USA
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28
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Improved DNA chip with poly(amidoamine) dendrimer peripherally modified with biotin and avidin. BIOTECHNOL BIOPROC E 2009. [DOI: 10.1007/s12257-008-0055-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Abstract
Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.
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Affiliation(s)
- Sascha Todt
- Center for Applied Genesensor-Technology, University of Bremen, , Bremen, Germany
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30
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Blair S, Williams L, Bishop J, Chagovetz A. Microarray temperature optimization using hybridization kinetics. Methods Mol Biol 2009; 529:171-196. [PMID: 19381979 DOI: 10.1007/978-1-59745-538-1_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In any microarray hybridization experiment, there are contributions at each probe spot due to the match and numerous mismatch target species (i.e., cross-hybridizations). One goal of temperature optimization is to minimize the contribution of mismatch species; however, achieving this goal may come at the expense of obtaining equilibrium reaction conditions. We employ two-component thermodynamic and kinetic models to study the trade-offs involved in temperature optimization. These models show that the maximum selectivity is achieved at equilibrium, but that the mismatch species controls the time to equilibrium via the competitive displacement mechanism. Also, selectivity is improved at lower temperatures. However, the time to equilibrium is also extended, so that greater selectivity cannot be achieved in practice. We also employ a two-color real-time microarray reader to experimentally demonstrate these effects by independently monitoring the match and mismatch species during multiplex hybridization. The only universal criterion that can be employed is to optimize temperature based upon attaining equilibrium reaction conditions. This temperature varies from one probe to another, but can be determined empirically using standard microarray experimentation methods.
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Affiliation(s)
- Steve Blair
- University of Utah, Salt Lake City, Utah, USA
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31
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Yu X, Schneiderhan-Marra N, Hsu HY, Bachmann J, Joos TO. Protein microarrays: effective tools for the study of inflammatory diseases. Methods Mol Biol 2009; 577:199-214. [PMID: 19718518 DOI: 10.1007/978-1-60761-232-2_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Inflammation is a defense reaction of an organism against harmful stimuli such as tissue injury or infectious agents. The relationship between the infecting microorganism and the immune, inflammatory, and coagulation responses of the host is intricately intertwined. Due to its complex nature, the molecular mechanisms of inflammation are not yet understood in detail and additional diagnostic tools are required to clarify further aspects. In recent years, protein microarray-based research has moved from being technology-based to application-oriented. Protein microarrays are perfect tools for studying inflammatory diseases. High-density protein arrays enable new classes of autoantibodies, which cause autoimmune diseases, to be discovered. Protein arrays consisting of miniaturized multiplexed sandwich immunoassays allow the simultaneous expression analysis of dozens of signaling molecules such as the cytokines and chemokines involved in the regulation of the immune system. The data enable statements to be made on the status of the disease and its progression as well as support for the clinicians in choosing patient-specific treatment. This chapter reviews the technology and the applications of protein microarrays in diagnosing and monitoring inflammatory diseases.
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Affiliation(s)
- Xiaobo Yu
- NMI Natural and Medical Sciences Institute, University of Tübingen, Reutlingen, Germany
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32
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Tan YH, Liu M, Nolting B, Go JG, Gervay-Hague J, Liu GY. A nanoengineering approach for investigation and regulation of protein immobilization. ACS NANO 2008; 2:2374-84. [PMID: 19206405 PMCID: PMC4512660 DOI: 10.1021/nn800508f] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
It is known that protein attachment to surfaces depends sensitively upon the local structure and environment of the binding sites at the nanometer scale. Using nanografting and reversal nanografting, both atomic force microscopy (AFM)-based lithography techniques, protein binding sites with well-defined local environments are designed and engineered with nanometer precision. Three proteins, goat antibiotin immunoglobulin G (IgG), lysozyme, and rabbit immunoglobulin G, are immobilized onto these engineered surfaces. Strong dependence on the dimension and spatial distribution of protein binding sites are revealed in antibody recognition, covalent attachment via primary amine residues and surface-bound aldehyde groups. This investigation indicates that AFM-based nanolithography enables the production of protein nanostructures, and more importantly, protein-surface interactions at a molecular level can be regulated by changing the binding domains and their local environment at nanometer scale.
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Affiliation(s)
- Yih Horng Tan
- Department of Chemistry, University of California, Davis, CA 95616
| | - Maozi Liu
- Department of Chemistry, University of California, Davis, CA 95616
| | - Birte Nolting
- Department of Chemistry, University of California, Davis, CA 95616
| | - Joan G. Go
- Department of Chemistry, University of California, Davis, CA 95616
| | | | - Gang-yu Liu
- Department of Chemistry, University of California, Davis, CA 95616
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33
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Matsudaira T, Tsuzuki S, Wada A, Suwa A, Kohsaka H, Tomida M, Ito Y. Automated microfluidic assay system for autoantibodies found in autoimmune diseases using a photoimmobilized autoantigen microarray. Biotechnol Prog 2008; 24:1384-92. [PMID: 19194953 DOI: 10.1002/btpr.63] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Takahiro Matsudaira
- Nano Medical Enginering Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama, Japan
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34
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Zhou Y, Liu A, Wang W, Du G. Using the Protein Chip to Screen Agonists and Antagonists of the Androgen Receptor. ACTA ACUST UNITED AC 2008; 13:276-84. [DOI: 10.1177/1087057108315881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Based on its important physical and pathological function, the androgen receptor (AR) is regarded as a significant drug target. In this report, the authors describe a novel strategy of protein chip technology to screen agonists and antagonists of AR. First, the AR ligand binding domain (AR-LBD) was expressed in Escherichia coli, purified, and then immobilized on a silane-polysaccharide surface of a protein chip. Second, the affinities of methyltestosterone (MT) and fluorescent-labeled testosterone for the AR-LBD protein chip were determined. Third, a converse strategy of the protein chip was tested to evaluate its reliability as a drug screening method. Fourth, a 10,067-compound library was screened to find new ligands of AR. From the results, the Kdof testosterone and the IC50of MT are consistent with the literature (0.61 vs. 0.49 nM 2.88 vs. 3.90 nM, respectively). The Z′ factor of the high-throughput screening (HTS) method was 0.76, which meets the requirement of drug screening (>0.4). Finally, 3 active ligands of AR were identified with their IC50values of 3.63, 2.19, and 1.71 µM, respectively. In summary, the novel strategy of the AR-LBD protein chip was suitable for HTS at the molecular level. ( Journal of Biomolecular Screening 2008:276-284)
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Affiliation(s)
- Yong Zhou
- National Center of Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, Ottawa Health Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Ailin Liu
- National Center of Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Wang
- The Key Laboratory of Biosynthesis, Ministry of Medicine, China, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guanhua Du
- National Center of Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China, , Institute of Materia Medica Chinese Academy of Medical Sciences and Peking Union Medical College 1 Xian Nong Tan Street Beijing, China, 100050
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35
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Gurard-Levin ZA, Mrksich M. Combining self-assembled monolayers and mass spectrometry for applications in biochips. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:767-800. [PMID: 20636097 DOI: 10.1146/annurev.anchem.1.031207.112903] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the self-assembled monolayers.
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Affiliation(s)
- Zachary A Gurard-Levin
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Illinois 60637, USA
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36
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Phillips MF, Lockett MR, Rodesch MJ, Shortreed MR, Cerrina F, Smith LM. In situ oligonucleotide synthesis on carbon materials: stable substrates for microarray fabrication. Nucleic Acids Res 2007; 36:e7. [PMID: 18084027 PMCID: PMC2248760 DOI: 10.1093/nar/gkm1103] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Glass has become the standard substrate for the preparation of DNA arrays. Typically, glass is modified using silane chemistries to provide an appropriate functional group for nucleic acid synthesis or oligonucleotide immobilization. We have found substantial issues with the stability of these surfaces as manifested in the unwanted release of oligomers from the surface when incubated in aqueous buffers at moderate temperatures. To address this issue, we have explored the use of carbon-based substrates. Here, we demonstrate in situ synthesis of oligonucleotide probes on carbon-based substrates using light-directed photolithographic phosphoramidite chemistry and evaluate the stabilities of the resultant DNA arrays compared to those fabricated on silanized glass slides. DNA arrays on carbon-based substrates are substantially more stable than arrays prepared on glass. This superior stability enables the use of high-density DNA arrays for applications involving high temperatures, basic conditions, or where serial hybridization and dehybridization is desired.
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Affiliation(s)
- Margaret F Phillips
- Department of Chemistry, University of Wisconsin - Madison, 1101 University Ave. Madison, Madison, WI 53706, USA
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37
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Strategies for label-free optical detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 109:395-432. [PMID: 17999039 DOI: 10.1007/10_2007_076] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A large number of methods using direct detection with label-free systems are known. They compete with the well-introduced fluorescence-based methods. However, recent applications take advantage of label-free detection in protein-protein interactions, high-throughput screening, and high-content screening. These new applications require new strategies for biosensors. It becomes more and more obvious that neither the transduction principle nor the recognition elements for the biomolecular interaction process alone determine the quality of the biosensor. Accordingly, the biosensor system has to be considered as a whole. This chapter focuses on strategies to optimize the detection platform and the biomolecular recognition layer. It concentrates on direct detection methods, with special focus on optical transduction. Since even this restriction still leaves a large number of methods, only microrefractometric and microreflectometric methods using planar transducers have been selected for a detailed description and a listing of applications. However, since many review articles on the physical principles exist, the description is kept short. Other methods are just mentioned in brief and for comparison. The outlook and the applications demonstrate the future perspectives of direct optical detection in bioanalytics.
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Abstract
Quantitative analysis of DNA microarray data is complicated by uncertainties inherent to the experimental setup. Using computer simulations and real-time experimental results, we have previously demonstrated effects of multiplex reactions on a single sensing zone of an array, which may be a leading factor in erroneous interpretation of experimental data. We suggest here that a simplified three-component kinetic model may present a sufficient approximation to describe the general case of DNA sensing in a complex sample milieu. We show that, by analyzing the real-time hybridization kinetics of a nontarget species, we can perform quantitative analysis of unlabeled targets of interest within a broad dynamic range of concentrations.
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39
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Kopf E, Zharhary D. Antibody arrays--an emerging tool in cancer proteomics. Int J Biochem Cell Biol 2007; 39:1305-17. [PMID: 17600752 DOI: 10.1016/j.biocel.2007.04.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 04/26/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
Cancer is a result of complex changes that occur in normal cells as they transform to become malignant and further when they become metastatic. These changes are not a consequence of a single protein but rather involve multiple proteins that function in pathways and networks. Thus, profiling cancer-associated changes requires simultaneous measurement of many proteins in a single sample. Identifying these changes may lead to the discovery of cancer-associated biomarkers that may assist in diagnosis, prognosis, patient monitoring and possibly for therapeutic purposes. Antibody arrays are a relatively new technology that enables one to perform multiplex high-throughput protein expression profiling. This review describes current technologies in antibody array and assay design, and presents a survey of the current literature on the use of these arrays in cancer research.
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Affiliation(s)
- Eliezer Kopf
- Sigma-Aldrich Israel Ltd., 3 Plaut Street, Park Rabin, Rehovot 76100, Israel
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40
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