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Sytu MRC, Cho DH, Hahm JI. Self-Assembled Block Copolymers as a Facile Pathway to Create Functional Nanobiosensor and Nanobiomaterial Surfaces. Polymers (Basel) 2024; 16:1267. [PMID: 38732737 PMCID: PMC11085100 DOI: 10.3390/polym16091267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Block copolymer (BCP) surfaces permit an exquisite level of nanoscale control in biomolecular assemblies solely based on self-assembly. Owing to this, BCP-based biomolecular assembly represents a much-needed, new paradigm for creating nanobiosensors and nanobiomaterials without the need for costly and time-consuming fabrication steps. Research endeavors in the BCP nanobiotechnology field have led to stimulating results that can promote our current understanding of biomolecular interactions at a solid interface to the never-explored size regimes comparable to individual biomolecules. Encouraging research outcomes have also been reported for the stability and activity of biomolecules bound on BCP thin film surfaces. A wide range of single and multicomponent biomolecules and BCP systems has been assessed to substantiate the potential utility in practical applications as next-generation nanobiosensors, nanobiodevices, and biomaterials. To this end, this Review highlights pioneering research efforts made in the BCP nanobiotechnology area. The discussions will be focused on those works particularly pertaining to nanoscale surface assembly of functional biomolecules, biomolecular interaction properties unique to nanoscale polymer interfaces, functionality of nanoscale surface-bound biomolecules, and specific examples in biosensing. Systems involving the incorporation of biomolecules as one of the blocks in BCPs, i.e., DNA-BCP hybrids, protein-BCP conjugates, and isolated BCP micelles of bioligand carriers used in drug delivery, are outside of the scope of this Review. Looking ahead, there awaits plenty of exciting research opportunities to advance the research field of BCP nanobiotechnology by capitalizing on the fundamental groundwork laid so far for the biomolecular interactions on BCP surfaces. In order to better guide the path forward, key fundamental questions yet to be addressed by the field are identified. In addition, future research directions of BCP nanobiotechnology are contemplated in the concluding section of this Review.
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Affiliation(s)
- Marion Ryan C. Sytu
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
| | - David H. Cho
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA;
| | - Jong-in Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
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2
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Cho DH, Hahm JI. Protein-Polymer Interaction Characteristics Unique to Nanoscale Interfaces: A Perspective on Recent Insights. J Phys Chem B 2021; 125:6040-6057. [PMID: 34101462 DOI: 10.1021/acs.jpcb.1c00684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein interactions at polymer interfaces represent a complex but ubiquitous phenomenon that demands an entirely different focus of investigation than what has been attempted before. With the advancement of nanoscience and nanotechnology, the nature of polymer materials interfacing proteins has evolved to exhibit greater chemical intricacy and smaller physical dimensions. Existing knowledge built from studying the interaction of macroscopic, chemically alike surfaces with an ensemble of protein molecules cannot be simply carried over to nanoscale protein-polymer interactions. In this Perspective, novel protein interaction phenomena driven by the presence of nanoscale polymer interfaces are discussed. Being able to discern discrete protein interaction events via simple visualization was crucial to attaining the much needed, direct experimental evidence of protein-polymer interactions at the single biomolecule level. Spatial and temporal tracking of particular proteins at specific polymer interfaces was made possible by resolving individual proteins simultaneously with those polymer nanodomains responsible for the protein interactions. Therefore, such single biomolecule level approaches taken to examine protein-polymer interaction mark a big departure from the mainstream approaches of collecting indirectly observed, ensemble-averaged protein signals on chemically simple substrates. Spearheading research efforts so far has led to inspiring initial discoveries of protein interaction mechanisms and kinetics that are entirely unique to nanoscale polymer systems. They include protein self-assembly/packing characteristics, protein-polymer interaction mechanisms/kinetics, and various protein functionalities on polymer nanoconstructs. The promising beginning and future of nanoscale protein-polymer research endeavors are presented in this article.
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Affiliation(s)
- David H Cho
- Department of Chemistry, Georgetown University, 37th & O Streets NW, Washington, District of Columbia 20057, United States
| | - Jong-In Hahm
- Department of Chemistry, Georgetown University, 37th & O Streets NW, Washington, District of Columbia 20057, United States
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3
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Metabolic Labeling and Structural Analysis of Glycosylphosphatidylinositols from Parasitic Protozoa. Methods Mol Biol 2019. [PMID: 31256378 DOI: 10.1007/978-1-4939-9055-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Glycosylphosphatidylinositol (GPI) is a complex glycolipid structure that acts as a membrane anchor for many cell-surface proteins of eukaryotes. GPI-anchored proteins are particularly abundant in protozoa and represent the major carbohydrate modification of many cell-surface parasite proteins. A minimal GPI-anchor precursor consists of core glycan (ethanolamine-PO4-Manα1-2Manα1-6Manα1-4GlcNH2) linked to the 6-position of the D-myo-inositol ring of phosphatidylinositol. Although the GPI core glycan is conserved in all organisms, many differences in additional modifications to GPI structures and biosynthetic pathways have been reported. The preassembled GPI-anchor precursor is post-translationally transferred to a variety of membrane proteins in the lumen of the endoplasmic reticulum in a transamidase-like reaction during which a C-terminal GPI attachment signal is released. Increasing evidence shows that a significant proportion of the synthesized GPIs are not used for protein anchoring, particularly in protozoa in which a large amount of free GPIs are being displayed at the cell surface. The characteristics of GPI biosynthesis are currently being explored for the development of parasite-specific inhibitors. Especially this pathway, at least for Trypanosoma brucei, has been validated as a drug target. Furthermore, thanks to an increase of new innovative strategies to produce pure synthetic carbohydrates, a novel era in the use of GPIs in diagnostic, anti-GPI antibody production, as well as parasitic protozoa GPI-based vaccine approach is developing fast.
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4
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Jiang Z, Guan J, Qian J, Zhan C. Peptide ligand-mediated targeted drug delivery of nanomedicines. Biomater Sci 2019; 7:461-471. [PMID: 30656305 DOI: 10.1039/c8bm01340c] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeted drug delivery is emerging as a promising strategy to achieve better clinical outcomes. Actively targeted drug delivery that utilizes overexpressed receptors or antigens on diseased tissues is receiving increasing scrutiny, especially due to the uncertainty of existence of the enhanced permeability and retention (EPR) effect in cancer patients. Peptide ligands are advantageous over other classes of targeting ligands due to their accessibility of high-throughput screening, ease of synthesis, high specificity and affinity, etc. In this review, we briefly summarize the resources of peptide ligands and discuss the pitfalls and perspectives of peptide ligand-mediated targeted delivery of nanomedicines.
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Affiliation(s)
- Zhuxuan Jiang
- Department of Pharmacology, School of Basic Medical Sciences & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200032, P.R. China.
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5
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Xie T, Chattoraj J, Mulcahey PJ, Kelleher NP, Del Gado E, Hahm JI. Revealing the principal attributes of protein adsorption on block copolymer surfaces with direct experimental evidence at the single protein level. NANOSCALE 2018; 10:9063-9076. [PMID: 29718032 DOI: 10.1039/c8nr01371c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding protein adsorption onto polymer surfaces is of great importance in designing biomaterials, improving bioanalytical devices, and controlling biofouling, to name a few examples. Although steady research efforts have been advancing this field, our knowledge of this ubiquitous and complex phenomenon is still limited. In this study, we elucidate competitive protein adsorption behaviors sequentially occurring onto nanoscale block copolymer (BCP) surfaces via combined experimental and computer simulation approaches. The model systems chosen for our investigation are immunoglobulin G and fibrinogen introduced in different orders into the self-assembled nanodomains of poly(styrene)-block-poly(methylmethacrylate). We unambiguously reveal the adsorption, desorption, and replacement events of the same protein molecules via single protein tracking with atomic force microscopy. We then ascertain adsorption-related behaviors such as lateral mobility and self-association of proteins. We provide the much-needed, direct experimental proof of sequential adsorption events at the biomolecular level, which was virtually nonexistent before. We determine key protein adsorption pathways and dominant tendencies of sequential protein adsorption. We also reveal preadsorbed surface-associated behaviors in sequential adsorption, distinct from situations involving initially empty surfaces. We perform Monte-Carlo simulations to further substantiate our experimental outcomes. Our endeavors in this study may facilitate a well-guided mechanistic understanding of protein-polymer interactions by providing definite experimental evidence of competitive, sequential adsorption at the nanoscale. Increasingly, biomaterial and biomedical applications rely on systems of multicomponent proteins and chemically intricate, nanoscale polymer surfaces. Hence, our findings can also be beneficial for the development of next-generation nanobiomaterials and nanobiosensors exploiting self-assembled BCP nanodomain surfaces.
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Affiliation(s)
- Tian Xie
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA.
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6
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Adeola HA, Van Wyk JC, Arowolo A, Ngwanya RM, Mkentane K, Khumalo NP. Emerging Diagnostic and Therapeutic Potentials of Human Hair Proteomics. Proteomics Clin Appl 2017; 12. [PMID: 28960873 DOI: 10.1002/prca.201700048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Indexed: 01/22/2023]
Abstract
The use of noninvasive human substrates to interrogate pathophysiological conditions has become essential in the post- Human Genome Project era. Due to its high turnover rate, and its long term capability to incorporate exogenous and endogenous substances from the circulation, hair testing is emerging as a key player in monitoring long term drug compliance, chronic alcohol abuse, forensic toxicology, and biomarker discovery, among other things. Novel high-throughput 'omics based approaches like proteomics have been underutilized globally in comprehending human hair morphology and its evolving use as a diagnostic testing substrate in the era of precision medicine. There is paucity of scientific evidence that evaluates the difference in drug incorporation into hair based on lipid content, and very few studies have addressed hair growth rates, hair forms, and the biological consequences of hair grooming or bleaching. It is apparent that protein-based identification using the human hair proteome would play a major role in understanding these parameters akin to DNA single nucleotide polymorphism profiling, up to single amino acid polymorphism resolution. Hence, this work seeks to identify and discuss the progress made thus far in the field of molecular hair testing using proteomic approaches, and identify ways in which proteomics would improve the field of hair research, considering that the human hair is mostly composed of proteins. Gaps in hair proteomics research are identified and the potential of hair proteomics in establishing a historic medical repository of normal and disease-specific proteome is also discussed.
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Affiliation(s)
- Henry A Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Jennifer C Van Wyk
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Afolake Arowolo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Reginald M Ngwanya
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Khwezikazi Mkentane
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
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7
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Peltomaa R, Benito-Peña E, Barderas R, Sauer U, González Andrade M, Moreno-Bondi MC. Microarray-Based Immunoassay with Synthetic Mimotopes for the Detection of Fumonisin B1. Anal Chem 2017; 89:6216-6223. [DOI: 10.1021/acs.analchem.7b01178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | - Ursula Sauer
- Center
for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Martin González Andrade
- Department
of Biochemistry, Faculty of Medicine, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán D.F., México
City 04510, México
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8
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Liu R, Li X, Xiao W, Lam KS. Tumor-targeting peptides from combinatorial libraries. Adv Drug Deliv Rev 2017; 110-111:13-37. [PMID: 27210583 DOI: 10.1016/j.addr.2016.05.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 02/07/2023]
Abstract
Cancer is one of the major and leading causes of death worldwide. Two of the greatest challenges in fighting cancer are early detection and effective treatments with no or minimum side effects. Widespread use of targeted therapies and molecular imaging in clinics requires high affinity, tumor-specific agents as effective targeting vehicles to deliver therapeutics and imaging probes to the primary or metastatic tumor sites. Combinatorial libraries such as phage-display and one-bead one-compound (OBOC) peptide libraries are powerful approaches in discovering tumor-targeting peptides. This review gives an overview of different combinatorial library technologies that have been used for the discovery of tumor-targeting peptides. Examples of tumor-targeting peptides identified from each combinatorial library method will be discussed. Published tumor-targeting peptide ligands and their applications will also be summarized by the combinatorial library methods and their corresponding binding receptors.
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Affiliation(s)
- Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA 95817, USA; University of California Davis Comprehensive Cancer Center, Sacramento, CA 95817, USA; Division of Hematology & Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA 95817, USA
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9
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Verma S, Verma V. Lithographic patterning of antibodies by direct lift-off and improved surface adhesion. Biofabrication 2017; 9:015012. [PMID: 28092639 DOI: 10.1088/1758-5090/9/1/015012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The inherent property of antibodies binding to their antigen with high specificity makes them a strong candidate for sensing and detection applications. Microscale patterning of antibodies is desired for the miniaturization of sensors and fundamental cell biology studies. However, existing methodologies to pattern antibodies at the microscale are multi-step. In this work, we demonstrate microscale patterning of antibodies on a glass coverslip in a single step photolithography process. The microscale features of the photoresist were generated on the coverslip using photolithography, and the antibody solution was incubated. Acetone lift-off of the antibody incubated photoresist, and subsequent washing by isopropanol (IPA), produced a micro-array of antibodies. The functionality of patterned primary antibody was confirmed using the corresponding antigen and strict controls. One of the striking features of this method of patterning is that the process steps and chemicals inherently improve the adhesion between the antibodies and glass without the need to functionalize the glass surface. We performed an ultrasonication test, detergent washing test, and Scotch tape test to show improved adhesion. Using appropriate controls, we show that the interaction taking place between the antibodies and the glass surface, after our process, is stronger than the simple physisorption taking place between the antibodies and the glass surface, without any treatment.
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Affiliation(s)
- Sankalp Verma
- Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, India
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10
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Sun YS. Use of Microarrays as a High-Throughput Platform for Label-Free Biosensing. ACTA ACUST UNITED AC 2015; 20:334-53. [DOI: 10.1177/2211068215577570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/28/2022]
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11
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Liu Z, Pourghiasian M, Radtke MA, Lau J, Pan J, Dias GM, Yapp D, Lin KS, Bénard F, Perrin DM. An Organotrifluoroborate for Broadly Applicable One-Step18F-Labeling. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406258] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Liu Z, Pourghiasian M, Radtke MA, Lau J, Pan J, Dias GM, Yapp D, Lin KS, Bénard F, Perrin DM. An organotrifluoroborate for broadly applicable one-step 18F-labeling. Angew Chem Int Ed Engl 2014; 53:11876-80. [PMID: 25196467 DOI: 10.1002/anie.201406258] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 11/12/2022]
Abstract
A new zwitterionic organotrifluoroborate is appended to three radiosynthons that afford undergo facile bioconjugation to several clinically relevant peptides and one enzyme inhibitor. Molecularly complex bioconjugates are (18)F-labeled in a single aqueous step in rapid time (<15 min) without HPLC purification to afford tracers in good yields (>200 mCi, 20-40%) at high specific activity (≥3 Ci/μmol) and at >98% purity. PET imaging shows in vivo stability and tumor uptake.
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Affiliation(s)
- Zhibo Liu
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T-1Z1 (Canada)
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13
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González-González M, Bartolome R, Jara-Acevedo R, Casado-Vela J, Dasilva N, Matarraz S, García J, Alcazar JA, Sayagues JM, Orfao A, Fuentes M. Evaluation of homo- and hetero-functionally activated glass surfaces for optimized antibody arrays. Anal Biochem 2014; 450:37-45. [PMID: 24440232 DOI: 10.1016/j.ab.2014.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/07/2014] [Indexed: 11/17/2022]
Abstract
Antibody arrays hold great promise for biomedical applications, but they are typically manufactured using chemically functionalized surfaces that still require optimization. Here, we describe novel hetero-functionally activated glass surfaces favoring oriented antibody binding for improved performance in protein microarray applications. Antibody arrays manufactured in our facility using the functionalization chemistries described here proved to be reproducible and stable and also showed good signal intensities. As a proof-of-principle of the glass surface functionalization protocols described in this article, we built antibody-based arrays functionalized with different chemistries that enabled the simultaneous detection of 71 human leukocyte membrane differentiation antigens commonly found in peripheral blood mononuclear cells. Such detection is specific and semi-quantitative and can be performed in a single assay under native conditions. In summary, the protocol described here, based on the use of antibody array technology, enabled the concurrent detection of a set of membrane proteins under native conditions in a specific, selective, and semi-quantitative manner and in a single assay.
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Affiliation(s)
- María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Raquel Bartolome
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | | | - Juan Casado-Vela
- Spanish National Research Council (CSIC)-Spanish National Biotechnology Centre (CNB), 28049 Madrid, Spain
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Jacinto García
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J A Alcazar
- Servicio de Cirugía, Hospital Clínico Universitario de Salamanca-IBSAL, 37007 Salamanca, Spain
| | - J M Sayagues
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, 37007 Salamanca, Spain.
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14
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Bissonnette L, Bergeron MG. Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine. Expert Rev Mol Diagn 2014; 6:433-50. [PMID: 16706745 DOI: 10.1586/14737159.6.3.433] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.
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Affiliation(s)
- Luc Bissonnette
- Département de Biologie Médicale (Microbiologie), Faculté de Médecine, Université Laval, Québec City, Canada.
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15
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Assessing the detection capacity of microarrays as bio/nanosensing platforms. BIOMED RESEARCH INTERNATIONAL 2013; 2013:310461. [PMID: 24324959 PMCID: PMC3845509 DOI: 10.1155/2013/310461] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/19/2013] [Indexed: 11/24/2022]
Abstract
Microarray is one of the most powerful detection systems with multiplexing and high throughput capability. It has significant potential as a versatile biosensing platform for environmental monitoring, pathogen detection, medical therapeutics, and drug screening to name a few. To date, however, microarray applications are still limited to preliminary screening of genome-scale transcription profiling or gene ontology analysis. Expanding the utility of microarrays as a detection tool for various biological and biomedical applications requires information about performance such as the limits of detection and quantification, which are considered as an essential information to decide the detection sensitivity of sensing devices. Here we present a calibration design that integrates detection limit theory and linear dynamic range to obtain a performance index of microarray detection platform using oligonucleotide arrays as a model system. Two different types of limits of detection and quantification are proposed by the prediction or tolerance interval for two common cyanine fluorescence dyes, Cy3 and Cy5. Besides oligonucleotide, the proposed method can be generalized to other microarray formats with various biomolecules such as complementary DNA, protein, peptide, carbohydrate, tissue, or other small biomolecules. Also, it can be easily applied to other fluorescence dyes for further dye chemistry improvement.
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16
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17
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Wu X, Chen H, Wang X. Can lung cancer stem cells be targeted for therapies? Cancer Treat Rev 2012; 38:580-8. [DOI: 10.1016/j.ctrv.2012.02.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/26/2012] [Accepted: 02/28/2012] [Indexed: 12/26/2022]
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18
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Lee JW. Evaluation of Microarray Sensitivity for DNA Profiling. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2012. [DOI: 10.5012/jkcs.2012.56.4.530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Hu L, Paul Fawcett J, Gu J. Protein target discovery of drug and its reactive intermediate metabolite by using proteomic strategy. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2012.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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20
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Landry JP, Fei Y, Zhu X. Simultaneous measurement of 10,000 protein-ligand affinity constants using microarray-based kinetic constant assays. Assay Drug Dev Technol 2011; 10:250-9. [PMID: 22192305 DOI: 10.1089/adt.2011.0406] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluorescence-based endpoint detection of microarrays with 10,000 or more molecular targets is a most useful tool for high-throughput profiling of biomolecular interactions, including screening large molecular libraries for novel protein ligands. However, endpoint fluorescence data such as images of reacted microarrays contain little information on kinetic rate constants, and the reliability of endpoint data as measures of binding affinity depends on reaction conditions and postreaction processing. We here report a simultaneous measurement of binding curves of a protein probe with 10,000 molecular targets in a microarray with an ellipsometry-based (label-free) optical scanner. The reaction rate constants extracted from these curves (k(on), k(off), and k(a)=k(on)/k(off)) are used to characterize the probe-target interactions instead of the endpoints. This work advances the microarray technology to a new milestone, namely, from an endpoint assay to a kinetic constant assay platform. The throughput of this binding curve assay platform is comparable to those at the National Institutes of Health Molecular Library Screening Centers, making it a practical method in screening compound libraries for novel ligands and for system-wide affinity profiling of proteins, viruses, or whole cells against diverse molecular targets.
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Affiliation(s)
- James P Landry
- Department of Physics, University of California at Davis, Davis, CA 95616, USA
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Proteomics in pancreatic cancer research. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:365350. [PMID: 22084685 PMCID: PMC3200191 DOI: 10.1155/2011/365350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/13/2011] [Accepted: 06/29/2011] [Indexed: 01/29/2023]
Abstract
Pancreatic cancer is a highly aggressive malignancy with a poor prognosis and deeply affects the life of people. Therefore, the earlier diagnosis and better treatments are urgently needed. In recent years, the proteomic technologies are well established and growing rapidly and have been widely applied in clinical applications, especially in pancreatic cancer research. In this paper, we attempt to discuss the development of current proteomic technologies and the application of proteomics to the field of pancreatic cancer research. This will explore the potential perspective in revealing pathogenesis, making the diagnosis earlier and treatment.
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Idikio HA. Human cancer classification: a systems biology- based model integrating morphology, cancer stem cells, proteomics, and genomics. J Cancer 2011; 2:107-15. [PMID: 21479129 PMCID: PMC3072616 DOI: 10.7150/jca.2.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 02/18/2011] [Indexed: 12/15/2022] Open
Abstract
Human cancer classification is currently based on the idea of cell of origin, light and electron microscopic attributes of the cancer. What is not yet integrated into cancer classification are the functional attributes of these cancer cells. Recent innovative techniques in biology have provided a wealth of information on the genomic, transcriptomic and proteomic changes in cancer cells. The emergence of the concept of cancer stem cells needs to be included in a classification model to capture the known attributes of cancer stem cells and their potential contribution to treatment response, and metastases. The integrated model of cancer classification presented here incorporates all morphology, cancer stem cell contributions, genetic, and functional attributes of cancer. Integrated cancer classification models could eliminate the unclassifiable cancers as used in current classifications. Future cancer treatment may be advanced by using an integrated model of cancer classification.
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Affiliation(s)
- Halliday A Idikio
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, ALBERTA T6G 2B7, CANADA
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Gehring AG, Tu SI. High-throughput biosensors for multiplexed food-borne pathogen detection. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:151-172. [PMID: 21689045 DOI: 10.1146/annurev-anchem-061010-114010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Incidental contamination of foods by pathogenic bacteria and/or their toxins is a serious threat to public health and the global economy. The presence of food-borne pathogens and toxins must be rapidly determined at various stages of food production, processing, and distribution. Producers, processors, regulators, retailers, and public health professionals need simple and cost-effective methods to detect different species or serotypes of bacteria and associated toxins in large numbers of food samples. This review addresses the desire to replace traditional microbiological plate culture with more timely and less cumbersome rapid, biosensor-based methods. Emphasis focuses on high-throughput, multiplexed techniques that allow for simultaneous testing of numerous samples, in rapid succession, for multiple food-borne analytes (primarily pathogenic bacteria and/or toxins).
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Affiliation(s)
- Andrew G Gehring
- Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania 19038, USA
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Barbey R, Kauffmann E, Ehrat M, Klok HA. Protein Microarrays Based on Polymer Brushes Prepared via Surface-Initiated Atom Transfer Radical Polymerization. Biomacromolecules 2010; 11:3467-79. [DOI: 10.1021/bm101297w] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Raphael Barbey
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland, and Zeptosens - A Division of Bayer (Schweiz) AG, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
| | - Ekkehard Kauffmann
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland, and Zeptosens - A Division of Bayer (Schweiz) AG, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
| | - Markus Ehrat
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland, and Zeptosens - A Division of Bayer (Schweiz) AG, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
| | - Harm-Anton Klok
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland, and Zeptosens - A Division of Bayer (Schweiz) AG, Benkenstrasse 254, CH-4108 Witterswil, Switzerland
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Kinoshita Y, Tayama T, Kitamura K, Salimullah M, Uchida H, Suzuki M, Husimi Y, Nishigaki K. Novel concept microarray enabling PCR and multistep reactions through pipette-free aperture-to-aperture parallel transfer. BMC Biotechnol 2010; 10:71. [PMID: 20923572 PMCID: PMC2959086 DOI: 10.1186/1472-6750-10-71] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 10/06/2010] [Indexed: 11/15/2022] Open
Abstract
Background The microarray has contributed to developing the omic analysis. However, as it depends basically on the surface reaction, it is hard to perform bulk reactions and sequential multistep reactions. On the other hand, the popular microplate technology, which has a great merit of being able to perform parallel multistep reactions, has come to its limit in increasing the number of wells (currently, up to 9600) and reducing the volume to deal with due to the difficulty in operations. Results Here, we report a novel microarray technology which enables us to explore advanced applications, termed microarray-with-manageable volumes (MMV). The technical essence is in the pipette-free direct parallel transfer from well to well performed by centrifugation, evading the evaporation and adsorption-losses during handling. By developing the MMV plate, accompanying devices and techniques, generation of multiple conditions (256 kinds) and performance of parallel multistep reactions, including PCR and in vitro translation reactions, have been made possible. These were demonstrated by applying the MMV technology to searching lysozyme-crystallizing conditions and selecting peptides aimed for Aβ-binding or cathepsin E-inhibition. Conclusions With the introduction of a novel concept microarray (MMV) technology, parallel and multistep reactions in sub-μL scale have become possible.
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Affiliation(s)
- Yasunori Kinoshita
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
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Azzouz N, Kamena F, Seeberger PH. Synthetic Glycosylphosphatidylinositol as Tools for Glycoparasitology Research. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:445-54. [DOI: 10.1089/omi.2009.0138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nahid Azzouz
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Research Campus, Golm, Germany, and Free University Berlin, Berlin, Germany
| | - Faustin Kamena
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Research Campus, Golm, Germany, and Free University Berlin, Berlin, Germany
| | - Peter H. Seeberger
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Research Campus, Golm, Germany, and Free University Berlin, Berlin, Germany
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Sun YS, Landry JP, Fei YY, Zhu XD, Luo JT, Wang XB, Lam KS. Macromolecular scaffolds for immobilizing small molecule microarrays in label-free detection of protein-ligand interactions on solid support. Anal Chem 2009; 81:5373-80. [PMID: 19563213 PMCID: PMC2751602 DOI: 10.1021/ac900889p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We explored two macromolecular scaffolds, bovine serum albumin (BSA) and polyvinyl alcohol (PVA), as chemically complementary platforms for immobilizing small molecule compounds on functionalized glass slides. We conjugated biotin molecules to BSA and amine-derivatized PVA and subsequently immobilized the conjugates on epoxy-functionalized glass slides through reaction of free amine residues on BSA and PVA with surface-bound epoxy groups. We studied binding reactions of such immobilized small molecule targets with solution-phase protein probes using an oblique-incidence reflectivity difference scanning optical microscope. The results showed that both BSA and amine-derivatized PVA were effective and efficient as carriers of small molecules with NHS residues and fluoric residues and for immobilization on epoxy-coated solid surfaces. A significant fraction of the conjugated small molecules retain their innate chemical activity.
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Affiliation(s)
- Y. S. Sun
- Department of Physics, University of California, Davis, California 95616
| | - J. P. Landry
- Department of Physics, University of California, Davis, California 95616
| | - Y. Y. Fei
- Department of Physics, University of California, Davis, California 95616
| | - X. D. Zhu
- Department of Physics, University of California, Davis, California 95616
| | - J. T. Luo
- School of Medicine, University of California at Davis, Sacramento, California 95817
| | - X. B. Wang
- School of Medicine, University of California at Davis, Sacramento, California 95817
| | - K. S. Lam
- School of Medicine, University of California at Davis, Sacramento, California 95817
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Ehricht R, Adelhelm K, Monecke S, Huelseweh B. Application of protein arraytubes to bacteria, toxin, and biological warfare agent detection. Methods Mol Biol 2009; 509:85-105. [PMID: 19212716 DOI: 10.1007/978-1-59745-372-1_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Microarray technology enables the fast and parallel analysis of a multitude of biologically relevant parameters. Not only nucleic acid-based tests, but also peptide, antigen, and antibody assays using different formats of microarrays evolved within the last decade. They offer the possibility to measure interactions in a miniaturised, economic, automated, and qualitative or quantitative way providing insights into the cellular machinery of diverse organisms. Examples of applications in research and diagnostics are, e.g., O-typing of pathogenic Escherichia coli, detection of bacterial toxins and other biological warfare agents (BW agents) from a variety of different samples, screening of complex antibody libraries, and epitope mapping. Conventional O- and H-serotyping methods can now be substituted by procedures applying DNA oligonucleotide and antibody-based microarrays. For simultaneous and sensitive detection of BW agents microarray-based tests are available, which include not only relevant viruses and bacteria, but also toxins. This application is not only restricted to the security and military sector but it can also be used in the fields of medical diagnostics or public health to detect, e.g., staphylococcal enterotoxins in food or clinical samples. Furthermore, the same technology could be used to detect antibodies against enterotoxins in human sera using a competitive assay. Protein and peptide microarrays can also be used for characterisation of antibodies. On one hand, peptide microarrays allow detailed epitope mapping. On the other hand, a set of different antibodies recognising the same antigen can be spotted as a microarray and labelled as detection antibodies. This approach makes it possible to test every combination, allowing to find the optimal pair of detection/capture antibody.
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29
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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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31
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Horlacher T, Seeberger PH. Carbohydrate arrays as tools for research and diagnostics. Chem Soc Rev 2008; 37:1414-22. [PMID: 18568167 DOI: 10.1039/b708016f] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In a very short time, carbohydrate microarrays have become important tools to investigate binding events that involve sugars. High throughput analysis of carbohydrate interactions with a wide range of binding partners, including proteins, RNA, whole cells and viruses, can be performed. Questions ranging from simple binding events to in-depth kinetic analysis can be addressed. This tutorial review summarizes methods to produce carbohydrate microarrays as well as their use. Some selected examples illustrate applications and the potential that these tools hold.
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Affiliation(s)
- Tim Horlacher
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology (ETH) Zürich, Wolfgang-Pauli-Str. 10, HCI F315, 8093, Zürich, Switzerland
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Ng JK, Ajikumar PK, Tang YC, Lee JY, Stephanopoulos G, Too HP. Spatially addressable protein array: ssDNA-directed assembly for antibody microarray. Electrophoresis 2007; 28:4638-44. [DOI: 10.1002/elps.200700183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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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Souplet V, Desmet R, Melnyk O. Imaging of protein layers with an optical microscope for the characterization of peptide microarrays. J Pept Sci 2007; 13:451-7. [PMID: 17559066 DOI: 10.1002/psc.866] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Solid-phase assays play a crucial role today in biological studies. These assays are based on the immobilization of probe molecules on a surface, which are able to capture specifically soluble receptors. In particular, peptide microarrays have emerged as powerful tools in a variety of applications. In this context, optical techniques that allow imaging of nanometer-thick biomolecular films, and thereby the characterization of microarrays, are of great interest. For this purpose, we used a recently disclosed wide-field optical imaging technique of surface nanostructures called Sarfus, which is based on the use of a standard optical microscope and antireflection substrates. We demonstrate here that this technique allows the imaging of the protein layers that result from the specific capture of antibodies by arrayed peptide probes with a spatial resolution of 0.45 microm. The relationship between the thickness of the antibody layer and peptide or antibody concentration was examined.
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Affiliation(s)
- Vianney Souplet
- UMR CNRS 8161-CNRS/Université de Lille 1 et 2/Institut Pasteur de Lille, Institut de Biologie de Lille, 59021 Lille, France
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Ajikumar PK, Ng JK, Tang YC, Lee JY, Stephanopoulos G, Too HP. Carboxyl-terminated dendrimer-coated bioactive interface for protein microarray: high-sensitivity detection of antigen in complex biological samples. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:5670-7. [PMID: 17388617 DOI: 10.1021/la063717u] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Protein microarrays are promising tools that can potentially enable high throughput proteomic screening in areas such as disease diagnosis and drug discovery. A critical aspect in the development of protein microarrays is the optimization of the array's surface chemistry to achieve the high sensitivity required for detection of proteins in cell lysate and other complex biological mixtures. In the present study, a high-density antibody array with minimal nonspecific cellular protein adsorption was prepared using a glass surface coated with a poly(propyleneimine) dendrimer terminated with carboxyl group (PAMAM-COOH). The carboxyl-terminated dendrimer-modified surface has almost similar nonspecific cellular protein adsorption when compared to an inert PEG-modified surface. In addition, the multiple functional sites available for reaction on the dendrimer surface facilitated high-density immobilization of antibodies and efficient capture of bioanalytes. Various molecules were tested for their ability to block or deactivate the reactive carboxyl surface after antibody immobilization to further reduce the nonspecific binding. A short oligoethylene glycol (NH2-d4-PEG-COOH), was found to significantly improve the signal-to-noise ratio of the assay, resulting in higher sensitivity. The properties and functional qualities of the various surfaces were characterized by contact angle and AFM measurements. Nonspecific protein adsorption and protein immobilization as a function of dendrimer generations and sensitivity of antigen capturing from a buffer (1 pM) as well as from the complex cell lysate (10 pM) system were examined. Our detailed experimental studies demonstrated a facile method of preparing surfaces with high protein loading and low nonspecific protein binding for the development of high sensitivity protein microarrays.
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Affiliation(s)
- Parayil Kumaran Ajikumar
- MEBCS Program, Singapore-MIT Alliance, National University of Singapore, 4 Engineering Drive 3, Singapore 117546.
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Konry T, Bouhifd M, Cosnier S, Whelan M, Valsesia A, Rossi F, Marks RS. Electrogenerated indium tin oxide-coated glass surface with photosensitive interfaces: Surface analysis. Biosens Bioelectron 2007; 22:2230-6. [PMID: 17156996 DOI: 10.1016/j.bios.2006.10.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2006] [Revised: 10/22/2006] [Accepted: 10/31/2006] [Indexed: 11/26/2022]
Abstract
We present herein a photo-immobilization technique for the localized and specific conjugation of biochip platforms with different proteinaceous bioreceptors, such as antigen or antibodies. This methodology based on a photoactivable electrogenerated polymer film, pyrrole-benzophenone, allows the covalent immobilization of biomolecules through light mediation. The surface-conductive glass platform electropolymerized with poly(pyrrole-benzophenone) thin film may then be used to affinity-coat the chip with molecular recognition probes. This glass chip electroconductive surface modification is done by the deposition of a thin layer of indium tin oxide (ITO). Thereafter, pyrrole-benzophenone monomers are electropolymerized onto the conductive metal oxide surface and then exposed to an antigen Staphylococcal Enterotoxin B (SEB)) solution and illuminated with UV light (wavelength approximately 345 nm) through a mask. As a result of the photochemical reaction, a pattern thin layer of the antigen was covalently bound to the benzophenone-modified surface. Then the sample to be analyzed, along with its specific target antibody (anti-SEB antibodies), is introduced onto the glass surface and left to react with the previously photo-immobilized antigen. When the immuno-reaction is completed, the specifically attached immunoglobulin analytes are detected by using secondary antibodies conjugated with Fluorescein isothiocyanate (FITC). The fluorescence signal emanating from the biochip surface is then quantified by two methods, using a filtered intensified charge-coupled device (CCD) camera and a grating spectrometer.
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Affiliation(s)
- Tania Konry
- The Department of Biotechnology Engineering, Faculty of Engineering Science, Ben Gurion University of the Negev, P.O. Box 653, Beer Sheva 84105, Israel
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Horlacher T, Seeberger PH. The utility of carbohydrate microarrays in glycomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 10:490-8. [PMID: 17233559 DOI: 10.1089/omi.2006.10.490] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Carbohydrate microarrays are powerful tools in glycomics. Interactions of different carbohydrate structures with a wide variety of biological targets, including proteins, RNA, viruses, and whole cells, have been investigated using this technique. Binding preferences and specificities, inhibition of interactions, enzymatic activities, and structure-function relationships have been determined. Screening and characterization of antibodies have been conducted using microarrays. Binding of whole cells to the arrays has been exploited to search for novel binding proteins and to detect bacteria in blood. Here, we review the different techniques for carbohydrate microarray production and application. To illustrate the utility of arrays for glycomics research, some select experiments are discussed in greater detail.
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Affiliation(s)
- Tim Horlacher
- Laboratory for Organic Chemistry, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
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Kussmann M. How to comprehensively analyse proteins and how this influences nutritional research. Clin Chem Lab Med 2007; 45:288-300. [PMID: 17378722 DOI: 10.1515/cclm.2007.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key platform within the "omic" technologies that also encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarises protein pre-separation, identification, quantification and modification/interaction analysis and puts them into perspective for nutritional R and D. Mass spectrometry has progressed with regard to mass accuracy, resolution and protein identification performance. Separation, depletion and enrichment techniques can increasingly cope with complexity and dynamic range of proteomic samples. Hence, proteomic studies currently provide a broader, albeit still incomplete, coverage of a given proteome. Proteomics adapted and applied to nutrition and health should demonstrate ingredient efficacy, deliver biomarkers for health and disease disposition, help in differentiating dietary responders from non-responders, and discover bioactive food components.
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Affiliation(s)
- Martin Kussmann
- BioAnalytical Science Department, Nestlé Research Centre, Nestec Ltd., Lausanne, Switzerland.
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Snopok B, Yurchenko M, Szekely L, Klein G, Kashuba E. SPR-based immunocapture approach to creating an interfacial sensing architecture: mapping of the MRS18-2 binding site on retinoblastoma protein. Anal Bioanal Chem 2006; 386:2063-73. [PMID: 17086389 DOI: 10.1007/s00216-006-0867-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 08/02/2006] [Accepted: 09/15/2006] [Indexed: 11/30/2022]
Abstract
Biosensor technologies based on optical readout are widely used in protein-protein interaction studies. Here we describe a fast and simple approach to the creation of oriented interfacial architectures for surface plasmon resonance (SPR) transducers, based on conventional biochemical procedures and custom reagents. The proposed protocol permits the oriented affinity-capture of GST fusion proteins by a specific antibody which is bound to protein A, which in turn has been immobilized on the transducer surface (after the surface has been modified by guanidine thiocyanate). The applicability of the method was demonstrated by studying the interaction between retinoblastoma tumor suppressor protein (pRb) and MRS18-2 proteins. The formation of the pRb-MRS18-2 protein complex was examined and the pRb binding site (A-box-spacer-B-box) was mapped. We have also shown that MRS18-2, which was detected as the Epstein-Barr virus-encoded EBNA-6 binding partner using the yeast two-hybrid system, binds to pRb in GST pull-down assays.
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Affiliation(s)
- Boris Snopok
- V. Lashkaryov Institute of Semiconductor Physics, NASU, Prospekt Nauki 41, 03028 Kiev-28, Ukraine
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Abstract
PURPOSE OF REVIEW Proteomics, the comprehensive analysis of a protein complement in a cell, tissue or biological fluid at a given time, is a key player in the family of -omic disciplines, which encompass genomics (gene analysis), transcriptomics (gene expression analysis) and metabolomics (metabolite profiling). This review summarizes the state of the art of proteomics technology and puts it into perspective for food-related research. Learning from proteomic experiences in the pharmaceutical context, this article may help to translate proteomics into nutrition and health. RECENT FINDINGS Mass spectrometric technology has progressed enormously with regard to mass accuracy, resolution and peptide sequencing power. Likewise, upstream separation, depletion and enrichment techniques now allow us to deal with the large complexity and wide dynamic range of proteomic samples more efficiently. Consequently, proteomic studies now provide a broader, but still far from complete, coverage of a given proteome. SUMMARY Proteomics adapted and applied to the context of nutrition and health has the potential to deliver biomarkers for health and comfort, reveal early indicators of disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components.
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Affiliation(s)
- Martin Kussmann
- Bioanalytical Science Department, Nestlé Research Center, Nestec Ltd., Lausanne, Switzerland.
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Abstract
The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomics-based information with other related research areas.
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Affiliation(s)
- Gil Alterovitz
- Division of Health Sciences and Technology, HST, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA.
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Gudiksen KL, Gitlin I, Whitesides GM. Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS. Proc Natl Acad Sci U S A 2006; 103:7968-72. [PMID: 16698920 PMCID: PMC1472413 DOI: 10.1073/pnas.0602816103] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper shows that proteins display an unexpectedly wide range of behaviors in buffers containing moderate (0.1-10 mM) concentrations of SDS (complete unfolding, formation of stable intermediate states, specific association with SDS, and various kinetic phenomena); capillary electrophoresis provides a convenient method of examining these behaviors. Examination of the dynamics of the response of proteins to SDS offers a way to differentiate and characterize proteins. Based on a survey of 18 different proteins, we demonstrate that proteins differ in the concentrations of SDS at which they denature, in the rates of unfolding in SDS, and in the profiles of the denaturation pathways. We also demonstrate that these differences can be exploited in the analysis of mixtures.
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Affiliation(s)
- Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
- *To whom correspondence should be addressed. E-mail:
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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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Cho EJ, Collett JR, Szafranska AE, Ellington AD. Optimization of aptamer microarray technology for multiple protein targets. Anal Chim Acta 2006; 564:82-90. [PMID: 17723365 DOI: 10.1016/j.aca.2005.12.038] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 12/08/2005] [Accepted: 12/12/2005] [Indexed: 10/25/2022]
Abstract
Aptamer-based microarrays for the quantitation of multiple protein analytes have been developed. A multiplex aptamer microarray was generated by printing two RNA aptamers (anti-lysozyme and anti-ricin) and two DNA aptamers (anti-IgE and anti-thrombin) on to either streptavidin (SA) or neutravidin (NA)-coated glass slides. However, substantial optimization was required in order to ensure the simultaneous function of the aptamer:analyte pairs. The effects of protein labeling, assay buffer, surface coating, and immobilization chemistry and orientation were investigated. A single buffer (PBS buffer containing 5 mM MgCl2 and 0.1% Tween 20) was found to work well with all the aptamers, even though this was not the buffer originally used in their selection, while neutravidin-coated slides yielded a lower detection limit, wider detection range, and more uniform background than streptavidin-coated slides. Incubation with Cy3-labeled proteins yielded sensitive, target-specific, and dose-dependent responses to each protein. Target protein concentrations as low as 72 pg/mL (5 pM, lysozyme), 15 ng/mL (0.5 nM, ricin), 1.9 ng/mL (0.01 nM, IgE), and 170 ng/mL (5 nM, thrombin) could be detected. These results show that aptamer arrays can potentially be used with numerous proteins in parallel, furthering the notion that aptamer arrays may be useful in proteomics.
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Affiliation(s)
- Eun Jeong Cho
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
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Haggarty SJ. The principle of complementarity: chemical versus biological space. Curr Opin Chem Biol 2005; 9:296-303. [PMID: 15939332 DOI: 10.1016/j.cbpa.2005.04.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/15/2005] [Indexed: 02/07/2023]
Abstract
Chemical genomics aims to systematically explore the interactions between small molecules and biological systems. These efforts aim to annotate genomes using the language of chemistry, and to provide information-rich profiles of chemical and biological systems. Here, I describe recent conceptual and experimental advances toward the goal of mapping multidimensional chemical and biological descriptor spaces. In doing so, I will focus on the complementary nature of these efforts, the importance of recognizing the distinction between computed versus observed descriptors, and highlight recent 'landmark' examples of small molecules discovered using phenotypic screens. Future computation and experimental advances will be needed to fully realize the goals of chemical genomics. For those willing to consider both local and global properties of chemical and biological space, and to venture into uncharted territory, there promises to be new vistas and principles to be discovered.
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Affiliation(s)
- Stephen J Haggarty
- Eli & Edythe L Broad Institute, 320 Charles Street, Cambridge, MA 02141, USA.
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Abstract
Two methods that use chemoselective ligation chemistry to prepare peptide and small-molecule microarrays are described here. The first method involves the functionalization of a glass slide with a glyoxylyl group, followed by chemoselective ligation of small molecules or peptides to the functionalized surface via a covalent bond. In the second method, peptides or small molecules are first conjugated to a macromolecular scaffold. The final ligand-scaffold conjugates are then spotted and adsorbed onto the solid surface. Three different assay methods to screen such chemical microarrays are described.
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Affiliation(s)
- Jan Marik
- Division of Hematology & Oncology, Department of Internal Medicine, UC Davis Cancer Center, University of California, Davis, USA
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Love DR, Pichler FB, Dodd A, Copp BR, Greenwood DR. Technology for high-throughput screens: the present and future using zebrafish. Curr Opin Biotechnol 2004; 15:564-71. [PMID: 15560983 DOI: 10.1016/j.copbio.2004.09.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The zebrafish is a popular vertebrate model organism with similar organ systems and gene sequences to humans. Zebrafish embryos are optically transparent enabling organ visualisation, which can be complemented with gene expression analysis at the transcript and protein levels. Furthermore, zebrafish can be treated with small molecules and drugs in a microtitre plate format for high-throughput analysis and for the identification and validation of drugs. High-throughput methodologies for use in zebrafish include phenotype-based visualisation, transcript studies using low-density DNA microarrays and proteomic analysis. These technologies offer significant whole-organism biological value in the drug discovery and drug development pipeline.
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Affiliation(s)
- Donald R Love
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1001, New Zealand.
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Bailey SN, Sabatini DM, Stockwell BR. Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens. Proc Natl Acad Sci U S A 2004; 101:16144-9. [PMID: 15534212 PMCID: PMC528944 DOI: 10.1073/pnas.0404425101] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We developed a microarray-based system for screening small molecules in mammalian cells. This system is compatible with image-based screens and requires fewer than 100 cells per compound. Each compound is impregnated in a 200-microm-diameter disc composed of biodegradable poly-(D),(L)-lactide/glycolide copolymer. Cells are seeded on top of these discs, and compounds slowly diffuse out, affecting proximal cells. In contrast with microtiter-based screening, this system does not involve the use of wells or walls between each compound-treated group of cells. We demonstrate detection of the effects of a single compound in a large microarray, that diverse compounds can be released in this format, and that extended release over several days is feasible. We performed a small synthetic lethal screen and identified a compound (macbecin II) that has reduced activity in cells with RNA interference-mediated decrease in the expression of tuberous sclerosis 2. Thus, we have developed a microarray-based screening system for testing the effects of small molecules on mammalian cells by using an imaging-based readout. This method will be useful to those performing small-molecule screens to discover new chemical tools and potential therapeutic agents.
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Affiliation(s)
- Steve N Bailey
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
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Schrattenholz A. Proteomics: how to control highly dynamic patterns of millions of molecules and interpret changes correctly? DRUG DISCOVERY TODAY. TECHNOLOGIES 2004; 1:1-8. [PMID: 24981261 DOI: 10.1016/j.ddtec.2004.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
"Proteomics" is essentially protein analysis and, until recently, could be described as an umbrella for a set of technology and bioinformatic platforms aimed at the comprehensive molecular description of the actual protein complement of a given sample. Today, it is typically associated with systems biology. In this context, powerful new technologies for differential complexity reduction promise to solve some of the most pressing problems in drug development. The resulting analytical challenges of unprecedented complexity are emerging as one of the last frontiers of molecular biology. Considerable progress has been made in characterizing rapid post-translational protein modifications in highly complex molecular signatures as key disease-related biomarkers from experimental model systems or clinical samples.: Section Editors: Wolfgang Fischer, Rob Hooft, and Michael Walker Identifying a potential protein drug target within a cell is a major challenge in modern drug discovery; techniques for screening the proteome are, therefore, an important tool. Major difficulties for target identification include the separation of proteins and their detection. The latest developments in techniques that master these challenges, such as SDS-PAGE and liquid chromatography in combination with isotopic labeling and staining techniques, are highlighted in this review. The authors evaluate the applicability of these approaches for specific tasks.
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Affiliation(s)
- André Schrattenholz
- ProteoSys AG, Carl-Zeiss-Str. 51, 55129 Mainz, Germany. http://www.proteosys.com
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