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Huff JL, Lynch MP, Nettikadan S, Johnson JC, Vengasandra S, Henderson E. Label-Free Protein and Pathogen Detection Using the Atomic Force Microscope. ACTA ACUST UNITED AC 2016; 9:491-7. [PMID: 15452335 DOI: 10.1177/1087057104268803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The atomic force microscope (AFM) uses a sharp micron-scale tip to scan and amplify surface features, providing exceptionally detailed topographical information with magnification on the order of ×106. This instrument is used extensively for quality control in the computer and semiconductor industries and is becoming a progressively more important tool in the biological sciences. Advantages of the AFM for biological application include the ability to obtain information in a direct, label-free manner and the ability to image in solution, providing real-time data acquisition under physiologically relevant conditions. A novel application of the AFM currently under development combines its surface profiling capabilities with fixed immuno-capture using antibodies immobilized in a nanoarray format. This provides a distinctive platform for direct, label-free detection and characterization of viral particles and other pathogens.
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Hirao I, Kimoto M. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:345-67. [PMID: 22850726 PMCID: PMC3422687 DOI: 10.2183/pjab.88.345] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/01/2012] [Indexed: 05/30/2023]
Abstract
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
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Affiliation(s)
- Ichiro Hirao
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan.
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3
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Brody EN, Gold L, Lawn RM, Walker JJ, Zichi D. High-content affinity-based proteomics: unlocking protein biomarker discovery. Expert Rev Mol Diagn 2011; 10:1013-22. [PMID: 21080818 DOI: 10.1586/erm.10.89] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single protein biomarkers measured with antibody-based affinity assays are the basis of molecular diagnostics in clinical practice today. There is great hope in discovering new protein biomarkers and combinations of protein biomarkers for advancing medicine through monitoring health, diagnosing disease, guiding treatment, and developing new therapeutics. The goal of high-content proteomics is to unlock protein biomarker discovery by measuring many (thousands) or all (∼23,000) proteins in the human proteome in an unbiased, data-driven approach. High-content proteomics has proven technically difficult due to the diversity of proteins, the complexity of relevant biological samples, such as blood and tissue, and large concentration ranges (in the order of 10(12) in blood). Mass spectrometry and affinity methods based on antibodies have dominated approaches to high-content proteomics. For technical reasons, neither has achieved adequate simultaneous performance and high-content. Here we review antibody-based protein measurement, multiplexed antibody-based protein measurement, and limitations of antibodies for high-content proteomics due to their inherent cross-reactivity. Finally, we review a new affinity-based proteomic technology developed from the ground up to solve the problem of high content with high sensitivity and specificity. Based on a new generation of slow off-rate modified aptamers (SOMAmers), this technology is unlocking biomarker discovery.
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Affiliation(s)
- Edward N Brody
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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4
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Abstract
In less than 40 years, aptamers have consolidated their role in biosensor development. Chemically related to nucleic acid probes, production of aptamers against targets of various sizes and compositions places them as ideal capture elements, alternative to more consolidated molecules such as antibodies. Thanks to their chemical simplicity and production, as well as their unique characteristics, aptamers have been successfully integrated in several innovative approaches. The incorporation of aptamers into the existing microarray technologies has lead to the reporting of various detection strategies, including direct fluorescence detection of fluorescent reporters, fluorescence anisotropy, FRET, SPR imaging, and electrochemical detection.
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Affiliation(s)
- Eva Baldrich
- Instituto de Microelectrónica de Barcelona (IMB-CNM), Barcelona, Spain.
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5
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Hiep HM, Yoshikawa H, Tamiya E. Interference Localized Surface Plasmon Resonance Nanosensor Tailored for the Detection of Specific Biomolecular Interactions. Anal Chem 2010; 82:1221-7. [DOI: 10.1021/ac902008x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ha Minh Hiep
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroyuki Yoshikawa
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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6
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Abstract
Aptamers are small single-stranded nucleic acids that fold into a well-defined three-dimensional structure. They show a high affinity and specificity for their target molecules and inhibit their biological functions. Aptamers belong to the nucleic acids family and can be synthesized by chemical or enzymatic procedures, or a combination of the two. They can, therefore, be considered as both chemical and biological substances. This Review summarizes the most convenient approaches to their preparation and new developments in the field of aptamers. The application of aptamers in chemical biology is also discussed.
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Affiliation(s)
- Günter Mayer
- Life and Medical Sciences, Prog. Unit Chemical Biology and Medicinal Chemistry, University of Bonn c/o Kekulé-Institute for Organic Chemistry and Biochemistry, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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7
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Dahdah DB, Morin I, Moreau MJJ, Dixon NE, Schaeffer PM. Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus-Ter complex. Chem Commun (Camb) 2009:3050-2. [PMID: 19462083 DOI: 10.1039/b900905a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.
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Affiliation(s)
- Dahdah B Dahdah
- Comparative Genomics Centre, School of Pharmacy & Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
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8
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9
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Espina V, Liotta LA, Petricoin EF. Reverse-phase protein microarrays for theranostics and patient tailored therapy. Methods Mol Biol 2009; 520:89-105. [PMID: 19381949 DOI: 10.1007/978-1-60327-811-9_7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Analysis of the genome provides important information about the somatic genetic changes existing in the tissue; however, it is the proteins that do the work of the cell. Diseases such as cancer are caused by derangements in cellular protein molecular networks and cell signaling pathways. These pathways contain a large and growing collection drug targets, governing cellular survival, proliferation, invasion, and cell death. The clinical utility of reverse-phase protein microarrays (RPPA), a new technology invented in our laboratory, lies in its ability to generate a functional map of known cell signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. Coupled with laser capture microdissection (LCM), the RPPA platform, the entire cellular proteome is immobilized on a substratum with subsequent immunodetection of the total levels and phosphorylated, or activated, state of cell signaling proteins. The results of which pathways are "in use" can then be correlated with biological and clinical information and serve as both a diagnostic and a therapeutic guide, thus providing a "theranostic" endpoint.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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10
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Espina V, Wulfkuhle JD, Calvert VS, Petricoin EF, Liotta LA. Reverse phase protein microarrays for monitoring biological responses. Methods Mol Biol 2008; 383:321-36. [PMID: 18217695 DOI: 10.1007/978-1-59745-335-6_21] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Cancer has a genomic and proteomic basis. Genomic information provides information about the somatic genetic changes existing in the tumor that provides a survival advantage driving neoplastic progression. On the other hand, proteomics aids in the identification of dysregulated cellular proteins, including known or novel drug targets, governing cellular survival, proliferation, invasion, and cell death. The clinical utility of reverse phase protein microarrays lies in their ability to generate a map of known cell signaling networks or pathways for an individual patient. This protein network map aids in identifying critical nodes or pathways that may serve as drug targets for individualized or combinatorial therapy. Reverse phase protein microarrays are one of the tools available for profiling the protein molecular pathways in a given cellular sample. This type of microarray can uniquely quantify phosphorylation states of proteins. An entire cellular proteome is immobilized on a substratum with subsequent immunodetection of total and activated forms of cell signaling proteins. The pattern of signal intensity generated by the protein spots can be correlated with biological and clinical information as diagnostic and prognostic indicators.
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Affiliation(s)
- Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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11
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Espina V, Wulfkuhle J, Calvert VS, Edmiston KH, Liotta LA, Petricoin EF. Development and Use of Reversed-Phase Protein Microarrays for Clinical Applications. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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12
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Kulbachinskiy AV. Methods for selection of aptamers to protein targets. BIOCHEMISTRY (MOSCOW) 2008; 72:1505-18. [PMID: 18282139 DOI: 10.1134/s000629790713007x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers are synthetic single-stranded RNA or DNA molecules capable of specific binding to other target molecules. In this review, the main aptamer properties are considered and methods for selection of aptamers against various protein targets are described. Special attention is given to the methods for directed selection of aptamers, which allow one to obtain ligands with specified properties.
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Affiliation(s)
- A V Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, pl. Kurchatova 2, 123182 Moscow, Russia.
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13
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Zichi D, Eaton B, Singer B, Gold L. Proteomics and diagnostics: Let's Get Specific, again. Curr Opin Chem Biol 2008; 12:78-85. [DOI: 10.1016/j.cbpa.2008.01.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 12/21/2022]
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Sathuluri RR, Yamamura S, Tamiya E. Microsystems technology and biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:285-350. [PMID: 17999038 DOI: 10.1007/10_2007_078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
This review addresses the recent developments in miniaturized microsystems or lab-on-a-chip devices for biosensing of different biomolecules: DNA, proteins, small molecules, and cells, especially at the single-molecule and single-cell level. In order to sense these biomolecules with sensitivity we have fabricated chip devices with respect to the biomolecule to be analyzed. The details of the fabrication are also dealt with in this review. We mainly developed microarray and microfluidic chip devices for DNA, protein, and cell analyses. In addition, we have introduced the porous anodic alumina layer chip with nanometer scale and gold nanoparticles for label-free sensing of DNA and protein interactions. We also describe the use of microarray and microfluidic chip devices for cell-based assays and single-cell analysis in drug discovery research.
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Affiliation(s)
- Ramachandra Rao Sathuluri
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
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15
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Espina V, Wulfkuhle J, Calvert VS, Liotta LA, Petricoin EF. Reverse phase protein microarrays for theranostics and patient-tailored therapy. Methods Mol Biol 2008; 441:113-28. [PMID: 18370315 DOI: 10.1007/978-1-60327-047-2_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although the genome provides information about the somatic genetic changes existing in the tissue and underpins pathology, it is the proteins that do the work of the cell and are functionally responsible for almost all disease processes. Moreover, many diseases such as cancer are a manifestation of deranged cellular protein molecular networks and cell-signaling pathways. These pathways contain a large and growing collection of drug targets, governing cellular survival, proliferation, invasion, and cell death. Thus, the promise of proteomics resides in the study of molecules that extend beyond correlation to causality. The clinical utility of reverse phase protein microarrays, a new technology invented in our laboratory, lies in its ability to generate a functional map of known cell-signaling networks or pathways for an individual patient obtained directly from a biopsy specimen. This patient-specific circuit diagram provides key information that identifies critical nodes or pathways that may serve as drug targets for individualized or combinatorial therapy through the quantification of phosphorylation states of proteins. Using this technique, the entire cellular proteome is immobilized on a substratum with subsequent immunodetection of the phosphorylated, or activated, state of cell-signaling proteins. The results of which pathways are "in use" can then be correlated with biological and clinical information and serve as both a diagnostic and a therapeutic guide: thus providing a "theranostic" endpoint.
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Affiliation(s)
- Virginia Espina
- Laboratory of Pathology, National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
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16
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Stoevesandt O, Taussig MJ. Affinity reagent resources for human proteome detection: initiatives and perspectives. Proteomics 2007; 7:2738-50. [PMID: 17639606 DOI: 10.1002/pmic.200700155] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Essential to the ambition of characterising fully the human proteome are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. Although a large number of affinity reagents are available commercially, their quality is often questionable and only a fraction of the proteome is covered. In order for more targets to be examined, there is a need for broad availability of panels of affinity reagents, including binders against proteins of unknown functions. The most familiar affinity reagents are antibodies and their fragments, but engineered forms of protein scaffolds and nucleic acid aptamers with similar diversity and binding properties are becoming viable alternatives. Recent initiatives in Europe and the USA have been established to improve both the availability and quality of reagents for affinity proteomics, with the ultimate aim of creating standardised collections of well-validated binding molecules for proteome analysis. As well as coordinating affinity reagent production through existing resources and technology providers, these projects aim to benchmark key molecular entities, tools, and applications, and establish the bioinformatics framework and databases needed. The benefits of such reagent resources will be seen in basic research, medicine and the biotechnology and pharmaceutical industries.
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Affiliation(s)
- Oda Stoevesandt
- Technology Research Group, The Babraham Institute, Cambridge, UK
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17
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Missailidis S, Perkins A. Update: aptamers as novel radiopharmaceuticals: their applications and future prospects in diagnosis and therapy. Cancer Biother Radiopharm 2007; 22:453-68. [PMID: 17803440 DOI: 10.1089/cbr.2007.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The production of biomaterials with the capacity to bind tightly and specifically to cell surface receptors of malignant cells can greatly benefit cancer diagnosis and treatment. Whereas antibodies have the ability to specifically recognize some tumor cell makers, their large size and immunogenecity markedly limit their value. The development of nuclease-resistant oligonucleotide agents, termed aptamers, offers an alternative to antibodies as targeting, diagnostic, and delivery agents. Using the systematic evolution of ligands by exponential enrichment (SELEX) methodology or other variations, one can select specific sequences that have appropriate binding affinities and specificities against clinically relevant markers from large libraries of oligonucleotide ligands. Aptamers have been found to bind their targets with high specificity and with dissociation constants in the subnanomolar or picomolar range. However, the possibility for the selected aptamers to be developed as targeting agents for diagnostic imaging or targeted radiotherapy purposes has yet to be realized. Peptide-coupling reactions between amino and carboxylic groups offer the possibility of labeling the aptamers with a number of chelators that, coupled with appropriate radionuclides, would generate novel targeted radiopharmaceuticals for the diagnosis and therapy of disease. The unparalleled combinatorial chemical diversity, small size, and modification ability of aptamers is expected to meet the criteria for robust, generic drug discovery technology and open new horizons for the development of future radiopharmaceuticals.
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Affiliation(s)
- Sotiris Missailidis
- Department of Chemistry, The Open University, Walton Hall, Milton Keynes, UK.
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18
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Abstract
The high affinity and specificity of aptamers make them ideal reagents for a wide range of analytical applications. It is not surprising that they are finding application in microfluidics as well. CE has proven to be an efficient technique for isolating aptamers. Aptamers have been used as affinity reagents in CE assays. Aptamer-based chromatography stationary phases have demonstrated unique selectivities. Possibly the application that holds the highest potential is aptamer microarrays for screening proteomic samples.
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19
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Radko SP, Rakhmetova SY, Bodoev NV, Archakov AI. Aptamers as affinity reagents for clinical proteomics. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2007. [DOI: 10.1134/s1990750807030043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Huang RP, Yang W, Yang D, Flowers L, Horowitz IR, Cao X, Huang R. The promise of cytokine antibody arrays in the drug discovery process. Expert Opin Ther Targets 2007; 9:601-15. [PMID: 15948677 DOI: 10.1517/14728222.9.3.601] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The introduction of cytokine antibody arrays has added a new approach for investigators to simultaneously measure multiple cytokine levels in biological samples. Several different platforms have been developed. The ability to measure hundreds of cytokine levels with high specificity and sensitivity within a very limited amount of samples is a powerful tool. Many investigators worldwide have applied this novel technology in their biomedical research, particularly in drug discovery. Undoubtedly, the technology will continue to be improved and the application increased in the next several years.
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Affiliation(s)
- Ruo-Pan Huang
- Division of Research, Department of Gynecology and Obstetrics, Emory University School of Medicine, 1639 Pierce Drive, Atlanta, GA 30322, USA.
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21
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Wulfkuhle JD, Edmiston KH, Liotta LA, Petricoin EF. Technology insight: pharmacoproteomics for cancer--promises of patient-tailored medicine using protein microarrays. ACTA ACUST UNITED AC 2006; 3:256-68. [PMID: 16683004 DOI: 10.1038/ncponc0485] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 02/07/2006] [Indexed: 11/09/2022]
Abstract
Patient-tailored medicine can be defined as the selection of specific therapeutics to treat disease in a particular individual based on genetic, genomic or proteomic information. While individualized treatments have been used in medicine for years, advances in cancer treatment have now generated a need to more precisely define and identify those patients who will derive the most benefit from new-targeted agents. Cellular signaling pathways are a protein-based network, and the intended drug effect is to disrupt aberrant protein phosphorylation-based enzymatic activity and epigenetic phenomena. Pharmacoproteomics, or the tailoring of therapy based on proteomic knowledge, will begin to take a central role in this process. A new type of protein array platform, the reverse-phase protein microarray, shows potential for providing detailed information about the state of the cellular 'circuitry' from small samples such as patient biopsy specimens. Measurements of hundreds of specific phosphorylated proteins that span large classes of important signaling pathways can be obtained at once from only a few thousand cells. Clinical implementation of these new proteomic tools to aid the clinical, medical and surgical oncologist in making decisions about patient care will now require thoughtful communication between practicing clinicians and research scientists.
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Affiliation(s)
- Julia D Wulfkuhle
- Center for Applied Proteomics Molecular Medicine, George Mason University, Manassas, VA, USA.
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22
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Endo T, Kerman K, Nagatani N, Hiepa HM, Kim DK, Yonezawa Y, Nakano K, Tamiya E. Multiple Label-Free Detection of Antigen−Antibody Reaction Using Localized Surface Plasmon Resonance-Based Core−Shell Structured Nanoparticle Layer Nanochip. Anal Chem 2006; 78:6465-75. [PMID: 16970322 DOI: 10.1021/ac0608321] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this research, a localized surface plasmon resonance (LSPR)-based bioanalysis method for developing multiarray optical nanochip suitable for screening bimolecular interactions is described. LSPR-based label-free monitoring enables to solve the problems of conventional methods that require large sample volumes and time-consuming labeling procedures. We developed a multiarray LSPR-based nanochip for the label-free detection of proteins. The multiarray format was constructed by a core-shell-structured nanoparticle layer, which provided 300 nanospots on the sensing surface. Antibodies were immobilized onto the nanospots using their interaction with Protein A. The concentrations of antigens were determined from the peak absorption intensity of the LSPR spectra. We demonstrated the capability of the array measurement using immunoglobulins (IgA, IgD, IgG, IgM), C-reactive protein, and fibrinogen. The detection limit of our label-free method was 100 pg/mL. Our nanochip is readily transferable to monitor the interactions of other biomolecules, such as whole cells or receptors, with a massively parallel detection capability in a highly miniaturized package. We anticipate that the direct label-free optical immunoassay of proteins reported here will revolutionize clinical diagnosis and accelerate the development of hand-held and user-friendly point-of-care devices.
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Affiliation(s)
- Tatsuro Endo
- Department of Mechano-Micro Engineering, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8502, Japan
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Chauveau F, Pestourie C, Tavitian B. [Aptamers: selection and scope of applications]. ACTA ACUST UNITED AC 2006; 54:251-8. [PMID: 16678359 DOI: 10.1016/j.patbio.2006.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 03/17/2006] [Indexed: 12/15/2022]
Abstract
Aptamers are short oligonucleotides selected from large combinatorial pools of sequences for their capacity to bind to many different targets ranging from small molecules (amino acids, antibiotics...) to proteins or nucleic acid structures. Aptamers present the same high specificity and affinity for their targets as antibodies. In addition to efficient binding, aptamers have been shown in many cases to display an inhibitory activity against their targets. Many aptamers are now being developed against biomedical relevant targets, and one aptamer that inhibits the human VEGF165 already received approval for the treatment of age-related macular degeneration. Here we discuss the principles and the practical way of selecting aptamers (SELEX technology) as well as the structural basis for their performance as ligands. A wide scope of applications is described - aptamers have been used as tools for studying nucleic acids/proteins interactions, detecting, purifying or imaging target molecules, regulating gene expression - and includes recent developments of aptamers for therapy and diagnosis.
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Affiliation(s)
- F Chauveau
- CEA, département de recherche médicale, service hospitalier Frédéric-Joliot, Inserm U803, Orsay, France
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24
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Proske D, Blank M, Buhmann R, Resch A. Aptamers--basic research, drug development, and clinical applications. Appl Microbiol Biotechnol 2005; 69:367-74. [PMID: 16283295 DOI: 10.1007/s00253-005-0193-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 08/16/2005] [Accepted: 09/14/2005] [Indexed: 01/28/2023]
Abstract
Since its discovery in the early 1990s, aptamer technology has progressed tremendously. Automated selection procedures now allow rapid identification of DNA and RNA sequences that can target a broad range of extra- and intracellular proteins with nanomolar affinities and high specificities. The unique binding properties of nucleic acids, which are amenable to various modifications, make aptamers perfectly suitable for different areas of biotechnology. Moreover, the approval of an aptamer for vascular endothelial growth factor by the US Food and Drug Administration highlights the potential of aptamers for therapeutic applications. This review summarizes recent developments and demonstrates that aptamers are valuable tools for diagnostics, purification processes, target validation, drug discovery, and even therapeutic approaches.
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Affiliation(s)
- Daniela Proske
- NascaCell IP GmbH, 3. OG, Modul D Max-Lebsche-Platz, 3181377 Munich, Germany.
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25
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Abstract
Aptamers are short single-stranded oligonucleotides that fold into well defined three-dimensional shapes allowing them to bind to and inhibit their targets with high affinity and specificity. Aptamers can be considered truly multifunctional tools, because they can be generated rapidly and applied for specific detection, inhibition, and characterization of proteins. Recent publications impressively confirm that aptamers can be used either as surrogate inhibitors for the identification of small molecule lead compounds or as biopharmaceuticals.
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Wulfkuhle J, Espina V, Liotta L, Petricoin E. Genomic and proteomic technologies for individualisation and improvement of cancer treatment. Eur J Cancer 2005; 40:2623-32. [PMID: 15541963 DOI: 10.1016/j.ejca.2004.05.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 05/20/2004] [Indexed: 01/03/2023]
Abstract
The development of microarray-based technologies for characterising tumours, both at the genomic and proteomic levels, has had a significant impact on the field of oncology. Gene expression profiling of various human tumour tissues has led to the identification of expression patterns related to disease outcome and drug resistance, as well as to the discovery of new therapeutic targets and insights into disease pathogenesis. Protein microarray technologies, such as reverse-phase protein arrays, provide the unique opportunity to profile tissues and assess the activity of signalling pathways within isolated cell populations. This technology can be used to identify patients likely to benefit from specific treatment modalities and also to monitor therapeutic response in samples obtained during and after treatment. Routine application of genomic and proteomic microarray technologies in clinical practice will require significant efforts to standardise the techniques, controls and reference standards, and analytical tools used. Extensive, independent validation using large, statistically-powered datasets will also be necessary. Inclusion of concomitant genomic and proteomic-based molecular profiling techniques into clinical trial protocols will bring us closer to the reality of patient-tailored therapy.
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Affiliation(s)
- Julia Wulfkuhle
- NCI/FDA Clinical Proteomics Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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27
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Sheehan KM, Calvert VS, Kay EW, Lu Y, Fishman D, Espina V, Aquino J, Speer R, Araujo R, Mills GB, Liotta LA, Petricoin EF, Wulfkuhle JD. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol Cell Proteomics 2005; 4:346-55. [PMID: 15671044 DOI: 10.1074/mcp.t500003-mcp200] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cancer can be defined as a deregulation or hyperactivity in the ongoing network of intracellular and extracellular signaling events. Reverse phase protein microarray technology may offer a new opportunity to measure and profile these signaling pathways, providing data on post-translational phosphorylation events not obtainable by gene microarray analysis. Treatment of ovarian epithelial carcinoma almost always takes place in a metastatic setting since unfortunately the disease is often not detected until later stages. Thus, in addition to elucidation of the molecular network within a tumor specimen, critical questions are to what extent do signaling changes occur upon metastasis and are there common pathway elements that arise in the metastatic microenvironment. For individualized combinatorial therapy, ideal therapeutic selection based on proteomic mapping of phosphorylation end points may require evaluation of the patient's metastatic tissue. Extending these findings to the bedside will require the development of optimized protocols and reference standards. We have developed a reference standard based on a mixture of phosphorylated peptides to begin to address this challenge.
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Affiliation(s)
- Katherine M Sheehan
- United States Food and Drug Administration (FDA)-NCI Clinical Proteomics Program, Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD, USA
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28
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Abstract
The potential for quickly isolating high affinity, highly selective ligands generated much excitement when SELEX was first described. Fifteen years later, SELEX has still not achieved widespread acceptance due to limitations in aptamer affinity, stability and throughput. Recent research is beginning to address these limitations though and SELEX is quickly regaining its standing as a hot topic in areas as diverse as drug discovery, chemical analysis, and even genomics and proteomics.
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Affiliation(s)
- Michael T Bowser
- University of Minnesota, Department of Chemistry, 207 Pleasant St. SE, Minneapolis, MN 55455, USA.
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29
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Espina V, Woodhouse EC, Wulfkuhle J, Asmussen HD, Petricoin EF, Liotta LA. Protein microarray detection strategies: focus on direct detection technologies. J Immunol Methods 2004; 290:121-33. [PMID: 15261576 DOI: 10.1016/j.jim.2004.04.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2004] [Indexed: 11/18/2022]
Abstract
Protein microarrays are being utilized for functional proteomic analysis, providing information not obtainable by gene arrays. Microarray technology is applicable for studying protein-protein, protein-ligand, kinase activity and posttranslational modifications of proteins. A precise and sensitive protein microarray, the direct detection or reverse-phase microarray, has been applied to ongoing clinical trials at the National Cancer Institute for studying phosphorylation events in EGF-receptor-mediated cell signaling pathways. The variety of microarray applications allows for multiple, creative microarray designs and detection strategies. Herein, we discuss detection strategies and challenges for protein microarray technology, focusing on direct detection of protein microarrays.
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Affiliation(s)
- Virginia Espina
- FDA-NCI Clinical Proteomics Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Room B1B53, Bldg. 10, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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30
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Kimoto M, Endo M, Mitsui T, Okuni T, Hirao I, Yokoyama S. Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. ACTA ACUST UNITED AC 2004; 11:47-55. [PMID: 15112994 DOI: 10.1016/j.chembiol.2003.12.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Revised: 10/20/2003] [Accepted: 10/22/2003] [Indexed: 11/20/2022]
Abstract
A photo-sensitive ribonucleotide of 5-iodo-2-oxo(1H) pyridine (Iy) capable of site-specific incorporation into transcripts was developed. The site-specific Iy incorporation into RNA was achieved by T7 transcription mediated by unnatural base pairing between Iy and its partner, 2-amino-6-(2-thienyl)purine (s). By this specific transcription, Iy was incorporated into an anti(Raf-1) RNA aptamer, which binds to human Raf-1 and inhibits the interaction between Raf-1 and Ras. Protein-dependent photo-dimerization of the aptamer was observed when Iy was located at specific positions in the aptamer, showing that the site-specific incorporation of the photo-sensitive component into RNA achieves highly specific crosslinking. This specific transcription mediated by the unnatural base pair would be a powerful tool for generating high-affinity RNA ligands and for analyzing RNA-RNA and RNA-protein interactions, as well as for constructing RNA-based nanostructures.
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Affiliation(s)
- Michiko Kimoto
- Protein Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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31
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Espina V, Dettloff KA, Cowherd S, Petricoin EF, Liotta LA. Use of proteomic analysis to monitor responses to biological therapies. Expert Opin Biol Ther 2004; 4:83-93. [PMID: 14680471 DOI: 10.1517/14712598.4.1.83] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Proteomics has the potential to revolutionise diagnosis and disease management. Serum protein pattern profiling by surface-enhanced laser desorption/ionisation time of flight (SELDI-TOF) mass spectrometry is emerging as a novel approach to discover protein patterns capable of distinguishing disease and disease-free states with high sensitivity and specificity. This method has shown great promise for early diagnosis of ovarian cancer and is being applied to a range of pathological states. Protein microarray technology is being evaluated as a new means to track biological responses to therapy. Through the measurement of key protein phosphorylation sites at different stages of disease progression or before and after treatment, protein signal pathways can be mapped and thus become the starting point for individualised therapy. Laser capture microdissection (LCM) coupled with immunostaining of protein microarrays allows isolation of pure cell populations and relative quantitation of phosphorylated and non-phosphorylated forms of the cell's key signalling proteins. This technology is currently in use at the National Institutes of Health in Phase II clinical trials of metastatic breast and ovarian cancer. Cell survival and apoptotic protein pathways are monitored as biological markers of disease progression in these clinical trials. Proteomic technologies, such as serum protein pattern profiling, combined with protein microarray technologies, constitute a new paradigm for detecting disease and monitoring disease response to therapy. Ultimately, proteomics and genomics will become integrated into cancer patient management through the design and tracking of individualised therapy.
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Affiliation(s)
- Virginia Espina
- National Cancer Institute, NIH, Building 10, Room B1B53, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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32
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Koch TH, Smith D, Tabacman E, Zichi DA. Kinetic analysis of site-specific photoaptamer-protein cross-linking. J Mol Biol 2004; 336:1159-73. [PMID: 15037076 DOI: 10.1016/j.jmb.2004.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 12/29/2003] [Accepted: 01/05/2004] [Indexed: 10/26/2022]
Abstract
ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.
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Affiliation(s)
- Tad H Koch
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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33
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Espina V, Petricoin EF, Liotta LA, Geho D. Application of sector protein microarrays to clinical samples. Clin Proteomics 2004. [DOI: 10.1385/cp:1:1:091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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34
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Blank K, Mai T, Gilbert I, Schiffmann S, Rankl J, Zivin R, Tackney C, Nicolaus T, Spinnler K, Oesterhelt F, Benoit M, Clausen-Schaumann H, Gaub HE. A force-based protein biochip. Proc Natl Acad Sci U S A 2003; 100:11356-60. [PMID: 12975526 PMCID: PMC208761 DOI: 10.1073/pnas.1934928100] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.
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Affiliation(s)
- K Blank
- nanotype, Lochhamer Schlag 12, 82166 Gräfelfing, Germany
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35
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36
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Albrecht C, Blank K, Lalic-Mülthaler M, Hirler S, Mai T, Gilbert I, Schiffmann S, Bayer T, Clausen-Schaumann H, Gaub HE. DNA: a programmable force sensor. Science 2003; 301:367-70. [PMID: 12869761 DOI: 10.1126/science.1084713] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Direct quantification of biomolecular interaction by single-molecule force spectroscopy has evolved into a powerful tool for materials and life sciences. We introduce an approach in which the unbinding forces required to break intermolecular bonds are measured in a differential format by comparison with a known reference bond (here, a short DNA duplex). In addition to a marked increase in sensitivity and force resolution, which enabled us to resolve single-base pair mismatches, this concept allows for highly specific parallel assays. This option was exploited to overcome cross-reactions of antibodies in a protein biochip application.
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37
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Sydor JR, Nock S. Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins. Proteome Sci 2003; 1:3. [PMID: 12831399 PMCID: PMC165414 DOI: 10.1186/1477-5956-1-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2003] [Accepted: 06/10/2003] [Indexed: 12/05/2022] Open
Abstract
The completion of the human genome sequence has led to a rapid increase in genetic information. The invention of DNA microarrays, which allow for the parallel measurement of thousands of genes on the level of mRNA, has enabled scientists to take a more global view of biological systems. Protein microarrays have a big potential to increase the throughput of proteomic research. Microarrays of antibodies can simultaneously measure the concentration of a multitude of target proteins in a very short period of time. The ability of protein microarrays to increase the quantity of data points in small biological samples on the protein level will have a major impact on basic biological research as well as on the discovery of new drug targets and diagnostic markers. This review highlights the current status of protein expression profiling arrays, their development, applications and limitations.
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Affiliation(s)
- Jens R Sydor
- Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, MA 02139, USA
| | - Steffen Nock
- Promab Biotechnologies Inc., 1300 Bancroft Ave, San Leandro, CA 94577, USA
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38
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Liotta LA, Espina V, Mehta AI, Calvert V, Rosenblatt K, Geho D, Munson PJ, Young L, Wulfkuhle J, Petricoin EF. Protein microarrays: meeting analytical challenges for clinical applications. Cancer Cell 2003; 3:317-25. [PMID: 12726858 DOI: 10.1016/s1535-6108(03)00086-2] [Citation(s) in RCA: 363] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Protein microarrays, one emerging class of proteomic technologies, have broad applications for discovery and quantitative analysis. A rapidly expanding use of this technology is the acquisition of information about the posttranslational modifications of proteins reflecting the activity state of signal pathways and networks, and is now employed for the analysis of biopsy samples in clinical trial research.
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Affiliation(s)
- Lance A Liotta
- FDA-NCI Clinical Proteomics Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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