251
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Koehler AN, Shamji AF, Schreiber SL. Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis. J Am Chem Soc 2003; 125:8420-1. [PMID: 12848532 DOI: 10.1021/ja0352698] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecule microarrays were screened to identify a small molecule ligand for Hap3p, a subunit of the yeast Hap2/3/4/5p transcription factor complex. The compound, named haptamide A, was determined to have a KD of 5.03 muM for binding to Hap3p using surface plasmon resonance analysis. Haptamide A also inhibited activation of a GDH1-lacZ reporter gene in a dose-dependent fashion. To explore structure-activity relationships, 11 derivatives of haptamide A were prepared using the same synthetic route that was developed for the original library synthesis. Analysis of dissociation constants and IC50 values for the reporter gene assay revealed a more potent inhibitor, haptamide B, with a KD of 330 nM. Whole-genome transcriptional profiling was used to compare effects of haptamide B with a hap3Delta yeast strain. Treatment with haptamide B, like the deletion mutant, reduced lactate-induced transcription of several genes from wild-type levels. Profiling the genetic "knockout" and the chemical genetic "knockdown" led to the identification of several genes that are regulated by Hap3p under nonfermentative conditions. These results demonstrate that a small molecule discovered using the small molecule microarray binding assay can permeate yeast cells and reach its target transcription factor protein in cells.
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Affiliation(s)
- Angela N Koehler
- Department of Chemistry and Chemical Biology, Harvard Biophysics Program, Howard Hughes Medical Institute, Harvard Institute of Chemistry and Cell Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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252
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Eastwood EL, Schaus SE. Borrelidin induces the transcription of amino acid biosynthetic enzymes via a GCN4-dependent pathway. Bioorg Med Chem Lett 2003; 13:2235-7. [PMID: 12798341 DOI: 10.1016/s0960-894x(03)00406-2] [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] [Indexed: 11/17/2022]
Abstract
Global cellular profiling of messenger RNA levels has been used to provide insight into the effects of the angiogenesis inhibitor borrelidin on the eukaryotic model organism Saccharomyces cerevisiae. The most notable result of treatment with borrelidin is the induction of amino acid biosynthetic enzymes in a time-dependent fashion. We have ascertained that induction of this pathway involves the GCN4 transcription factor. This conclusion was determined by treating a yeast strain lacking this gene and observing the absence of increased gene transcription under Gcn4p control.
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Affiliation(s)
- Erin L Eastwood
- Department of Chemistry, Metcalf Center for Science and Engineering, Boston University, 590 Commonwealth Avenue, MA 02215, Boston, USA
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253
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Abstract
Proteomics, the systematic evaluation of changes in the protein constituency of a cell, is more than just the generation of lists of proteins that increase or decrease in expression as a cause or consequence of disease. The ultimate goal is to characterize the information flow through protein pathways that interconnect the extracellular microenvironment with the control of gene transcription. The nature of this information can be a cause or a consequence of disease processes. Clinical applications of proteomics involve the use of proteomic technologies at the bedside. The analysis of human cancer as a model for how proteomics can have an impact at the bedside is now employing several new proteomic technologies that are being developed for early detection, therapeutic targeting and finally, patient-tailored therapy.
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Affiliation(s)
- Emanuel F Petricoin
- U. S. Food and Drug Administration-National Cancer Institute Clinical Proteomics Program, Center for Biologic Evaluation and Research, U. S. Food and Drug Administration, Rockville, MD 20852, USA.
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254
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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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255
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Abstract
To address the worsening problem of antibiotic-resistant bacteria there is an urgent need to develop new antibiotics. Comparative genomics and molecular genetics are being applied to produce lists of essential new targets for compound screening programmes. Combinatorial chemistry and structural biology are being applied to rapidly explore and optimize the interactions between lead compounds and their biological targets. Several compounds that have been identified from target-based screens are now in development, but technical and economic constraints might result in a trickle, rather than a flood, of new antibiotics onto the market in the near future.
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Affiliation(s)
- Diarmaid Hughes
- Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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256
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Feng Y. A marriage of chemistry and biology. CHINESE SCIENCE BULLETIN-CHINESE 2003. [DOI: 10.1007/bf03184204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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257
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Abstract
Proteomics is the study of the function of all expressed proteins. Tremendous progress has been made in the past few years in generating large-scale data sets for protein-protein interactions, organelle composition, protein activity patterns and protein profiles in cancer patients. But further technological improvements, organization of international proteomics projects and open access to results are needed for proteomics to fulfil its potential.
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Affiliation(s)
- Mike Tyers
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Canada M5G 1X5.
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258
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Abstract
The long-term challenge of proteomics is enormous: to define the identities, quantities, structures and functions of complete complements of proteins, and to characterize how these properties vary in different cellular contexts. One critical step in tackling this goal is the generation of sets of clones that express a representative of each protein of a proteome in a useful format, followed by the analysis of these sets on a genome-wide basis. Such studies enable genetic, biochemical and cell biological technologies to be applied on a systematic level, leading to the assignment of biochemical activities, the construction of protein arrays, the identification of interactions, and the localization of proteins within cellular compartments.
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Affiliation(s)
- Eric Phizicky
- University of Rochester School of Medicine, Department of Biochemistry and Biophysics, Box 712, 601 Elmwood Avenue, Rochester, New York 14642, USA.
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259
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Abstract
The potential medical applications of microarrays and in vitro diagnostic devices for global assessments of DNA sequence variations, relative RNA abundance and measurements of proteins have generated much excitement, and some skepticism, within the biomedical community. It has been suggested that within the next decade these microarrays and diagnostic devices will be routinely used in the selection, assessment and quality control of the best drugs for pharmaceutical development, at the bedside for diagnostics and for clinical monitoring of both desired and adverse outcomes of therapeutic interventions. Realizing such potential will be a challenge to the entire scientific community as often breakthroughs which show great promise at the bench fail to meet the requirements of clinicians and regulatory scientists, and to make the transition into common clinical and regulatory practice. The development of a co-operative framework between regulators, product sponsors and technology experts will be essential for realizing the revolutionary promise these platforms could have on the evolution of drug development, regulatory science, the practice of medicine and public health.
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Affiliation(s)
- Ali M Ardekani
- Department of Therapeutic Proteins, CBER, FDA, Bethesda, MD 20892, USA.
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260
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Naffin JL, Han Y, Olivos HJ, Reddy MM, Sun T, Kodadek T. Immobilized peptides as high-affinity capture agents for self-associating proteins. CHEMISTRY & BIOLOGY 2003; 10:251-9. [PMID: 12670539 DOI: 10.1016/s1074-5521(03)00049-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
There is currently great interest in the fabrication of protein-detecting arrays comprised of large numbers of immobilized protein capture agents. While most efforts in this arena have focused on the use of biomolecules such as antibodies and nucleic acid aptamers as capture agents, synthetic species have many potential advantages. However, synthetic molecules isolated from combinatorial libraries generally do not bind target proteins with the high affinity necessary for array applications. Here, we demonstrate that simple linear peptides bind dimeric proteins tenaciously when immobilized, although they exhibit only modest affinity in solution. These data show that high-affinity bidentate capture agents for dimeric proteins can be created by simply immobilizing modest-affinity ligands on a surface at high density, bypassing the requirement for careful optimization of linker length and geometry that is normally required to create a high-affinity solution bidentate ligand.
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Affiliation(s)
- Jacqueline L Naffin
- Department of Internal Medicine, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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261
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Abstract
The genomic era has brought with it a basic change in experimentation, enabling researchers to look more comprehensively at biological systems. The sequencing of the human genome coupled with advances in automation and parallelization technologies have afforded a fundamental transformation in the drug target discovery paradigm, towards systematic whole genome and proteome analyses. In conjunction with novel proteomic techniques, genome-wide annotation of function in cellular models is possible. Overlaying data derived from whole genome sequence, expression and functional analysis will facilitate the identification of causal genes in disease and significantly streamline the target validation process. Moreover, several parallel technological advances in small molecule screening have resulted in the development of expeditious and powerful platforms for elucidating inhibitors of protein or pathway function. Conversely, high-throughput and automated systems are currently being used to identify targets of orphan small molecules. The consolidation of these emerging functional genomics and drug discovery technologies promises to reap the fruits of the genomic revolution.
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Affiliation(s)
- Sumit K Chanda
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
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262
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Abstract
Pharmaceutical companies are facing an urgent need to both increase their lead compound and clinical candidate portfolios and satisfy market demands for continued innovation and revenue growth. Here, we outline an emerging approach that attempts to facilitate and alleviate many of the current drug discovery issues and problems. This is, in part, achieved through the systematic integration of technologies, which results in a superior output of data and information, thereby enhancing our understanding of biological function, chemico-biological interactions and, ultimately, drug discovery. Systems biology is one new discipline that is positioned to significantly impact this process.
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263
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Abstract
Forward chemical genetics is a new method to systematize the discovery and use of small molecules as tools for basic biological research. This approach requires three basic components: a library of compounds; an assay, in which the library is screened for a cellular or organismal phenotype; and a method to trace an active compound to its biological target. Bioactive compounds have traditionally been isolated from natural product extracts, although 'diversity-oriented synthesis' and commercial compound collections are gaining in prominence. New techniques, such as image-based screening and the cytoblot method, have increased the throughput of phenotypic assays. Strategies are also being developed to streamline target identification using molecular biological approaches.
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Affiliation(s)
- R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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264
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Taitt CR, Anderson GP, Lingerfelt BM, Feldstein SMJ, Ligler FS. Nine-analyte detection using an array-based biosensor. Anal Chem 2002; 74:6114-20. [PMID: 12498211 DOI: 10.1021/ac0260185] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fluorescence-based multianalyte immunosensor has been developed for simultaneous analysis of multiple samples. While the standard 6 x 6 format of the array sensor has been used to analyze six samples for six different analytes, this same format has the potential to allow a single sample to be tested for 36 different agents. The method described herein demonstrates proof of principle that the number of analytes detectable using a single array can be increased simply by using complementary mixtures of capture and tracer antibodies. Mixtures were optimized to allow detection of closely related analytes without significant cross-reactivity. Following this facile modification of patterning and assay procedures, the following nine targets could be detected in a single 3 x 3 array: Staphylococcal enterotoxin B, ricin, cholera toxin, Bacillus anthracis Sterne, Bacillus globigii, Francisella tularensis LVS, Yersiniapestis F1 antigen, MS2 coliphage, and Salmonella typhimurium. This work maximizes the efficiency and utility of the described array technology, increasing only reagent usage and cost; production and fabrication costs are not affected.
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Affiliation(s)
- Chris Rowe Taitt
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA.
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265
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Petricoin EF, Hackett JL, Lesko LJ, Puri RK, Gutman SI, Chumakov K, Woodcock J, Feigal DW, Zoon KC, Sistare FD. Medical applications of microarray technologies: a regulatory science perspective. Nat Genet 2002; 32 Suppl:474-9. [PMID: 12454641 DOI: 10.1038/ng1029] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The potential medical applications of microarrays have generated much excitement, and some skepticism, within the biomedical community. Some researchers have suggested that within the decade microarrays will be routinely used in the selection, assessment, and quality control of the best drugs for pharmaceutical development, as well as for disease diagnosis and for monitoring desired and adverse outcomes of therapeutic interventions. Realizing this potential will be a challenge for the whole scientific community, as breakthroughs that show great promise at the bench often fail to meet the requirements of clinicians and regulatory scientists. The development of a cooperative framework among regulators, product sponsors, and technology experts will be essential for realizing the revolutionary promise that microarrays hold for drug development, regulatory science, medical practice and public health.
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Affiliation(s)
- Emanuel F Petricoin
- Division of Therapeutic Products, Office of Therapeutics Research and Review, Center for Biologics Evaluation and Research, FDA, Bethesda, Maryland 20892, USA.
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266
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Elia G, Silacci M, Scheurer S, Scheuermann J, Neri D. Affinity-capture reagents for protein arrays. Trends Biotechnol 2002; 20:S19-22. [PMID: 12570155 DOI: 10.1016/s1471-1931(02)00201-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The simultaneous identification and quantitative measurement of the production levels of thousands of different proteins in a biological specimen remains an unachieved goal of modern proteomic research. Advances in the development of microarray-based platforms for highly parallel detection of proteins have therefore received a considerable impulse during the last few years. Here, we review the existing reagents for affinity capture of protein targets, as well as the techniques used for their immobilization on solid supports and methods for the detection of binding events, underlining the problems and the opportunities in this continuously evolving research field.
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Affiliation(s)
- Giuliano Elia
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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267
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Olivos HJ, Alluri PG, Reddy MM, Salony D, Kodadek T. Microwave-assisted solid-phase synthesis of peptoids. Org Lett 2002; 4:4057-9. [PMID: 12423085 DOI: 10.1021/ol0267578] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microwave irradiation reduces the reaction time for the solid-phase synthesis of peptoids. Under these conditions, coupling of each residue requires only 1 min. The purity and yields of peptoids synthesized in this way are as good as or better than those achieved using standard methods. [reaction: see text]
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Affiliation(s)
- Hernando J Olivos
- Center for Biomedical Inventions, Departments of Internal Medicine and Molecular Biology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-8573, USA
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268
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Affiliation(s)
- Bradley E Bernstein
- Department of Chemistry and Chemical Biology, Bauer Center for Genomics Research and the Howard Hughes Medical Institute, Harvard University, 02138, Cambridge, MA, USA
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269
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Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA. Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 2002; 1:683-95. [PMID: 12209149 DOI: 10.1038/nrd891] [Citation(s) in RCA: 443] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ultimate goal of proteomics is to characterize the information flow through protein networks. This information can be a cause, or a consequence, of disease processes. Clinical proteomics is an exciting new subdiscipline of proteomics that involves the application of proteomic technologies at the bedside, and cancer, in particular, is a model disease for studying such applications. Here, we describe proteomic technologies that are being developed to detect cancer earlier, to discover the next generation of targets and imaging biomarkers, and finally to tailor the therapy to the patient.
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Affiliation(s)
- Emanuel F Petricoin
- FDA-NCI Clinical Proteomics Program, Division of Therapeutic Proteins, Center for Biologic Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
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270
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Vuyisich M, Beal PA. Controlling protein activity with ligand-regulated RNA aptamers. CHEMISTRY & BIOLOGY 2002; 9:907-13. [PMID: 12204690 DOI: 10.1016/s1074-5521(02)00185-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Controlling the activity of a protein is necessary for defining its function in vivo. RNA aptamers are capable of inhibiting proteins with high affinity and specificity, but this effect is not readily reversible. We describe a general method for discovering aptamers that bind and inhibit their target protein, but addition of a specific small molecule disrupts the protein-RNA complex. A SELEX protocol was used to raise RNA aptamers to the DNA repair enzyme, formamidopyrimidine glycosylase (Fpg), and neomycin was employed in each round to dissociate Fpg-bound RNAs. We identified an RNA molecule able to completely inhibit Fpg at 100 nM concentration. Importantly, Fpg activity is recovered by the addition of neomycin. We envision these ligand-regulated aptamers (LIRAs) as valuable tools in the study of biological phenomena in which the timing of molecular events is critical.
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Affiliation(s)
- Momchilo Vuyisich
- Department of Chemistry, University of Utah, Salt Lake City 84112, USA
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271
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272
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Abstract
Small molecules were created by diversity-oriented synthesis and subsequently subjected to microarray-based screening for their ability to bind a protein of interest. This general two-step method proved powerful in generating highly specific modulators of protein function.
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Affiliation(s)
- Jie Chen
- Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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