101
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Best MD. Click Chemistry and Bioorthogonal Reactions: Unprecedented Selectivity in the Labeling of Biological Molecules. Biochemistry 2009; 48:6571-84. [DOI: 10.1021/bi9007726] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Michael D. Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996
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102
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Abstract
Glycosylation is an essential form of post-translational modification that regulates intracellular and extracellular processes. Regrettably, conventional biochemical and genetic methods often fall short for the study of glycans, because their structures are often not precisely defined at the genetic level. To address this deficiency, chemists have developed technologies to perturb glycan biosynthesis, profile their presentation at the systems level, and perceive their spatial distribution. These tools have identified potential disease biomarkers and ways to monitor dynamic changes to the glycome in living organisms. Still, glycosylation remains the underexplored frontier of many biological systems. In this Account, we focus on research in our laboratory that seeks to transform the study of glycan function from a challenge to routine practice.
In studies of proteins and nucleic acids, functional studies have often relied on genetic manipulations to perturb structure. Though not directly subject to mutation, we can determine glycan structure−function relationships by synthesizing defined glycoconjugates or by altering natural glycosylation pathways. Chemical syntheses of uniform glycoproteins and polymeric glycoprotein mimics have facilitated the study of individual glycoconjugates in the absence of glycan microheterogeneity. Alternatively, selective inhibition or activation of glycosyltransferases or glycosidases can define the biological roles of the corresponding glycans. Investigators have developed tools including small molecule inhibitors, decoy substrates, and engineered proteins to modify cellular glycans. Current approaches offer a precision approaching that of genetic control. Genomic and proteomic profiling form a basis for biological discovery. Glycans also present a rich matrix of information that adapts rapidly to changing environs. Glycomic and glycoproteomic analyses via microarrays and mass spectrometry are beginning to characterize alterations in glycans that correlate with disease. These approaches have already identified several cancer biomarkers. Metabolic labeling can identify recently synthesized glycans and thus directly track glycan dynamics. This approach can highlight changes in physiology or environment and may be more informative than steady-state analyses. Together, glycomic and metabolic labeling techniques provide a comprehensive description of glycosylation as a foundation for hypothesis generation. Direct visualization of proteins via the green fluorescent protein (GFP) and its congeners has revolutionized the field of protein dynamics. Similarly, the ability to perceive the spatial organization of glycans could transform our understanding of their role in development, infection, and disease progression. Fluorescent tagging in cultured cells and developing organisms has revealed important insights into the dynamics of these structures during growth and development. These results have highlighted the need for additional imaging probes.
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Affiliation(s)
| | - Carolyn R. Bertozzi
- The Molecular Foundry, Lawrence Berkeley National Laboratory, B-84 Hildebrand Hall, Berkeley, California 94720-1460
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103
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Pianowski Z, Gorska K, Oswald L, Merten CA, Winssinger N. Imaging of mRNA in Live Cells Using Nucleic Acid-Templated Reduction of Azidorhodamine Probes. J Am Chem Soc 2009; 131:6492-7. [DOI: 10.1021/ja809656k] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zbigniew Pianowski
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Laurence Oswald
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Christoph A. Merten
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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104
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Furukawa K, Abe H, Hibino K, Sako Y, Tsuneda S, Ito Y. Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells. Bioconjug Chem 2009; 20:1026-36. [DOI: 10.1021/bc900040t] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kayo Hibino
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasushi Sako
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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105
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2343] [Impact Index Per Article: 156.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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106
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Pan J, Downing JA, McHale JL, Xian M. A fluorogenic dye activated by S-nitrosothiols. MOLECULAR BIOSYSTEMS 2009; 5:918-20. [DOI: 10.1039/b822283e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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107
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Abstract
Molecular imaging enables visualization of specific molecules in vivo and without substantial perturbation to the target molecule's environment. Glycans are appealing targets for molecular imaging but are inaccessible with conventional approaches. Classic methods for monitoring glycans rely on molecular recognition with probe-bearing lectins or antibodies, but these techniques are not well suited to in vivo imaging. In an emerging strategy, glycans are imaged by metabolic labeling with chemical reporters and subsequent ligation to fluorescent probes. This technique has enabled visualization of glycans in living cells and in live organisms such as zebrafish. Molecular imaging with chemical reporters offers a new avenue for probing changes in the glycome that accompany development and disease.
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108
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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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109
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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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110
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Malashikhin S, Finney NS. Fluorescent Signaling Based on Sulfoxide Profluorophores: Application to the Visual Detection of the Explosive TATP. J Am Chem Soc 2008; 130:12846-7. [DOI: 10.1021/ja802989v] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergey Malashikhin
- Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Nathaniel S. Finney
- Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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111
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Abe H, Wang J, Furukawa K, Oki K, Uda M, Tsuneda S, Ito Y. A reduction-triggered fluorescence probe for sensing nucleic acids. Bioconjug Chem 2008; 19:1219-26. [PMID: 18476727 DOI: 10.1021/bc800014d] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a reduction-triggered fluorescence probe with a new fluorogenic compound derivatized from Rhodamine for sensing oligonucleotides. The chemistry to activate the compound involves the reaction between the azide group of rhodamine derivatives and the reducing reagents, with the fluorescence signal appearing after reduction of the azide group. The signal/background ratio of this fluorogenic compound reached 2100-fold enhancement in fluorescence intensity. Dithio-1,4-threitol or triphenylphosphine as reducing reagents were successfully utilized for this chemistry to be introduced into the DNA probe. The genetic detection requires that two strands of DNA bind onto target oligonucleotides, one probe carrying a reducible fluorogenic compound while the other carries the reducing reagents. The reaction proceeds automatically without any enzymes or reagents under biological conditions to produce a fluorescence signal within 10-20 min in the presence of target DNA or RNA. In addition, the probe was very stable under biological conditions, even such extreme conditions as pH 5 solution, pH 10 solution, or high temperature (90 degrees C) with no undesirable background signal. The probes were successfully applied to the detection of oligonucleotides at the single nucleotide level in solution and endogenous RNA in bacterial cells.
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Affiliation(s)
- Hiroshi Abe
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan.
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112
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Recent advances in chemical proteomics: exploring the post-translational proteome. J Chem Biol 2008; 1:17-26. [PMID: 19568795 DOI: 10.1007/s12154-008-0002-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Accepted: 02/18/2008] [Indexed: 12/21/2022] Open
Abstract
Identification and quantification of multiple proteins from complex mixtures is a central theme in post-genomic biology. Despite recent progress in high-throughput proteomics, proteomic analysis of post-translationally modified (PTM) proteins remains particularly challenging. This mini-review introduces the emerging field of chemical proteomics and reviews recent advances in chemical proteomic technology that are offering striking new insights into the functional biology of post-translational modification.
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113
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Hangauer MJ, Bertozzi CR. A FRET-based fluorogenic phosphine for live-cell imaging with the Staudinger ligation. Angew Chem Int Ed Engl 2008; 47:2394-7. [PMID: 18306205 DOI: 10.1002/anie.200704847] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew J Hangauer
- Department of Chemistry and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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114
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Guo HM, Minakawa M, Tanaka F. Fluorogenic Imines for Fluorescent Detection of Mannich-Type Reactions of Phenols in Water. J Org Chem 2008; 73:3964-6. [DOI: 10.1021/jo8003293] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hai-Ming Guo
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Maki Minakawa
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Fujie Tanaka
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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115
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Hangauer M, Bertozzi C. A FRET-Based Fluorogenic Phosphine for Live-Cell Imaging with the Staudinger Ligation. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704847] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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116
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117
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Pianowski ZL, Winssinger N. Fluorescence-based detection of single nucleotide permutation in DNA via catalytically templated reaction. Chem Commun (Camb) 2008:3820-2. [PMID: 18217658 DOI: 10.1039/b709611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Templated reduction of low fluorescence azidocoumarin-PNA conjugate to high fluorescence aminocoumarin was achieved using a catalytic amount of DNA with single nucleotide resolution.
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Affiliation(s)
- Zbigniew L Pianowski
- Laboratoire de Chimie Organique et Bioorganique, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur-CNRS, 8 allée Gaspard Monge, 67083 Strasbourg, France
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118
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Rozhkov R, Davisson VJ, Bergstrom D. Fluorogenic Transformations Based on Formation of CC Bonds Catalyzed by Palladium: An Efficient Approach for High Throughput Optimizations and Kinetic Studies. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200700384] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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119
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120
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Dilek Ö, Bane SL. Synthesis of boron dipyrromethene fluorescent probes for bioorthogonal labeling. Tetrahedron Lett 2007; 49:1413-1416. [PMID: 31439966 DOI: 10.1016/j.tetlet.2007.12.052] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Seven 5-substituted 3-hydrazinyl derivatives of 3a, 4a-diaza-4,4-difluoro-8-phenyl boron dipyrromethene (BODIPY) were prepared for use as bioorthogonal fluorescent labels of aldehydes and ketones. The absorption energies can be tuned to absorb visible light over a large span of wavelengths by changing the nature of the 5-substituent. Optical properties of the hydrazones formed with these molecules are affected by the nature of the electrophile such that aliphatic and aromatic hydrazones can be differentiated from each other and from unreacted fluorophore.
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Affiliation(s)
- Özlem Dilek
- State University of New York at Binghamton, Department of Chemistry, Vestal Parkway, Binghamton, NY 13902, USA
| | - Susan L Bane
- State University of New York at Binghamton, Department of Chemistry, Vestal Parkway, Binghamton, NY 13902, USA
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121
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Baskin J, Bertozzi C. Bioorthogonal Click Chemistry: Covalent Labeling in Living Systems. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200740086] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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122
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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123
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Chang PV, Prescher JA, Hangauer MJ, Bertozzi CR. Imaging cell surface glycans with bioorthogonal chemical reporters. J Am Chem Soc 2007; 129:8400-1. [PMID: 17579403 PMCID: PMC2535820 DOI: 10.1021/ja070238o] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pamela V Chang
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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124
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Kosiova I, Janicova A, Kois P. Synthesis of coumarin or ferrocene labeled nucleosides via Staudinger ligation. Beilstein J Org Chem 2006; 2:23. [PMID: 17137496 PMCID: PMC1779791 DOI: 10.1186/1860-5397-2-23] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 11/30/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reaction of azides with triaryl phosphines under mild conditions gives iminophosphoranes which can react with almost any kind of electrophilic reagent, e.g. aldehydes/ketones to form imines or esters to form amides. This so-called Staudinger ligation has been employed in a wide range of applications as a general tool for bioconjugation including specific labeling of nucleic acids. RESULTS A new approach for the preparation of labeled nucleosides via intermolecular Staudinger ligation is described. Reaction of azidonucleosides with triphenylphosphine lead to iminophosphorane intermediates, which react subsequently with derivatives of coumarin or ferrocene to form coumarin or ferrocene labeled nucleosides. Fluorescent properties of coumarin labeled nucleosides are determined. CONCLUSION New coumarin and ferrocene labeled nucleosides were prepared via intermolecular Staudinger ligation. This reaction joins the fluorescent coumarin and biospecific nucleoside to the new molecule with promising fluorescent and electrochemical properties. The isolated yields of products depend on the structure of azidonucleoside and carboxylic acids. A detailed study of the kinetics of the Staudinger ligation with nucleoside substrates is in progress.
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Affiliation(s)
- Ivana Kosiova
- Comenius University, Faculty of Natural Sciences, Department of Organic Chemistry, Mlynska dolina, Pavilon CH2, SK-84215 Bratislava, Slovak Republic
| | - Andrea Janicova
- Comenius University, Faculty of Natural Sciences, Department of Organic Chemistry, Mlynska dolina, Pavilon CH2, SK-84215 Bratislava, Slovak Republic
| | - Pavol Kois
- Comenius University, Faculty of Natural Sciences, Department of Organic Chemistry, Mlynska dolina, Pavilon CH2, SK-84215 Bratislava, Slovak Republic
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125
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126
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Beatty KE, Liu JC, Xie F, Dieterich DC, Schuman EM, Wang Q, Tirrell DA. Fluorescence Visualization of Newly Synthesized Proteins in Mammalian Cells. Angew Chem Int Ed Engl 2006; 45:7364-7. [PMID: 17036290 DOI: 10.1002/anie.200602114] [Citation(s) in RCA: 250] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kimberly E Beatty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
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127
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Bräse S, Gil C, Knepper K, Zimmermann V. Organic azides: an exploding diversity of a unique class of compounds. Angew Chem Int Ed Engl 2006; 44:5188-240. [PMID: 16100733 DOI: 10.1002/anie.200400657] [Citation(s) in RCA: 1626] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Since the discovery of organic azides by Peter Griess more than 140 years ago, numerous syntheses of these energy-rich molecules have been developed. In more recent times in particular, completely new perspectives have been developed for their use in peptide chemistry, combinatorial chemistry, and heterocyclic synthesis. Organic azides have assumed an important position at the interface between chemistry, biology, medicine, and materials science. In this Review, the fundamental characteristics of azide chemistry and current developments are presented. The focus will be placed on cycloadditions (Huisgen reaction), aza ylide chemistry, and the synthesis of heterocycles. Further reactions such as the aza-Wittig reaction, the Sundberg rearrangement, the Staudinger ligation, the Boyer and Boyer-Aubé rearrangements, the Curtius rearrangement, the Schmidt rearrangement, and the Hemetsberger rearrangement bear witness to the versatility of modern azide chemistry.
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Affiliation(s)
- Stefan Bräse
- Institut für Organische Chemie, Universität Karlsruhe TH, Germany.
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128
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Azoulay M, Tuffin G, Sallem W, Florent JC. A new drug-release method using the Staudinger ligation. Bioorg Med Chem Lett 2006; 16:3147-9. [PMID: 16621529 DOI: 10.1016/j.bmcl.2006.03.073] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 03/16/2006] [Accepted: 03/17/2006] [Indexed: 11/26/2022]
Abstract
Many drugs induce severe side-effects caused by their lack of selectivity. One way to overcome this problem is to design a specific system which releases a free drug in a controlled manner. Herein we describe a new way to liberate a drug from a prodrug using the Staudinger ligation as the trigger.
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Affiliation(s)
- Michel Azoulay
- UMR 176 CNRS/Institut Curie, Centre de Recherche, 26 rue d'Ulm, F-75248 Paris Cedex 05, France
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129
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Takaoka Y, Tsutsumi H, Kasagi N, Nakata E, Hamachi I. One-Pot and Sequential Organic Chemistry on an Enzyme Surface to Tether a Fluorescent Probe at the Proximity of the Active Site with Restoring Enzyme Activity. J Am Chem Soc 2006; 128:3273-80. [PMID: 16522109 DOI: 10.1021/ja057926x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new and simple method to tether a functional molecule at the proximity of the active site of an enzyme has been successfully developed without any activity loss. The one-pot sequential reaction was conducted on a surface of human carbonic anhydrase II (hCAII) based on the affinity labeling and the subsequent hydrazone/oxime exchange reaction. The reaction proceeds in a greater than 90% yield in the overall steps under mild conditions. The enzymatic activity assay demonstrated that the release of the affinity ligand from the active site of hCAII concurrently occurred with the replacement by the aminooxy derivatives, so that it restored the enzymatic activity from the completely suppressed state of the labeled hCAII. Such restoring of the activity upon the sequential modification is quite unique compared to conventional affinity labeling methods. The peptide mapping experiment revealed that the labeling reaction was selectively directed to His-3 or His-4, located on a protein surface proximal to the active site. When the fluorescent probe was tethered using the present sequential chemistry, the engineered hCAII can act as a fluorescent biosensor toward the hCAII inhibitors. This clearly indicates the two advantages of this method, that is (i) the modification is directed to the proximity of the active site and (ii) the sequential reaction re-opens the active site cavity of the target enzyme.
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Affiliation(s)
- Yousuke Takaoka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 812-8581, Japan
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130
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Laughlin ST, Agard NJ, Baskin JM, Carrico IS, Chang PV, Ganguli AS, Hangauer MJ, Lo A, Prescher JA, Bertozzi CR. Metabolic Labeling of Glycans with Azido Sugars for Visualization and Glycoproteomics. Methods Enzymol 2006; 415:230-50. [PMID: 17116478 DOI: 10.1016/s0076-6879(06)15015-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The staggering complexity of glycans renders their analysis extraordinarily difficult, particularly in living systems. A recently developed technology, termed metabolic oligosaccharide engineering, enables glycan labeling with probes for visualization in cells and living animals, and enrichment of specific glycoconjugate types for proteomic analysis. This technology involves metabolic labeling of glycans with a specifically reactive, abiotic functional group, the azide. Azido sugars are fed to cells and integrated by the glycan biosynthetic machinery into various glycoconjugates. The azido sugars are then covalently tagged, either ex vivo or in vivo, using one of two azide-specific chemistries: the Staudinger ligation, or the strain-promoted [3+2] cycloaddition. These reactions can be used to tag glycans with imaging probes or epitope tags, thus enabling the visualization or enrichment of glycoconjugates. Applications to noninvasive imaging and glycoproteomic analyses are discussed.
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Affiliation(s)
- Scott T Laughlin
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, USA
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131
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Durek T, Becker CFW. Protein semi-synthesis: New proteins for functional and structural studies. ACTA ACUST UNITED AC 2005; 22:153-72. [PMID: 16188500 DOI: 10.1016/j.bioeng.2005.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 12/19/2022]
Abstract
Our ability to alter and control the structure and function of biomolecules, and of proteins in particular, will be of utmost importance in order to understand their respective biological roles in complex systems such as living organisms. This challenge has prompted the development of powerful modern techniques in the fields of molecular biology, physical biochemistry and chemical biology. These fields complement each other and their successful combination has provided unique insights into protein structure and function at the level of isolated molecules, cells and organisms. Chemistry is without doubt most suited for introducing subtle changes into biomolecules down to the atomic level, but often struggles when it comes to large targets, such as proteins. In this review, we attempt to give an overview of modern and broadly applicable techniques that permit chemical synthesis to be applied to complex protein targets in order to gain control over their structure and function. As will be demonstrated, these approaches offer unique possibilities in our efforts to understand the molecular basis of protein functioning in vitro and in vivo. We will discuss modern synthetic reactions that can be applied to proteins and give examples of recent highlights. Another focus of this review will be the application of inteins as versatile protein engineering tools.
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Affiliation(s)
- Thomas Durek
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
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132
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Bräse S, Gil C, Knepper K, Zimmermann V. Organische Azide - explodierende Vielfalt bei einer einzigartigen Substanzklasse. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400657] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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133
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Blencowe A, Hayes W. Development and application of diazirines in biological and synthetic macromolecular systems. SOFT MATTER 2005; 1:178-205. [PMID: 32646075 DOI: 10.1039/b501989c] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many different reagents and methodologies have been utilised for the modification of synthetic and biological macromolecular systems. In addition, an area of intense research at present is the construction of hybrid biosynthetic polymers, comprised of biologically active species immobilised or complexed with synthetic polymers. One of the most useful and widely applicable techniques available for functionalisation of macromolecular systems involves indiscriminate carbene insertion processes. The highly reactive and non-specific nature of carbenes has enabled a multitude of macromolecular structures to be functionalised without the need for specialised reagents or additives. The use of diazirines as stable carbene precursors has increased dramatically over the past twenty years and these reagents are fast becoming the most popular photophors for photoaffinity labelling and biological applications in which covalent modification of macromolecular structures is the basis to understanding structure-activity relationships. This review reports the synthesis and application of a diverse range of diazirines in macromolecular systems.
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Affiliation(s)
- Anton Blencowe
- School of Chemistry, The University of Reading, Whiteknights, Reading, Berkshire, UKRG6 6AD.
| | - Wayne Hayes
- School of Chemistry, The University of Reading, Whiteknights, Reading, Berkshire, UKRG6 6AD.
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134
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135
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Cai J, Li X, Yue X, Taylor JS. Nucleic acid-triggered fluorescent probe activation by the Staudinger reaction. J Am Chem Soc 2005; 126:16324-5. [PMID: 15600325 DOI: 10.1021/ja0452626] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly sequence specific and sensitive detection systems for DNA or RNA in vivo would be of great use in biology and medicine for monitoring gene expression and diagnosing diseased cells. Herein we describe a new nucleic acid-triggered fluorescent probe system that is activated by a biocompatible and chemoselective Staudinger reaction.
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Affiliation(s)
- Jianfeng Cai
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, Missouri 63130, USA
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136
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Abstract
Chemistry-driven strategies for modifying, controlling and monitoring protein function in vitro and in vivo have attracted widespread interest among chemists in recent years. Several strategies have now emerged that complement standard genetics-based approaches, and they are being increasingly adopted by biologists to address issues in relevant contexts from cells to animals. With the development of these chemical biology tools, we might be approaching a time when detailed quantitative analysis of protein function, to a degree previously available only in reconstituted systems, is attainable in an in vivo setting.
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Affiliation(s)
- Michael E Hahn
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, Box 223, New York, NY 10021, USA
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137
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Restituyo JA, Comstock LR, Petersen SG, Stringfellow T, Rajski SR. Conversion of aryl azides to O-alkyl imidates via modified Staudinger ligation. Org Lett 2004; 5:4357-60. [PMID: 14601999 DOI: 10.1021/ol035635s] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] o-Carboalkoxy triarylphosphines are shown to react with aryl azides to provide Staudinger ligation products bearing O-alkyl imidate linkages. This is in contrast to alkyl azides whose ligation to o-carboalkoxy triarylphosphines has been reported to yield amide-linked materials. This extension of the Staudinger ligation for coupling of abiotic reagents under biocompatible conditions highlights the utility of commercially available triarylphosphines through which suitable linkers can be attached via an ester moiety.
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Affiliation(s)
- José A Restituyo
- The School of Pharmacy and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53705, USA
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138
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Sivakumar K, Xie F, Cash BM, Long S, Barnhill HN, Wang Q. A Fluorogenic 1,3-Dipolar Cycloaddition Reaction of 3-Azidocoumarins and Acetylenes†. Org Lett 2004; 6:4603-6. [PMID: 15548086 DOI: 10.1021/ol047955x] [Citation(s) in RCA: 562] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition reaction of nonfluorescent 3-azidocoumarins and terminal alkynes afforded intense fluorescent 1,2,3-triazole products. The mild condition of this reaction allowed us to construct a large library of pure fluorescent coumarin dyes. Since both azide and alkyne are quite inert to biological systems, this reaction has potential in bioconjugation and bioimaging applications. [reaction: see text]
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Affiliation(s)
- Krishnamoorthy Sivakumar
- Department of Chemistry & Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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139
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Zhou Z, Fahrni CJ. A fluorogenic probe for the copper(I)-catalyzed azide-alkyne ligation reaction: modulation of the fluorescence emission via 3(n,pi)-1(pi,pi) inversion. J Am Chem Soc 2004; 126:8862-3. [PMID: 15264794 DOI: 10.1021/ja049684r] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemoselective ligation reactions represent a powerful approach for labeling of proteins or small molecules in a biological environment. We report here a fluorogenic probe that is activated by click chemistry, a highly versatile bio-orthogonal and chemoselective ligation reaction which is based on the azide moiety as the functional group. The electron-donating properties of the triazole ring that is formed in the course of the coupling reaction was effectively utilized to modulate the fluorescence output of an electronically coupled coumarin fluorophore. Under physiological conditions the probe is essentially nonfluorescent and undergoes a bright emission enhancement upon ligation with an azide. Time-resolved emission spectroscopy and semiempirical quantum-mechanical calculations suggest that the fluorescence switching is due to an inversion of the energy ordering of the emissive 1(pi,pi*) and nonemissive 3(n,pi*) excited states. The rapid kinetics of the ligation reaction render the probe attractive for a wide range of applications in biology, analytical chemistry, or material science.
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Affiliation(s)
- Zhen Zhou
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 770 State Street, Atlanta, Georgia 30332, USA
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140
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Miller GP, Kool ET. Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry. J Org Chem 2004; 69:2404-10. [PMID: 15049637 DOI: 10.1021/jo035765e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields. Further, we demonstrate high-yielding conversions of DNA-azides to 5'-amines, and of thiocarbamates to 5'-thiols. Finally, we report a new, one-pot conversion of naturally substituted 5'-OH oligonucleotides (again on the solid support) to 5'-amino-oligonucleotides. All of the above reactions are demonstrated in multiple sequence contexts. Most of the procedures are automatable.
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Affiliation(s)
- Gregory P Miller
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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141
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Abstract
8-Azido-5'-aziridino-5'-deoxyadenosine (6), a novel cofactor mimic, was synthesized in nine steps from commercially available 2',3'-isopropylideneadenosine in approximately 4% overall yield. Crucial to this success was a very unorthodox phthalimide cleavage procedure, C8 azidation prior to aziridination and late stage alkylation of the 5' amino group with iodoethanol necessitated by the high degree of lability endowed by the aryl azide moiety. Aziridine 6 is envisioned as a useful biochemical tool by which to probe DNA and protein methylation patterns.
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Affiliation(s)
- Lindsay R Comstock
- University of Wisconsin-Madison, School of Pharmacy, 777 Highland Avenue, Madison, Wisconsin 53705, USA
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142
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143
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Chinchilla R, Nájera C, Yus M. Metalated Heterocycles and Their Applications in Synthetic Organic Chemistry. Chem Rev 2004; 104:2667-722. [PMID: 15137804 DOI: 10.1021/cr020101a] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rafael Chinchilla
- Departamento de Química Orgánica and Instituto de Síntesis Orgánica, Facultad de Ciencias, Universidad de Alicante, Apartado 99, 03080 Alicante, Spain.
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144
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Luchansky SJ, Hang HC, Saxon E, Grunwell JR, Yu C, Dube DH, Bertozzi CR. Constructing azide-labeled cell surfaces using polysaccharide biosynthetic pathways. Methods Enzymol 2003; 362:249-72. [PMID: 12968369 DOI: 10.1016/s0076-6879(03)01018-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sarah J Luchansky
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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145
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Abstract
[reaction: see text] An efficient method for the synthesis of functionalized rhodamine derivatives has been developed. Multigram quantities of these water-soluble fluorophores can be prepared from inexpensive precursors and purified without the use of chromatography. A series of protein-reactive functional groups has been installed through subsequent reactions, providing materials for biomolecule modification. For multicolor applications, a solid-phase purification strategy has been developed to afford rhodamine derivatives possessing a wide range of spectral properties.
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Affiliation(s)
- Trung Nguyen
- Department of Chemistry, University of California-Berkeley, Berkeley, California 94720-1460, USA
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