201
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Li F, Zhang H, Sun Y, Pan Y, Zhou J, Wang J. Expanding the Genetic Code for Photoclick Chemistry inE. coli, Mammalian Cells, andA. thaliana. Angew Chem Int Ed Engl 2013; 52:9700-4. [DOI: 10.1002/anie.201303477] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/24/2013] [Indexed: 12/25/2022]
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202
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Making connections--strategies for single molecule fluorescence biophysics. Curr Opin Chem Biol 2013; 17:691-8. [PMID: 23769868 PMCID: PMC3989056 DOI: 10.1016/j.cbpa.2013.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/02/2013] [Accepted: 05/17/2013] [Indexed: 11/28/2022]
Abstract
The single-molecule approach yields exciting insights for many biomolecular applications. There are significant challenges to achieve main-stream single-molecule measurements. New labelling chemistries enable multiple tagged molecules in vitro and in live cells. Single-molecule pull-down expands the toolbox complementing co-immunoprecipitation. Breaking the single-molecule concentration barrier is within reach.
Fluorescence spectroscopy and fluorescence microscopy carried out on the single molecule level are elegant methods to decipher complex biological systems; it can provide a wealth of information that frequently is obscured in the averaging of ensemble measurements. Fluorescence can be used to localise a molecule, study its binding with interaction partners and ligands, or to follow conformational changes in large multicomponent systems. Efficient labelling of proteins and nucleic acids is very important for any fluorescence method, and equally the development of novel fluorophores has been crucial in making biomolecules amenable to single molecule fluorescence methods. In this paper we review novel coupling strategies that permit site-specific and efficient labelling of proteins. Furthermore, we will discuss progressive single molecule approaches that allow the detection of individual molecules and biomolecular complexes even directly isolated from cellular extracts at much higher and much lower concentrations than has been possible so far.
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203
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Kim CH, Axup JY, Schultz PG. Protein conjugation with genetically encoded unnatural amino acids. Curr Opin Chem Biol 2013; 17:412-9. [PMID: 23664497 DOI: 10.1016/j.cbpa.2013.04.017] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
The site-specific incorporation of unnatural amino acids with orthogonal chemical reactivity into proteins enables the synthesis of structurally defined protein conjugates. Amino acids containing ketone, azide, alkyne, alkene, and tetrazine side chains can be genetically encoded in response to nonsense and frameshift codons. These bio-orthogonal chemical handles allow precise control over the site and stoichiometry of conjugation, and have enabled medicinal chemistry-like optimization of the physical and biological properties of protein conjugates, especially the next-generation protein therapeutics.
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Affiliation(s)
- Chan Hyuk Kim
- California Institute for Biomedical Research, 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States
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204
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Li J, Lin S, Wang J, Jia S, Yang M, Hao Z, Zhang X, Chen PR. Ligand-Free Palladium-Mediated Site-Specific Protein Labeling Inside Gram-Negative Bacterial Pathogens. J Am Chem Soc 2013; 135:7330-8. [DOI: 10.1021/ja402424j] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jie Li
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shixian Lin
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jie Wang
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shang Jia
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Maiyun Yang
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyang Hao
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Zhang
- College of Chemistry and Chemical
Engineering, Lanzhou University, Lanzhou
730000, China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules
Center, Beijing National Laboratory for Molecular Sciences, Department
of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
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205
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Krueger AT, Imperiali B. Fluorescent Amino Acids: Modular Building Blocks for the Assembly of New Tools for Chemical Biology. Chembiochem 2013; 14:788-99. [DOI: 10.1002/cbic.201300079] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 12/16/2022]
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206
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Albayrak C, Swartz JR. Cell-free co-production of an orthogonal transfer RNA activates efficient site-specific non-natural amino acid incorporation. Nucleic Acids Res 2013; 41:5949-63. [PMID: 23589624 PMCID: PMC3675464 DOI: 10.1093/nar/gkt226] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We describe a new cell-free protein synthesis (CFPS) method for site-specific incorporation of non-natural amino acids (nnAAs) into proteins in which the orthogonal tRNA (o-tRNA) and the modified protein (i.e. the protein containing the nnAA) are produced simultaneously. Using this method, 0.9–1.7 mg/ml of modified soluble super-folder green fluorescent protein (sfGFP) containing either p-azido-l-phenylalanine (pAzF) or p-propargyloxy-l-phenylalanine (pPaF) accumulated in the CFPS solutions; these yields correspond to 50–88% suppression efficiency. The o-tRNA can be transcribed either from a linearized plasmid or from a crude PCR product. Comparison of two different o-tRNAs suggests that the new platform is not limited by Ef-Tu recognition of the acylated o-tRNA at sufficiently high o-tRNA template concentrations. Analysis of nnAA incorporation across 12 different sites in sfGFP suggests that modified protein yields and suppression efficiencies (i.e. the position effect) do not correlate with any of the reported trends. Sites that were ineffectively suppressed with the original o-tRNA were better suppressed with an optimized o-tRNA (o-tRNAopt) that was evolved to be better recognized by Ef-Tu. This new platform can also be used to screen scissile ribozymes for improved catalysis.
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Affiliation(s)
- Cem Albayrak
- Department of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, CA 94305, USA
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207
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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208
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Budisa N. Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs). Curr Opin Biotechnol 2013; 24:591-8. [PMID: 23537814 DOI: 10.1016/j.copbio.2013.02.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 01/26/2023]
Abstract
The number of constituent amino acids in ribosomally synthetized and post-translationally modified peptide natural products (RiPPs) is restricted to the 20 canonical amino acids. Microorganisms with an engineered genetic code are capable of delivering the biological, chemical, or physical properties of many unnatural or synthetic noncanonical amino acids, ncAAs (in different combinations of their numbers and chemistry) precisely defined by the chemist at the bench. In this way, post-translational modifications (PTMs) which make RiPPs chemically extremely rich can be augmented by the co-translational insertion of ncAAs. This will dramatically expand the chemical and functional space of these molecules and enable the design of novel and unique sequence combinations with improved specificity, stability, membrane permeability and even better oral availability.
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Affiliation(s)
- Nediljko Budisa
- Technische Universität Berlin (Berlin Institute of Technology), Department of Chemistry, Biocatalysis Group, Müller-Breslau-Straße 10, D-10623 Berlin, Germany.
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209
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Schmidt MJ, Summerer D. Durch rotes Licht kontrollierte Protein-RNA-Vernetzung mit einem genetisch kodierten Furan. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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210
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Red-Light-Controlled Protein-RNA Crosslinking with a Genetically Encoded Furan. Angew Chem Int Ed Engl 2013; 52:4690-3. [DOI: 10.1002/anie.201300754] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Indexed: 12/12/2022]
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211
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Nadler A, Schultz C. The power of fluorogenic probes. Angew Chem Int Ed Engl 2013; 52:2408-10. [PMID: 23339134 DOI: 10.1002/anie.201209733] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 12/18/2022]
Abstract
A definite turn-on: Turning on fluorescence only where successful labeling is happening sounds as desirable as delivering a drug only where the drug target resides. New fluorogenic xanthene derivatives from the Bertozzi research group are getting us closer to "magic bullet" dyes.
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Affiliation(s)
- André Nadler
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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212
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213
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Lukinavičius G, Umezawa K, Olivier N, Honigmann A, Yang G, Plass T, Mueller V, Reymond L, Corrêa IR, Luo ZG, Schultz C, Lemke EA, Heppenstall P, Eggeling C, Manley S, Johnsson K. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nat Chem 2013; 5:132-9. [PMID: 23344448 DOI: 10.1038/nchem.1546] [Citation(s) in RCA: 642] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/28/2012] [Indexed: 12/19/2022]
Abstract
The ideal fluorescent probe for bioimaging is bright, absorbs at long wavelengths and can be implemented flexibly in living cells and in vivo. However, the design of synthetic fluorophores that combine all of these properties has proved to be extremely difficult. Here, we introduce a biocompatible near-infrared silicon-rhodamine probe that can be coupled specifically to proteins using different labelling techniques. Importantly, its high permeability and fluorogenic character permit the imaging of proteins in living cells and tissues, and its brightness and photostability make it ideally suited for live-cell super-resolution microscopy. The excellent spectroscopic properties of the probe combined with its ease of use in live-cell applications make it a powerful new tool for bioimaging.
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Affiliation(s)
- Gražvydas Lukinavičius
- Ecole Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering (ISIC), National Centre of Competence in Research (NCCR) in Chemical Biology, 1015 Lausanne, Switzerland
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214
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Wang T, Pfisterer A, Kuan SL, Wu Y, Dumele O, Lamla M, Müllen K, Weil T. Cross-conjugation of DNA, proteins and peptides via a pH switch. Chem Sci 2013. [DOI: 10.1039/c3sc22015j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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215
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Chigrinova M, McKay CS, Beaulieu LPB, Udachin KA, Beauchemin AM, Pezacki JP. Rearrangements and addition reactions of biarylazacyclooctynones and the implications to copper-free click chemistry. Org Biomol Chem 2013; 11:3436-41. [DOI: 10.1039/c3ob40683k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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216
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Tyagi S, Lemke EA. Genetically encoded click chemistry for single-molecule FRET of proteins. Methods Cell Biol 2013; 113:169-87. [PMID: 23317903 DOI: 10.1016/b978-0-12-407239-8.00009-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Single molecule Fluorescence Resonance Energy Transfer (FRET) has been widely applied to study structure, function and dynamics of complex biological systems. Labeling of proteins at specific positions with fluorescent dyes is a challenging and key step for any single molecule FRET measurement. Genetic code expansion has facilitated site specific incorporation of unnatural amino acids into proteins. These unnatural amino acid bears bioorthognal functional groups that provide opportunity to install a unique chemical handle into proteins. Propargyllysine is an unnatural amino acid which, when incorporated into a protein, can be exploited to attach commercially available fluorescent azide dyes through copper-catalyzed alkyne-azide cycloaddition click reaction (also known as click reaction). We describe here an optimized strategy to combine synthesis of propargyllysine, its genetic incorporation in the protein and click reaction to site-specifically label the protein with azide derivative of Alexa® 488. Later the protein is labeled at unique cysteine residue via maleimide coupling chemistry with acceptor Alexa® 594 dye to yield double labeled protein as required for any single molecule FRET experiments.
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Affiliation(s)
- Swati Tyagi
- EMBL, Structural and Computational Biology Unit, Heidelberg, Germany
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217
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Herner A, Nikić I, Kállay M, Lemke EA, Kele P. A new family of bioorthogonally applicable fluorogenic labels. Org Biomol Chem 2013; 11:3297-306. [DOI: 10.1039/c3ob40296g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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218
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Milles S, Lemke EA. What precision-protein-tuning and nano-resolved single molecule sciences can do for each other. Bioessays 2012; 35:65-74. [DOI: 10.1002/bies.201200094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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219
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Koo H, Lee S, Na JH, Kim SH, Hahn SK, Choi K, Kwon IC, Jeong SY, Kim K. Bioorthogonal Copper-Free Click Chemistry In Vivo for Tumor-Targeted Delivery of Nanoparticles. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206703] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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220
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Koo H, Lee S, Na JH, Kim SH, Hahn SK, Choi K, Kwon IC, Jeong SY, Kim K. Bioorthogonal copper-free click chemistry in vivo for tumor-targeted delivery of nanoparticles. Angew Chem Int Ed Engl 2012; 51:11836-40. [PMID: 23081905 DOI: 10.1002/anie.201206703] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Heebeom Koo
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seongbuk-gu, Seoul 136-791, Korea
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221
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Liang Y, Mackey JL, Lopez SA, Liu F, Houk KN. Control and Design of Mutual Orthogonality in Bioorthogonal Cycloadditions. J Am Chem Soc 2012; 134:17904-7. [DOI: 10.1021/ja309241e] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yong Liang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,
United States
| | - Joel L. Mackey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,
United States
| | - Steven A. Lopez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,
United States
| | - Fang Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,
United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095,
United States
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222
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Jang S, Sachin K, Lee HJ, Kim DW, Lee HS. Development of a simple method for protein conjugation by copper-free click reaction and its application to antibody-free Western blot analysis. Bioconjug Chem 2012; 23:2256-61. [PMID: 23039792 DOI: 10.1021/bc300364z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
There are currently many methods available for labeling proteins in order to study their structure and function. However, the utility of these methods is hampered by low efficiency, slow reaction rates, nonbiocompatible reaction conditions, large-sized labeling groups, and the requirement of specific side chains such as cysteine or lysine. In this study, a simple and efficient method for protein labeling was developed, in which an azide-containing amino acid was introduced into a protein and conjugated to a labeling reagent by strain-promoted azide-alkyne cycloaddition (SPAAC). This method allowed us to label proteins by simply mixing a protein and a labeling reagent in physiological conditions with a labeling yield of approximately 80% in 120 min. In addition, the specificity of SPAAC made it possible to analyze the expression level of a protein quantitatively by simple mixing and SDS-PAGE analysis with no need for antibodies or multistep incubations. Because the genetic incorporation of the azide-containing amino acid can be generally applied to any protein and the SPAAC reaction is highly specific, this method should prove useful for labeling and analyzing proteins.
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Affiliation(s)
- Sohye Jang
- Department of Chemistry, Sogang University, Seoul 121-742, Republic of Korea
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223
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Coltharp C, Xiao J. Superresolution microscopy for microbiology. Cell Microbiol 2012; 14:1808-18. [PMID: 22947061 DOI: 10.1111/cmi.12024] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 08/14/2012] [Accepted: 08/16/2012] [Indexed: 11/28/2022]
Abstract
This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of superresolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate superresolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics & Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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224
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Palomo JM. Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes. Org Biomol Chem 2012; 10:9309-18. [PMID: 23023600 DOI: 10.1039/c2ob26409a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.
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Affiliation(s)
- Jose M Palomo
- Departamento de Biocatálisis. Instituto de Catálisis (CSIC). C/ Marie Curie 2. Cantoblanco. Campus UAM, 28049 Madrid, Spain.
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225
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Yu Z, Pan Y, Wang Z, Wang J, Lin Q. Genetically encoded cyclopropene directs rapid, photoclick-chemistry-mediated protein labeling in mammalian cells. Angew Chem Int Ed Engl 2012; 51:10600-4. [PMID: 22997015 DOI: 10.1002/anie.201205352] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/21/2012] [Indexed: 12/21/2022]
Abstract
We just click: Genetic incorporation of a cyclopropene amino acid CpK (see scheme) site-specifically into proteins in E. coli and mammalian cells was achieved using an orthogonal aminoacyl-tRNA synthetase/tRNA(CUA) pair (CpKRS/MbtRNA(CUA)). Cyclopropene exhibited fast reaction kinetics in the photoclick reaction and allowed rapid (ca. 2 min) labeling of proteins.
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Affiliation(s)
- Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
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226
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Genetically Encoded Cyclopropene Directs Rapid, Photoclick-Chemistry-Mediated Protein Labeling in Mammalian Cells. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205352] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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227
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Borrmann A, Milles S, Plass T, Dommerholt J, Verkade JMM, Wiessler M, Schultz C, van Hest JCM, van Delft FL, Lemke EA. Genetic encoding of a bicyclo[6.1.0]nonyne-charged amino acid enables fast cellular protein imaging by metal-free ligation. Chembiochem 2012; 13:2094-9. [PMID: 22945333 DOI: 10.1002/cbic.201200407] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 01/14/2023]
Abstract
Visualizing biomolecules by fluorescent tagging is a powerful method for studying their behaviour and function inside cells. We prepared and genetically encoded an unnatural amino acid (UAA) that features a bicyclononyne moiety. This UAA offered exceptional reactivity in strain-promoted azide-alkyne cycloadditions. Kinetic measurements revealed that the UAA reacted also remarkably fast in the inverse-electron-demand Diels-Alder cycloaddition with tetrazine-conjugated dyes. Genetic encoding of the new UAA inside mammalian cells and its subsequent selective labeling at low dye concentrations demonstrate the usefulness of the new amino acid for future imaging studies.
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Affiliation(s)
- Annika Borrmann
- Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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228
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Chakrabarty R, Stang PJ. Post-assembly functionalization of organoplatinum(II) metallacycles via copper-free click chemistry. J Am Chem Soc 2012; 134:14738-41. [PMID: 22917086 DOI: 10.1021/ja3070073] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe the use of a strain-promoted copper-free click reaction in the post-self-assembly functionalization of organoplatinum(II) metallacycles. The coordination-driven self-assembly of a 120° cyclooctyne-tethered dipyridyl donor with 60° and 120° di-Pt(II) acceptors forms molecular rhomboids and hexagons bearing cyclooctynes. These species undergo post-self-assembly [3+2] Huisgen cycloaddition with a variety of azides to give functionalized ensembles under mild conditions.
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Affiliation(s)
- Rajesh Chakrabarty
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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229
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Yushchenko DA, Zhang M, Yan Q, Waggoner AS, Bruchez MP. Genetically targetable and color-switching fluorescent probe. Chembiochem 2012; 13:1564-8. [PMID: 22777954 DOI: 10.1002/cbic.201200334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Indexed: 11/10/2022]
Abstract
Color bind: We have developed a probe TMR-para-MG that switches its fluorescence emission upon binding to a fluorogen-activating protein (FAP). In cells that express FAP, this dye labels target sites in one color and mitochondria in another color, thus it might be a suitable tool for monitoring changes in mitochondrial membrane potential.
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Affiliation(s)
- Dmytro A Yushchenko
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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230
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Schmidt MJ, Summerer D. A Need for Speed: Genetic Encoding of Rapid Cycloaddition Chemistries for Protein Labelling in Living Cells. Chembiochem 2012; 13:1553-7. [DOI: 10.1002/cbic.201200321] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Indexed: 01/08/2023]
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231
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Rutkowska A, Schultz C. Protein Tango: The Toolbox to Capture Interacting Partners. Angew Chem Int Ed Engl 2012; 51:8166-76. [DOI: 10.1002/anie.201201717] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Indexed: 11/07/2022]
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232
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233
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van Berkel SS, Brauch S, Gabriel L, Henze M, Stark S, Vasilev D, Wessjohann LA, Abbas M, Westermann B. Traceless tosylhydrazone-based triazole formation: a metal-free alternative to strain-promoted azide-alkyne cycloaddition. Angew Chem Int Ed Engl 2012; 51:5343-6. [PMID: 22514135 DOI: 10.1002/anie.201108850] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sander S van Berkel
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Halle, Germany
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234
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van Berkel SS, Brauch S, Gabriel L, Henze M, Stark S, Vasilev D, Wessjohann LA, Abbas M, Westermann B. “Spurlose” Tosylhydrazon-basierte Triazolsynthese: eine metallfreie Alternative zur ringspannungskatalysierten Azid-Alkin- Cycloaddition. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108850] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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235
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Plass T, Milles S, Koehler C, Szymański J, Mueller R, Wießler M, Schultz C, Lemke EA. Amino Acids for Diels-Alder Reactions in Living Cells. Angew Chem Int Ed Engl 2012; 51:4166-70. [DOI: 10.1002/anie.201108231] [Citation(s) in RCA: 277] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/17/2012] [Indexed: 01/03/2023]
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236
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Plass T, Milles S, Koehler C, Szymański J, Mueller R, Wießler M, Schultz C, Lemke EA. Amino Acids for Diels-Alder Reactions in Living Cells. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108231] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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237
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Wang L, Peng S, Danence LJT, Gao Y, Wang J. Amine-Catalyzed [3+2] Huisgen Cycloaddition Strategy for the Efficient Assembly of Highly Substituted 1,2,3-Triazoles. Chemistry 2012; 18:6088-93. [DOI: 10.1002/chem.201103393] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/14/2012] [Indexed: 11/10/2022]
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238
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Kaya E, Vrabel M, Deiml C, Prill S, Fluxa VS, Carell T. A Genetically Encoded Norbornene Amino Acid for the Mild and Selective Modification of Proteins in a Copper-Free Click Reaction. Angew Chem Int Ed Engl 2012; 51:4466-9. [DOI: 10.1002/anie.201109252] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Indexed: 12/31/2022]
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239
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Kaya E, Vrabel M, Deiml C, Prill S, Fluxa VS, Carell T. Genetische Kodierung einer Norbornen-Aminosäure zur milden und selektiven Modifikation von Proteinen mit einer kupferfreien Klick-Reaktion. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201109252] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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240
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Abstract
Copper(I) is able to catalyze Huisgen 1,3-dipolar cycloaddition in a "click" fashion. This copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction presents excellent chemoselectivity and occurs over a wide-range of reaction conditions. It shows tolerance to variation in both pH and solvent polarity, thereby facilitating the ligation of peptides and proteins to produce peptidomimetics and synthetic proteins. In addition, the only product formed is a 1,4-disubstituted-1,2,3-triazole moiety, in many aspects resembling the natural peptide bond, including hydrogen-bonding capability, planarity, distance between the 1 and 4 substituents, and conformational restriction of the peptide backbone; thus the triazole-backbone-modified peptide, in which a triazole replaces the amide bond, may be anticipated to present a secondary structure similar to that of its natural counterpart. This Focus Review describes the scope and applications of copper(I)-catalyzed alkyne–azide cycloaddition in synthetic peptide/protein chemistry.
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Affiliation(s)
- Xuechen Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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241
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Heaney F. Nitrile Oxide/Alkyne Cycloadditions - A Credible Platform for Synthesis of Bioinspired Molecules by Metal-Free Molecular Clicking. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101823] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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242
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Milles S, Tyagi S, Banterle N, Koehler C, VanDelinder V, Plass T, Neal AP, Lemke EA. Click strategies for single-molecule protein fluorescence. J Am Chem Soc 2012; 134:5187-95. [PMID: 22356317 DOI: 10.1021/ja210587q] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule methods have matured into central tools for studies in biology. Foerster resonance energy transfer (FRET) techniques, in particular, have been widely applied to study biomolecular structure and dynamics. The major bottleneck for a facile and general application of these studies arises from the need to label biological samples site-specifically with suitable fluorescent dyes. In this work, we present an optimized strategy combining click chemistry and the genetic encoding of unnatural amino acids (UAAs) to overcome this limitation for proteins. We performed a systematic study with a variety of clickable UAAs and explored their potential for high-resolution single-molecule FRET (smFRET). We determined all parameters that are essential for successful single-molecule studies, such as accessibility of the probes, expression yield of proteins, and quantitative labeling. Our multiparameter fluorescence analysis allowed us to gain new insights into the effects and photophysical properties of fluorescent dyes linked to various UAAs for smFRET measurements. This led us to determine that, from the extended tool set that we now present, genetically encoding propargyllysine has major advantages for state-of-the-art measurements compared to other UAAs. Using this optimized system, we present a biocompatible one-step dual-labeling strategy of the regulatory protein RanBP3 with full labeling position freedom. Our technique allowed us then to determine that the region encompassing two FxFG repeat sequences adopts a disordered but collapsed state. RanBP3 serves here as a prototypical protein that, due to its multiple cysteines, size, and partially disordered structure, is not readily accessible to any of the typical structure determination techniques such as smFRET, NMR, and X-ray crystallography.
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Affiliation(s)
- Sigrid Milles
- EMBL, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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243
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Yao JZ, Uttamapinant C, Poloukhtine A, Baskin JM, Codelli JA, Sletten EM, Bertozzi CR, Popik VV, Ting AY. Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition. J Am Chem Soc 2012; 134:3720-8. [PMID: 22239252 PMCID: PMC3306817 DOI: 10.1021/ja208090p] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methods for targeting of small molecules to cellular proteins can allow imaging with fluorophores that are smaller, brighter, and more photostable than fluorescent proteins. Previously, we reported targeting of the blue fluorophore coumarin to cellular proteins fused to a 13-amino acid recognition sequence (LAP), catalyzed by a mutant of the Escherichia coli enzyme lipoic acid ligase (LplA). Here, we extend LplA-based labeling to green- and red-emitting fluorophores by employing a two-step targeting scheme. First, we found that the W37I mutant of LplA catalyzes site-specific ligation of 10-azidodecanoic acid to LAP in cells, in nearly quantitative yield after 30 min. Second, we evaluated a panel of five different cyclooctyne structures and found that fluorophore conjugates to aza-dibenzocyclooctyne (ADIBO) gave the highest and most specific derivatization of azide-conjugated LAP in cells. However, for targeting of hydrophobic fluorophores such as ATTO 647N, the hydrophobicity of ADIBO was detrimental, and superior targeting was achieved by conjugation to the less hydrophobic monofluorinated cyclooctyne (MOFO). Our optimized two-step enzymatic/chemical labeling scheme was used to tag and image a variety of LAP fusion proteins in multiple mammalian cell lines with diverse fluorophores including fluorescein, rhodamine, Alexa Fluor 568, ATTO 647N, and ATTO 655.
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Affiliation(s)
- Jennifer Z. Yao
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
| | - Chayasith Uttamapinant
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
| | - Andrei Poloukhtine
- Bioconjugate Technologies, LLC, 7850 E. Evans Road, Ste 107, Scottsdale, Arizona, 85260
| | - Jeremy M. Baskin
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Julian A. Codelli
- Department of Chemistry, California Institute of Technology, 1200 East California Boulevard. Pasadena, California 91125
| | - Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720, and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Vladimir V. Popik
- Department of Chemistry, Complex Carbohydrate Research Center, University of Georgia, Athens, 30602
| | - Alice Y. Ting
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue. Cambridge, Massachusetts 02139
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244
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Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 2012; 13:168-82. [DOI: 10.1038/nrm3286] [Citation(s) in RCA: 271] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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245
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Neumann H. Rewiring translation - Genetic code expansion and its applications. FEBS Lett 2012; 586:2057-64. [PMID: 22710184 DOI: 10.1016/j.febslet.2012.02.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 02/02/2012] [Accepted: 02/02/2012] [Indexed: 12/19/2022]
Abstract
With few minor variations, the genetic code is universal to all forms of life on our planet. It is difficult to imagine that one day organisms might exist that use an entirely different code to translate the information of their genome. Recent developments in the field of synthetic biology, however, have opened the gate to their creation. The genetic code of several organisms has been expanded by the heterologous expression of evolved aminoacyl-tRNA synthetase/tRNA(CUA) pairs that mediate the incorporation of unnatural amino acids in response to amber codons. These UAAs introduce exciting new features into proteins, such as spectroscopic probes, UV-inducible crosslinkers, and functional groups for bioorthogonal conjugations or posttranslational modifications. Orthogonal ribosomes provide a parallel translational machinery in Escherichia coli that has lost its evolutionary constraints. Evolved variants of these ribosomes translate amber or quadruplet codons with massively enhanced efficiency. Here, I review these recent developments emphasizing their tremendous potential to facilitate biochemical and cell biological studies.
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Affiliation(s)
- Heinz Neumann
- Institute for Microbiology and Genetics, Justus-von-Liebig Weg 11, Georg-August University Göttingen, 37077 Göttingen, Germany.
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246
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Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 2012; 403:2089-102. [PMID: 22322380 DOI: 10.1007/s00216-012-5784-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/17/2012] [Accepted: 01/23/2012] [Indexed: 02/02/2023]
Abstract
The information used to build proteins is stored in the genetic material of every organism. In nature, ribosomes use 20 native amino acids to synthesize proteins in most circumstances. However, laboratory efforts to expand the genetic repertoire of living cells and organisms have successfully encoded more than 80 nonnative amino acids in E. coli, yeast, and other eukaryotic systems. The selectivity, fidelity, and site-specificity provided by the technology have enabled unprecedented flexibility in manipulating protein sequences and functions in cells. Various biophysical probes can be chemically conjugated or directly incorporated at specific residues in proteins, and corresponding analytical techniques can then be used to answer diverse biological questions. This review summarizes the methodology of genetic code expansion and its recent progress, and discusses the applications of commonly used analytical methods.
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247
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Seitchik JL, Peeler JC, Taylor MT, Blackman ML, Rhoads TW, Cooley RB, Refakis C, Fox JM, Mehl RA. Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with trans-cyclooctenes. J Am Chem Soc 2012; 134:2898-901. [PMID: 22283158 DOI: 10.1021/ja2109745] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bioorthogonal ligation methods with improved reaction rates and less obtrusive components are needed for site-specifically labeling proteins without catalysts. Currently no general method exists for in vivo site-specific labeling of proteins that combines fast reaction rate with stable, nontoxic, and chemoselective reagents. To overcome these limitations, we have developed a tetrazine-containing amino acid, 1, that is stable inside living cells. We have site-specifically genetically encoded this unique amino acid in response to an amber codon allowing a single 1 to be placed at any location in a protein. We have demonstrated that protein containing 1 can be ligated to a conformationally strained trans-cyclooctene in vitro and in vivo with reaction rates significantly faster than most commonly used labeling methods.
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Affiliation(s)
- Jason L Seitchik
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, USA
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248
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Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol 2012; 23:751-7. [PMID: 22237016 DOI: 10.1016/j.copbio.2011.12.027] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 12/20/2011] [Indexed: 02/02/2023]
Abstract
The expansion of the genetic code is gradually becoming a core discipline in Synthetic Biology. It offers the best possible platform for the transfer of numerous chemical reactions and processes from the chemical synthetic laboratory into the biochemistry of living cells. The incorporation of biologically occurring or chemically synthesized non-canonical amino acids into recombinant proteins and even proteomes via reprogrammed protein translation is in the heart of these efforts. Orthogonal pairs consisting of aminoacyl-tRNA synthetase and its cognate tRNA proved to be a general tool for the assignment of certain codons of the genetic code with a maximum degree of chemical liberty. Here, we highlight recent developments that should provide a solid basis for the development of generalist tools enabling a controlled variation of chemical composition in proteins and even proteomes. This will take place in the frame of a greatly expanded genetic code with emancipated codons liberated from the current function or with totally new coding units.
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249
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Buckley BR, Heaney H. Mechanistic Investigations of Copper(I)-Catalysed Alkyne–Azide Cycloaddition Reactions. TOPICS IN HETEROCYCLIC CHEMISTRY 2012. [DOI: 10.1007/7081_2011_71] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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250
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Singh I, Freeman C, Heaney F. Efficient Synthesis of DNA Conjugates by Strain-Promoted Azide-Cyclooctyne Cycloaddition in the Solid Phase. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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