151
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Merten H, Brandl F, Plückthun A, Zangemeister-Wittke U. Antibody-Drug Conjugates for Tumor Targeting-Novel Conjugation Chemistries and the Promise of non-IgG Binding Proteins. Bioconjug Chem 2015; 26:2176-85. [PMID: 26086208 DOI: 10.1021/acs.bioconjchem.5b00260] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antibody-drug conjugates (ADCs) have emerged as a promising class of anticancer agents, combining the specificity of antibodies for tumor targeting and the destructive potential of highly potent drugs as payload. An essential component of these immunoconjugates is a bifunctional linker capable of reacting with the antibody and the payload to assemble a functional entity. Linker design is fundamental, as it must provide high stability in the circulation to prevent premature drug release, but be capable of releasing the active drug inside the target cell upon receptor-mediated endocytosis. Although ADCs have demonstrated an increased therapeutic window, compared to conventional chemotherapy in recent clinical trials, therapeutic success rates are still far from optimal. To explore other regimes of half-life variation and drug conjugation stoichiometries, it is necessary to investigate additional binding proteins which offer access to a wide range of formats, all with molecularly defined drug conjugation. Here, we delineate recent progress with site-specific and biorthogonal conjugation chemistries, and discuss alternative, biophysically more stable protein scaffolds like Designed Ankyrin Repeat Proteins (DARPins), which may provide such additional engineering opportunities for drug conjugates with improved pharmacological performance.
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Affiliation(s)
- Hannes Merten
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Fabian Brandl
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Pharmacology, University of Bern , Inselspital INO-F, CH-3010 Bern, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Uwe Zangemeister-Wittke
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,Institute of Pharmacology, University of Bern , Inselspital INO-F, CH-3010 Bern, Switzerland
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152
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Tian H, Sakmar TP, Huber T. Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR. Chembiochem 2015; 16:1314-22. [PMID: 25962668 PMCID: PMC5287413 DOI: 10.1002/cbic.201500030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Genetically encoded p-azido-phenylalanine (azF) residues in G protein-coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne-modified (DIBO-modified) fluorescent probes by means of strain-promoted [3+2] azide-alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent-solubilized receptors exhibit up to 1000-fold rate enhancement relative to azF residues on water-exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle-enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.
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Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
- Department of Neurobiology, Care Sciences and Society, Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Alfred Nobels Allé 23, 141 57 Huddinge (Sweden).
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, 1230 York Avenue, New York, NY 10065 (USA).
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153
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Lim SI, Hahn YS, Kwon I. Site-specific albumination of a therapeutic protein with multi-subunit to prolong activity in vivo. J Control Release 2015; 207:93-100. [PMID: 25862515 PMCID: PMC4430413 DOI: 10.1016/j.jconrel.2015.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 02/03/2015] [Accepted: 04/05/2015] [Indexed: 11/21/2022]
Abstract
Albumin fusion/conjugation (albumination) has been an effective method to prolong in vivo half-life of therapeutic proteins. However, its broader application to proteins with complex folding pathway or multi-subunit is restricted by incorrect folding, poor expression, heterogeneity, and loss of native activity of the proteins linked to albumin. We hypothesized that the site-specific conjugation of albumin to a permissive site of a target protein will expand the utilities of albumin as a therapeutic activity extender to proteins with a complex structure. We show here the genetic incorporation of a non-natural amino acid (NNAA) followed by chemoselective albumin conjugation to prolong therapeutic activity in vivo. Urate oxidase (Uox), a therapeutic enzyme for treatment of hyperuricemia, is a homotetramer with multiple surface lysines, limiting conventional approaches for albumination. Incorporation of p-azido-l-phenylalanine into two predetermined positions of Uox allowed site-specific linkage of dibenzocyclooctyne-derivatized human serum albumin (HSA) through strain-promoted azide-alkyne cycloaddition (SPAAC). The bio-orthogonality of SPAAC resulted in the production of a chemically well-defined conjugate, Uox-HSA, with a retained enzymatic activity. Uox-HSA had a half-life of 8.8 h in mice, while wild-type Uox had a half-life of 1.3 h. The AUC increased 5.5-fold (1657 vs. 303 mU/mL x h). These results clearly demonstrated that site-specific albumination led to the prolonged enzymatic activity of Uox in vivo. Site-specific albumination enabled by NNAA incorporation and orthogonal chemistry demonstrates its promise for the development of long-acting protein therapeutics with high potency and safety.
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Affiliation(s)
- Sung In Lim
- Department of Chemical Engineering, University of Virginia, VA 22904, United States
| | - Young S Hahn
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, VA 22908, United States
| | - Inchan Kwon
- Department of Chemical Engineering, University of Virginia, VA 22904, United States; School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 500-712, Republic of Korea.
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154
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Tyagi S, Lemke EA. Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids. Curr Opin Struct Biol 2015; 32:66-73. [DOI: 10.1016/j.sbi.2015.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/24/2015] [Accepted: 02/05/2015] [Indexed: 10/23/2022]
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155
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Abstract
Antibody conjugates are important in many areas of medicine and biological research, and antibody-drug conjugates (ADCs) are becoming an important next generation class of therapeutics for cancer treatment. Early conjugation technologies relied upon random conjugation to multiple amino acid side chains, resulting in heterogeneous mixtures of labeled antibody. Recent studies, however, strongly support the notion that site-specific conjugation produces a homogeneous population of antibody conjugates with improved pharmacologic properties over randomly coupled molecules. Genetically incorporated unnatural amino acids (uAAs) allow unique orthogonal coupling strategies compared to those used for the 20 naturally occurring amino acids. Thus, uAAs provide a novel paradigm for creation of next generation ADCs. Additionally, uAA-based site-specific conjugation could also empower creation of additional multifunctional conjugates important as biopharmaceuticals, diagnostics, or reagents.
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Affiliation(s)
- Trevor J Hallam
- †Sutro Biopharma, 310 Utah Avenue, Suite 150, South San Francisco, California 94080, United States
| | - Erik Wold
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alan Wahl
- §Ambrx, Inc. 10975 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vaughn V Smider
- ‡The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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156
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Yang M, Li J, Chen PR. Transition metal-mediated bioorthogonal protein chemistry in living cells. Chem Soc Rev 2015; 43:6511-26. [PMID: 24867400 DOI: 10.1039/c4cs00117f] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Considerable attention has been focused on improving the biocompatibility of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), a hallmark of bioorthogonal reaction, in living cells. Besides creating copper-free versions of click chemistry such as strain promoted azide-alkyne cycloaddition (SPAAC), a central effort has also been made to develop various Cu(I) ligands that can prevent the cytotoxicity of Cu(I) ions while accelerating the CuAAC reaction. Meanwhile, additional transition metals such as palladium have been explored as alternative sources to promote a bioorthogonal conjugation reaction on cell surface, as well as within an intracellular environment. Furthermore, transition metal mediated chemical conversions beyond conjugation have also been utilized to manipulate protein activity within living systems. We highlight these emerging examples that significantly enriched our protein chemistry toolkit, which will likely expand our view on the definition and applications of bioorthogonal chemistry.
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Affiliation(s)
- Maiyun Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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157
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Abstract
Antibody-drug conjugates are an important and emerging drug class for the treatment of cancer. Recent evidence strongly suggests that site-specific drug conjugation results in a homogenous population of molecules with more favorable activity and pharmacokinetic properties than randomly conjugated antibodies. Unnatural amino acids (uAAs) can be incorporated in recombinant proteins to enable unique orthogonal chemistries in comparison to the side chains of the natural 20 amino acids. Thus, uAAs present a novel platform for which to create next-generation antibody-drug conjugates. Furthermore, site-specific conjugation through uAAs can also enpower unique small molecule, bispecific, multispecific and other conjugates that could be important constructs for therapeutics, diagnostics and research reagents. Here, we review the progress in uAA incorporation and conjugate construction through both cell-based and -free approaches.
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158
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Hu C, Chan SI, Sawyer EB, Yu Y, Wang J. Metalloprotein design using genetic code expansion. Chem Soc Rev 2015; 43:6498-510. [PMID: 24699759 DOI: 10.1039/c4cs00018h] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
More than one third of all proteins are metalloproteins. They catalyze important reactions such as photosynthesis, nitrogen fixation and CO2 reduction. Metalloproteins such as the olfactory receptors also serve as highly elaborate sensors. Here we review recent developments in functional metalloprotein design using the genetic code expansion approach. We show that, through the site-specific incorporation of metal-chelating unnatural amino acids (UAAs), proton and electron transfer mediators, and UAAs bearing bioorthogonal reaction groups, small soluble proteins can recapitulate and expand the important functions of complex metalloproteins. Further developments along this route may result in cell factories and live-cell sensors with unprecedented efficiency and selectivity.
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Affiliation(s)
- Cheng Hu
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.
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159
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Nikić I, Kang JH, Girona GE, Aramburu IV, Lemke EA. Labeling proteins on live mammalian cells using click chemistry. Nat Protoc 2015; 10:780-91. [DOI: 10.1038/nprot.2015.045] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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160
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Schulz S, Kramm K, Werner F, Grohmann D. Fluorescently labeled recombinant RNAP system to probe archaeal transcription initiation. Methods 2015; 86:10-8. [PMID: 25912642 DOI: 10.1016/j.ymeth.2015.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/14/2015] [Accepted: 04/16/2015] [Indexed: 10/24/2022] Open
Abstract
The transcriptional apparatus is one of the most complex cellular machineries and in order to fully appreciate the behavior of these protein-nucleic acid assemblies one has to understand the molecular details of the system. In addition to classical biochemical and structural studies, fluorescence-based techniques turned out as an important--and sometimes the critical--tool to obtain information about the molecular mechanisms of transcription. Fluorescence is not only a multi-modal parameter that can report on molecular interactions, environment and oligomerization status. Measured on the single-molecule level it also informs about the heterogeneity of the system and gives access to distances and distance changes in the molecular relevant nanometer regime. A pre-requisite for fluorescence-based measurements is the site-specific incorporation of one or multiple fluorescent dyes. In this respect, the archaeal transcription system is ideally suited as it is available in a fully recombinant form and thus allows for site-specific modification via sophisticated labeling schemes. The application of fluorescence based approaches to the archaeal transcription apparatus changed our understanding of the molecular mechanisms and dynamics that drive archaeal transcription and unraveled the architecture of transcriptional complexes not amenable to structural interrogation.
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Affiliation(s)
- Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
| | - Kevin Kramm
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany
| | - Finn Werner
- RNAP Laboratory, University College London, Institute of Structural and Molecular Biology, Division of Biosciences, Gower St, London WC1E 6BT, UK
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany.
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161
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Li N, Ramil CP, Lim RKV, Lin Q. A genetically encoded alkyne directs palladium-mediated protein labeling on live mammalian cell surface. ACS Chem Biol 2015; 10:379-84. [PMID: 25347611 PMCID: PMC4340352 DOI: 10.1021/cb500649q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
The merging of site-specific incorporation
of small bioorthogonal
functional groups into proteins via amber codon suppression with bioorthogonal
chemistry has created exciting opportunities to extend the power of
organic reactions to living systems. Here we show that a new alkyne
amino acid can be site-selectively incorporated into mammalian proteins
via a known orthogonal pyrrolysyl-tRNA synthetase/tRNACUA pair and directs an unprecedented, palladium-mediated cross-coupling
reaction-driven protein labeling on live mammalian cell surface. A
comparison study with the alkyne-encoded proteins in vitro indicated that this terminal alkyne is better suited for the palladium-mediated
cross-coupling reaction than the copper-catalyzed click chemistry.
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Affiliation(s)
- Nan Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Carlo P. Ramil
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Reyna K. V. Lim
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, United States
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162
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Affiliation(s)
- Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili , C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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163
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Wan JP, Hu D, Liu Y, Sheng S. Azide-Free Synthesis of 1,2,3-Triazoles: New Opportunity for Sustainable Synthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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164
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Borrmann A, Fatunsin O, Dommerholt J, Jonker AM, Löwik DWPM, van Hest JCM, van Delft FL. Strain-Promoted Oxidation-Controlled Cyclooctyne–1,2-Quinone Cycloaddition (SPOCQ) for Fast and Activatable Protein Conjugation. Bioconjug Chem 2015; 26:257-61. [DOI: 10.1021/bc500534d] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Annika Borrmann
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Olumide Fatunsin
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Jan Dommerholt
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Anika M. Jonker
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Dennis W. P. M. Löwik
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Jan C. M. van Hest
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Floris L. van Delft
- Bioorganic Chemistry and
Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
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165
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Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment - Expanding the chemistry in biology. Chem Sci 2015; 6:50-69. [PMID: 28553457 PMCID: PMC5424465 DOI: 10.1039/c4sc01534g] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/14/2014] [Indexed: 12/18/2022] Open
Abstract
Over the last decade, the ability to genetically encode unnatural amino acids (UAAs) has evolved rapidly. The programmed incorporation of UAAs into recombinant proteins relies on the reassignment or suppression of canonical codons with an amino-acyl tRNA synthetase/tRNA (aaRS/tRNA) pair, selective for the UAA of choice. In order to achieve selective incorporation, the aaRS should be selective for the designed tRNA and UAA over the endogenous amino acids and tRNAs. Enhanced selectivity has been achieved by transferring an aaRS/tRNA pair from another kingdom to the organism of interest, and subsequent aaRS evolution to acquire enhanced selectivity for the desired UAA. Today, over 150 non-canonical amino acids have been incorporated using such methods. This enables the introduction of a large variety of structures into proteins, in organisms ranging from prokaryote, yeast and mammalian cells lines to whole animals, enabling the study of protein function at a level that could not previously be achieved. While most research to date has focused on the suppression of 'non-sense' codons, recent developments are beginning to open up the possibility of quadruplet codon decoding and the more selective reassignment of sense codons, offering a potentially powerful tool for incorporating multiple amino acids. Here, we aim to provide a focused review of methods for UAA incorporation with an emphasis in particular on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems. Our hope is that this will help rationalize the design of systems for incorporation of unexplored unnatural amino acids, as well as novel applications for those already known.
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Affiliation(s)
- Anaëlle Dumas
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Lukas Lercher
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher D Spicer
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
| | - Benjamin G Davis
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK .
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166
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Tuley A, Wang YS, Fang X, Kurra Y, Rezenom YH, Liu WR. The genetic incorporation of thirteen novel non-canonical amino acids. Chem Commun (Camb) 2014; 50:2673-5. [PMID: 24473369 DOI: 10.1039/c3cc49068h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Thirteen novel non-canonical amino acids were synthesized and tested for suppression of an amber codon using a mutant pyrrolysyl-tRNA synthetase-tRNA(Pyl)(CUA) pair. Suppression was observed with varied efficiencies. One non-canonical amino acid in particular contains an azide that can be applied for site-selective protein labeling.
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Affiliation(s)
- Alfred Tuley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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167
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New developments in spin labels for pulsed dipolar EPR. Molecules 2014; 19:16998-7025. [PMID: 25342554 PMCID: PMC6271499 DOI: 10.3390/molecules191016998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
Spin labelling is a chemical technique that enables the integration of a molecule containing an unpaired electron into another framework for study. Given the need to understand the structure, dynamics, and conformational changes of biomacromolecules, spin labelling provides a relatively non-intrusive technique and has certain advantages over X-ray crystallography; which requires high quality crystals. The technique relies on the design of binding probes that target a functional group, for example, the thiol group of a cysteine residue within a protein. The unpaired electron is typically supplied through a nitroxide radical and sterically shielded to preserve stability. Pulsed electron paramagnetic resonance (EPR) techniques allow small magnetic couplings to be measured (e.g., <50 MHz) providing information on single label probes or the dipolar coupling between multiple labels. In particular, distances between spin labels pairs can be derived which has led to many protein/enzymes and nucleotides being studied. Here, we summarise recent examples of spin labels used for pulse EPR that serve to illustrate the contribution of chemistry to advancing discoveries in this field.
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168
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McKay CS, Finn MG. Click chemistry in complex mixtures: bioorthogonal bioconjugation. CHEMISTRY & BIOLOGY 2014; 21:1075-101. [PMID: 25237856 PMCID: PMC4331201 DOI: 10.1016/j.chembiol.2014.09.002] [Citation(s) in RCA: 551] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/18/2023]
Abstract
The selective chemical modification of biological molecules drives a good portion of modern drug development and fundamental biological research. While a few early examples of reactions that engage amine and thiol groups on proteins helped establish the value of such processes, the development of reactions that avoid most biological molecules so as to achieve selectivity in desired bond-forming events has revolutionized the field. We provide an update on recent developments in bioorthogonal chemistry that highlights key advances in reaction rates, biocompatibility, and applications. While not exhaustive, we hope this summary allows the reader to appreciate the rich continuing development of good chemistry that operates in the biological setting.
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Affiliation(s)
- Craig S McKay
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M G Finn
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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169
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Martin SE, Ganguly T, Munske GR, Fulton MD, Hopkins MR, Berkman CE, Black ME. Development of inhibitor-directed enzyme prodrug therapy (IDEPT) for prostate cancer. Bioconjug Chem 2014; 25:1752-60. [PMID: 25157916 PMCID: PMC4198102 DOI: 10.1021/bc500362n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Prostate
cancer (PCa) is the second most common cause of cancer
death among American men after lung cancer. Unfortunately, current
therapies do not provide effective treatments for patients with advanced,
metastatic, or hormone refractory disease. Therefore, we seek to generate
therapeutic agents for a novel PCa treatment strategy by delivering
a suicide enzyme (yCDtriple) to a cell membrane bound biomarker
found on PCa cells (prostate-specific membrane antigen (PSMA)). This
approach has resulted in a new PCa treatment strategy reported here
as inhibitor-directed enzyme prodrug therapy (IDEPT). The therapeutic
agents described were generated using a click chemistry reaction between
the unnatural amino acid (p-azidophenylalanine (pAzF)) incorporated into yCDtriple and the dibenzylcyclooctyne
moiety of our PSMA targeting agent (DBCO-PEG4-AH2-TG97). After characterization of the therapeutic agents, we demonstrate
significant PCa cell killing of PSMA-positive cells. Importantly,
we demonstrate that this click chemistry approach can be used to efficiently
couple a therapeutic protein to a targeting agent and may be applicable
to the ablation of other types of cancers and/or malignancies.
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Affiliation(s)
- Stacy E Martin
- School of Molecular Biosciences and §Department of Chemistry, Washington State University , Pullman, Washington 99164-7520, United States
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170
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Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun 2014; 5:4740. [PMID: 25190082 DOI: 10.1038/ncomms5740] [Citation(s) in RCA: 710] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.
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Affiliation(s)
- Christopher D Spicer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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171
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Kurra Y, Odoi KA, Lee YJ, Yang Y, Lu T, Wheeler SE, Torres-Kolbus J, Deiters A, Liu WR. Two rapid catalyst-free click reactions for in vivo protein labeling of genetically encoded strained alkene/alkyne functionalities. Bioconjug Chem 2014; 25:1730-8. [PMID: 25158039 PMCID: PMC4166034 DOI: 10.1021/bc500361d] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Detailed
kinetic analyses of inverse electron-demand Diels–Alder
cycloaddition and nitrilimine-alkene/alkyne 1,3-diploar cycloaddition
reactions were conducted and the reactions were applied for rapid
protein bioconjugation. When reacted with a tetrazine or a diaryl
nitrilimine, strained alkene/alkyne entities including norbornene, trans-cyclooctene, and cyclooctyne displayed rapid kinetics.
To apply these “click” reactions for site-specific protein
labeling, five tyrosine derivatives that contain a norbornene, trans-cyclooctene, or cyclooctyne entity were genetically
encoded into proteins in Escherichia coli using an engineered pyrrolysyl-tRNA synthetase-tRNACUAPyl pair. Proteins
bearing these noncanonical amino acids were successively labeled with
a fluorescein tetrazine dye and a diaryl nitrilimine both in vitro
and in living cells.
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Affiliation(s)
- Yadagiri Kurra
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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172
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Torres-Kolbus J, Chou C, Liu J, Deiters A. Synthesis of non-linear protein dimers through a genetically encoded Thiol-ene reaction. PLoS One 2014; 9:e105467. [PMID: 25181502 PMCID: PMC4152134 DOI: 10.1371/journal.pone.0105467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/21/2014] [Indexed: 11/19/2022] Open
Abstract
Site-specific incorporation of bioorthogonal unnatural amino acids into proteins provides a useful tool for the installation of specific functionalities that will allow for the labeling of proteins with virtually any probe. We demonstrate the genetic encoding of a set of alkene lysines using the orthogonal PylRS/PylTCUA pair in Escherichia coli. The installed double bond functionality was then applied in a photoinitiated thiol-ene reaction of the protein with a fluorescent thiol-bearing probe, as well as a cysteine residue of a second protein, showing the applicability of this approach in the formation of heterogeneous non-linear fused proteins.
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Affiliation(s)
- Jessica Torres-Kolbus
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chungjung Chou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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173
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Raulf A, Spahn CK, Zessin PJM, Finan K, Bernhardt S, Heckel A, Heilemann M. Click chemistry facilitates direct labelling and super-resolution imaging of nucleic acids and proteins†Electronic supplementary information (ESI) available. See DOI: 10.1039/c4ra01027bClick here for additional data file. RSC Adv 2014; 4:30462-30466. [PMID: 25580242 PMCID: PMC4285124 DOI: 10.1039/c4ra01027b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/27/2014] [Indexed: 12/21/2022] Open
Abstract
We demonstrate high-density labelling of cellular DNA and RNA using click chemistry and perform confocal and super-resolution microscopy. We visualize the crescent and ring-like structure of densely packed RNA in nucleoli. We further demonstrate click chemistry with unnatural amino acids for super-resolution imaging of outer-membrane proteins of E. coli.
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Affiliation(s)
- Anika Raulf
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Christoph K Spahn
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | - Patrick J M Zessin
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
| | | | - Stefan Bernhardt
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology , Goethe-University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
| | - Mike Heilemann
- Institute of Physical & Theoretical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany .
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174
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Rutkowska A, Plass T, Hoffmann JE, Yushchenko DA, Feng S, Schultz C. T-CrAsH: A Heterologous Chemical Crosslinker. Chembiochem 2014; 15:1765-8. [DOI: 10.1002/cbic.201402189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Indexed: 01/12/2023]
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175
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Denk C, Svatunek D, Filip T, Wanek T, Lumpi D, Fröhlich J, Kuntner C, Mikula H. Development of a (18) F-labeled tetrazine with favorable pharmacokinetics for bioorthogonal PET imaging. Angew Chem Int Ed Engl 2014; 53:9655-9. [PMID: 24989029 DOI: 10.1002/anie.201404277] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 05/09/2014] [Indexed: 11/07/2022]
Abstract
A low-molecular-weight (18) F-labeled tetrazine derivative was developed as a highly versatile tool for bioorthogonal PET imaging. Prosthetic groups and undesired carrying of (18) F through additional steps were evaded by direct (18) F-fluorination of an appropriate tetrazine precursor. Reaction kinetics of the cycloaddition with trans-cyclooctenes were investigated by applying quantum chemical calculations and stopped-flow measurements in human plasma; the results indicated that the labeled tetrazine is suitable as a bioorthogonal probe for the imaging of dienophile-tagged (bio)molecules. In vitro and in vivo investigations revealed high stability and PET/MRI in mice showed fast homogeneous biodistribution of the (18) F-labeled tetrazine that also passes the blood-brain barrier. An in vivo click experiment confirmed the bioorthogonal behavior of this novel tetrazine probe. Due to favorable chemical and pharmacokinetic properties this bioorthogonal agent should find application in bioimaging and biomedical research.
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Affiliation(s)
- Christoph Denk
- Institut für Angewandte Synthesechemie, Technische Universität Wien (TUW) (Austria)
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176
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Denk C, Svatunek D, Filip T, Wanek T, Lumpi D, Fröhlich J, Kuntner C, Mikula H. Entwicklung eines18F-markierten Tetrazins mit vorteilhaften pharmakokinetischen Eigenschaften für die bioorthogonale Positronenemissionstomographie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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177
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Herner A, Estrada Girona G, Nikić I, Kállay M, Lemke EA, Kele P. New generation of bioorthogonally applicable fluorogenic dyes with visible excitations and large Stokes shifts. Bioconjug Chem 2014; 25:1370-4. [PMID: 24932756 DOI: 10.1021/bc500235p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthesis of a set of new, azide bearing, biorthogonally applicable fluorogenic dyes with large Stokes shifts is presented herein. To assess the fluorogenic performance of these new dyes we have labeled a genetically modulated, cyclooctyne-bearing protein in lysate medium. Studies showed that the labels produce specific signal with minimal background fluorescence. We also provide theoretical insights into the design of such fluorogenic labels.
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Affiliation(s)
- András Herner
- "Lendület" Chemical Biology Research Group, Research Centre for Natural Sciences, Institute of Organic Chemistry, Hungarian Academy of Sciences , Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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178
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Abstract
We report the synthesis of active polymers of superfolder green fluorescent protein (sfGFP) in one step using Click chemistry. Up to six copies of the non-natural amino acids (nnAAs) p-azido-l-phenylalanine (pAzF) or p-propargyloxy-l-phenylalanine (pPaF) were site-specifically inserted into sfGFP by cell-free protein synthesis (CFPS). sfGFP containing two or three copies of these nnAAs were coupled by copper-catalyzed azide-alkyne cycloaddition to synthesize linear or branched protein polymers, respectively. The protein polymers retained ≥63% of their specific activity (i.e., fluorescence) after coupling. Polymerization of a concentrated solution of triply substituted sfGFP resulted in fluorescent macromolecular particles. Our method can be generalized to synthesize polymers of a protein or copolymers of any two or more proteins, and the conjugation sites can be determined exactly by standard genetic manipulation. Polymers of proteins and small molecules can also be created with this technology to make a new class of scaffolds or biomaterials.
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Affiliation(s)
- Cem Albayrak
- Department
of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, California 94305, United States
| | - James R. Swartz
- Department
of Chemical Engineering, Stanford University, 381 North-South Mall, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, 318 Campus Drive, Stanford, California 94305, United States
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179
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Tharp JM, Wang YS, Lee YJ, Yang Y, Liu WR. Genetic incorporation of seven ortho-substituted phenylalanine derivatives. ACS Chem Biol 2014; 9:884-90. [PMID: 24451054 PMCID: PMC3997995 DOI: 10.1021/cb400917a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Seven
phenylalanine derivatives with small ortho substitutions
were genetically encoded in Escherichia coli and
mammalian cells at an amber codon using a previously reported,
rationally designed pyrrolysyl-tRNA synthetase mutant (PylRS(N346A/C348A))
coupled with tRNACUAPyl. Ortho substitutions of the phenylalanine
derivatives reported herein include three halides, methyl, methoxy,
nitro, and nitrile. These compounds have the potential for use in
multiple biochemical and biophysical applications. Specifically, we
demonstrated that o-cyano-phenylalanine could be
used as a selective sensor to probe the local environment of proteins
and applied this to study protein folding/unfolding. For six of these
compounds this constitutes the first report of their genetic incorporation
in living cells. With these compounds the total number of substrates
available for PylRS(N346A/C348A) is increased to nearly 40, which
demonstrates that PylRS(N346A/C348A) is able to recognize phenylalanine
with a substitution at any side-chain aromatic position as a substrate.
To our knowledge, PylRS(N346A/C348A) is the only aminoacyl-tRNA synthetase
with such a high substrate promiscuity.
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Affiliation(s)
- Jeffery M. Tharp
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yane-Shih Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yan-Jiun Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yanyan Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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180
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Schmidt MJ, Weber A, Pott M, Welte W, Summerer D. Structural basis of furan-amino acid recognition by a polyspecific aminoacyl-tRNA-synthetase and its genetic encoding in human cells. Chembiochem 2014; 15:1755-60. [PMID: 24737732 DOI: 10.1002/cbic.201402006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 11/05/2022]
Abstract
The site-selective introduction of photo-crosslinking groups into proteins enables the discovery and mapping of weak and/or transient protein interactions with high spatiotemporal resolution, both in vitro and in vivo. We report the genetic encoding of a furan-based, photo-crosslinking amino acid in human cells; it can be activated with red light, thus offering high penetration depths in biological samples. This is achieved by activation of the amino acid and charging to its cognate tRNA by a pyrrolysyl-tRNA-synthetase (PylRS) mutant with broad polyspecificity. To gain insights into the recognition of this amino acid and to provide a rationale for its polyspecificity, we solved three crystal structures of the PylRS mutant: in its apo-form, in complex with adenosine 5'-(β,γ-imido)triphosphate (AMP-PNP) and in complex with the AMP ester of the furan amino acid. These structures provide clues for the observed polyspecificity and represent a promising starting point for the engineering of PylRS mutants with further increased substrate scope.
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Affiliation(s)
- Moritz J Schmidt
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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181
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Wallace S, Chin JW. Strain-promoted sydnone bicyclo-[6.1.0]-nonyne cycloaddition†Electronic supplementary information (ESI) available: Full experimental details, 1H/ 13C NMR spectral data, protein synthesis and purification. See DOI: 10.1039/c3sc53332h. Chem Sci 2014; 5:1742-1744. [PMID: 25580211 PMCID: PMC4285100 DOI: 10.1039/c3sc53332h] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/22/2014] [Indexed: 01/28/2023] Open
Abstract
The discovery and exploration of bioorthogonal chemical reactions and the biosynthetic incorporation of their components into biomolecules for specific labelling is an important challenge. Here we describe the reaction of a phenyl sydnone 1,3-dipole with a bicyclononyne dipolarophile. This strain-promoted reaction proceeds without transition metal catalysis in aqueous buffer, at physiological temperature, and pressure with a rate comparable to that of other bioorthogonal reactions. We demonstrate the quantitative and specific labelling of a genetically encoded bicyclononyne with a sydnone fluorophore conjugate, demonstrating the utility of this approach for bioorthogonal protein labelling.
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Affiliation(s)
- Stephen Wallace
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK . ; http://www.2.mrc-lmb.cam.ac.uk/ccsb/
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK . ; http://www.2.mrc-lmb.cam.ac.uk/ccsb/
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182
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Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes. Proc Natl Acad Sci U S A 2014; 111:5456-61. [PMID: 24706769 DOI: 10.1073/pnas.1322727111] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. Such activatable probes with near-infrared (NIR) emission would be ideal for in vivo imaging but have proven difficult to engineer. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. We used the probes for mammalian cell surface imaging and, in conjunction with a new class of cyclooctyne D-amino acids, for visualization of bacterial peptidoglycan without the need to wash away unreacted probe.
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183
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Lang K, Chin JW. Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 2014; 114:4764-806. [PMID: 24655057 DOI: 10.1021/cr400355w] [Citation(s) in RCA: 786] [Impact Index Per Article: 78.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kathrin Lang
- Medical Research Council Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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184
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Wan W, Tharp JM, Liu WR. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1059-70. [PMID: 24631543 DOI: 10.1016/j.bbapap.2014.03.002] [Citation(s) in RCA: 284] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/01/2014] [Accepted: 03/05/2014] [Indexed: 11/16/2022]
Abstract
The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNA(Pyl). Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low selectivity toward its substrate α-amine, and low selectivity toward the anticodon of tRNA(Pyl). These unique but ordinary features of PylRS as an aminoacyl-tRNA synthetase allow the Pyl incorporation machinery to be easily engineered for the genetic incorporation of more than 100 non-canonical amino acids (NCAAs) or α-hydroxy acids into proteins at amber codon and the reassignment of other codons such as ochre UAA, opal UGA, and four-base AGGA codons to code NCAAs.
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Affiliation(s)
- Wei Wan
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77845, USA.
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185
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Sletten EM, de Almeida G, Bertozzi CR. A homologation approach to the synthesis of difluorinated cycloalkynes. Org Lett 2014; 16:1634-7. [PMID: 24588780 PMCID: PMC3993865 DOI: 10.1021/ol500260d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Difluorinated cyclooctynes are important
reagents for labeling
azido-biomolecules through copper-free click chemistry. Here, a safe,
scalable synthesis of a difluorinated cyclooctyne is reported, which
involves a key homologation/ring-expansion reaction. Sequential ring
expansions were also employed to synthesize and study a novel difluorinated
cyclononyne.
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Affiliation(s)
- Ellen M Sletten
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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186
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Abstract
Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals (C. elegans and D. melanogaster) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl-transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. Combining chemoselective reactions with encoded amino acids has facilitated the installation of posttranslational modifications, as well as rapid derivatization with diverse fluorophores for imaging.
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Affiliation(s)
- Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 OQH, United Kingdom;
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187
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Gahlmann A, Moerner WE. Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging. Nat Rev Microbiol 2014; 12:9-22. [PMID: 24336182 DOI: 10.1038/nrmicro3154] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The ability to detect single molecules in live bacterial cells enables us to probe biological events one molecule at a time and thereby gain knowledge of the activities of intracellular molecules that remain obscure in conventional ensemble-averaged measurements. Single-molecule fluorescence tracking and super-resolution imaging are thus providing a new window into bacterial cells and facilitating the elucidation of cellular processes at an unprecedented level of sensitivity, specificity and spatial resolution. In this Review, we consider what these technologies have taught us about the bacterial cytoskeleton, nucleoid organization and the dynamic processes of transcription and translation, and we also highlight the methodological improvements that are needed to address a number of experimental challenges in the field.
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Affiliation(s)
- Andreas Gahlmann
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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188
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Nikić I, Plass T, Schraidt O, Szymański J, Briggs JAG, Schultz C, Lemke EA. Minimal Tags for Rapid Dual-Color Live-Cell Labeling and Super-Resolution Microscopy. Angew Chem Int Ed Engl 2014; 53:2245-9. [DOI: 10.1002/anie.201309847] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 12/21/2022]
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189
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Schnelle, zweifarbige Proteinmarkierung an lebenden Zellen für die hochauflösende Mikroskopie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309847] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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190
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Schmidt MJ, Borbas J, Drescher M, Summerer D. A Genetically Encoded Spin Label for Electron Paramagnetic Resonance Distance Measurements. J Am Chem Soc 2014; 136:1238-41. [DOI: 10.1021/ja411535q] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Moritz J. Schmidt
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Borbas
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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191
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Otsuka S, Szymborska A, Ellenberg J. Imaging the assembly, structure, and function of the nuclear pore inside cells. Methods Cell Biol 2014; 122:219-38. [PMID: 24857732 DOI: 10.1016/b978-0-12-417160-2.00010-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nuclear pore complex (NPC) mediates selective transport across the nuclear envelope (NE) and plays crucial roles in several additional cellular functions. In higher eukaryotes, the NPC and the NE disassemble and reassemble during cell division and live-cell imaging has been a powerful tool to analyze these dynamic processes. Here, we present a method for the kinetic analysis of postmitotic NPC assembly and reestablishment of transport competence in intact cells by multicolor 4D imaging and photoswitching. By applying the methods we have established previously using normal rat kidney to HeLa cells, we demonstrate the conservation of NPC assembly in different mammalian cells. We recently showed that the molecular organization of the NPC can be studied by combining stochastic super-resolution microscopy with single-particle averaging and present this method here in detail.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Szymborska
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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192
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Jung JE, Lee SY, Park H, Cha H, Ko W, Sachin K, Kim DW, Chi DY, Lee HS. Genetic incorporation of unnatural amino acids biosynthesized from α-keto acids by an aminotransferase. Chem Sci 2014. [DOI: 10.1039/c3sc51617b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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193
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Gattner MJ, Ehrlich M, Vrabel M. Sulfonyl azide-mediated norbornene aziridination for orthogonal peptide and protein labeling. Chem Commun (Camb) 2014; 50:12568-71. [DOI: 10.1039/c4cc04117h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we show that electron-deficient sulfonyl azides can be used for selective functionalization of norbornene containing peptides and proteins.
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Affiliation(s)
- Michael J. Gattner
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
| | - Michael Ehrlich
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
| | - Milan Vrabel
- Department of Chemistry
- Ludwig-Maximilians-University
- 81377 Munich, Germany
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194
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Yang H, Srivastava P, Zhang C, Lewis JC. A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition. Chembiochem 2013; 15:223-7. [PMID: 24376040 DOI: 10.1002/cbic.201300661] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Indexed: 12/29/2022]
Abstract
Strain-promoted azide-alkyne cycloaddition (SPAAC) can be used to generate artificial metalloenzymes (ArMs) from scaffold proteins containing a p-azido-L-phenylalanine (Az) residue and catalytically active bicyclononyne-substituted metal complexes. The high efficiency of this reaction allows rapid ArM formation when using Az residues within the scaffold protein in the presence of cysteine residues or various reactive components of cellular lysate. In general, cofactor-based ArM formation allows the use of any desired metal complex to build unique inorganic protein materials. SPAAC covalent linkage further decouples the native function of the scaffold from the installation process because it is not affected by native amino acid residues; as long as an Az residue can be incorporated, an ArM can be generated. We have demonstrated the scope of this method with respect to both the scaffold and cofactor components and established that the dirhodium ArMs generated can catalyze the decomposition of diazo compounds and both Si-H and olefin insertion reactions involving these carbene precursors.
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Affiliation(s)
- Hao Yang
- Department of Chemistry, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637 (USA)
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195
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Lee CY, Held R, Sharma A, Baral R, Nanah C, Dumas D, Jenkins S, Upadhaya S, Du W. Copper-granule-catalyzed microwave-assisted click synthesis of polyphenol dendrimers. J Org Chem 2013; 78:11221-8. [PMID: 24127771 PMCID: PMC3875327 DOI: 10.1021/jo401603d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Syringaldehyde- and vanillin-based antioxidant dendrimers were synthesized via microwave-assisted alkyne-azide 1,3-dipolar cycloaddition using copper granules as a catalyst. The use of Cu(I) as a catalyst resulted in copper contaminated dendrimers. To produce copper-free antioxidant dendrimers for biological applications, Cu(I) was substituted with copper granules. Copper granules were ineffective at both room temperature and under reflux conditions (<5% yield). However, they were an excellent catalyst when dendrimer synthesis was performed under microwave irradiation, giving yields up to 94% within 8 h. ICP-mass analysis of the antioxidant dendrimers obtained with this method showed virtually no copper contamination (9 ppm), which was the same as the background level. The synthesized antioxidants, free from copper contamination, demonstrated potent radical scavenging with IC50 values of less than 3 μM in the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. In comparison, dendrimers synthesized from Cu(I)-catalyzed click chemistry showed a high level of copper contamination (4800 ppm) and no detectable antioxidant activity.
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Affiliation(s)
- Choon Young Lee
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Rich Held
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Ajit Sharma
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Rom Baral
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Cyprien Nanah
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Dan Dumas
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Shannon Jenkins
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Samik Upadhaya
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Wenjun Du
- Department of Chemistry, Central Michigan University, Mount Pleasant, MI 48859, USA
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196
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Zhang H, Feng G, Guo Y, Zhou D. Robust and specific ratiometric biosensing using a copper-free clicked quantum dot-DNA aptamer sensor. NANOSCALE 2013; 5:10307-15. [PMID: 24056667 PMCID: PMC3814187 DOI: 10.1039/c3nr02897f] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/13/2013] [Indexed: 05/30/2023]
Abstract
We report herein the successful preparation of a compact and functional CdSe-ZnS core-shell quantum dot (QD)-DNA conjugate via highly efficient copper-free "click chemistry" (CFCC) between a dihydro-lipoic acid-polyethylene glycol-azide (DHLA-PEG-N3) capped QD and a cyclooctyne modified DNA. This represents an excellent balance between the requirements of high sensitivity, robustness and specificity for the QD-FRET (Förster resonance energy transfer) based sensor as confirmed by a detailed FRET analysis on the QD-DNA conjugate, yielding a relatively short donor-acceptor distance of ~5.8 nm. We show that this CFCC clicked QD-DNA conjugate is not only able to retain the native fluorescence quantum yield (QY) of the parent DHLA-PEG-N3 capped QD, but also well-suited for robust and specific biosensing; it can directly quantitate, at the pM level, both labelled and unlabelled complementary DNA probes with a good SNP (single-nucleotide polymorphism) discrimination ability in complex media, e.g. 10% human serum via target-binding induced FRET changes between the QD donor and the dye acceptor. Furthermore, this sensor has also been successfully exploited for the detection, at the pM level, of a specific protein target (thrombin) via the encoded anti-thrombin aptamer sequence in the QD-DNA conjugate.
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Affiliation(s)
- Haiyan Zhang
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ;
| | - Guoqiang Feng
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education , College of Chemistry , Central China Normal University , 152 Luoyu Road , Wuhan 430079 , P.R. China
| | - Yuan Guo
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ;
| | - Dejian Zhou
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ;
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197
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Schneider S, Gattner MJ, Vrabel M, Flügel V, López-Carrillo V, Prill S, Carell T. Structural Insights into Incorporation of Norbornene Amino Acids for Click Modification of Proteins. Chembiochem 2013; 14:2114-8. [DOI: 10.1002/cbic.201300435] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 12/13/2022]
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198
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Kamber DN, Nazarova LA, Liang Y, Lopez SA, Patterson DM, Shih HW, Houk KN, Prescher JA. Isomeric Cyclopropenes Exhibit Unique Bioorthogonal Reactivities. J Am Chem Soc 2013; 135:13680-3. [DOI: 10.1021/ja407737d] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [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
| | - Steven A. Lopez
- 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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199
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Zhang WH, Otting G, Jackson CJ. Protein engineering with unnatural amino acids. Curr Opin Struct Biol 2013; 23:581-7. [DOI: 10.1016/j.sbi.2013.06.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 12/20/2022]
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200
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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. [DOI: 10.1002/ange.201303477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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