51
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Monitoring conformational dynamics with single-molecule fluorescence energy transfer: applications in nucleosome remodeling. Methods Enzymol 2012; 513:59-86. [PMID: 22929765 PMCID: PMC5023429 DOI: 10.1016/b978-0-12-391938-0.00003-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Due to its ability to track distance changes within individual molecules or molecular complexes on the nanometer scale and in real time, single-molecule fluorescence resonance energy transfer (single-molecule FRET) is a powerful tool to tackle a wide range of important biological questions. Using our recently developed single-molecule FRET assay to monitor nucleosome translocation as an illustrative example, we describe here in detail how to set up, carry out, and analyze single-molecule FRET experiments that provide time-dependent information on biomolecular processes.
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52
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Slavoff SA, Liu DS, Cohen JD, Ting AY. Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. J Am Chem Soc 2011; 133:19769-76. [PMID: 22098454 DOI: 10.1021/ja206435e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report a new method, Interaction-Dependent PRobe Incorporation Mediated by Enzymes, or ID-PRIME, for imaging protein-protein interactions (PPIs) inside living cells. ID-PRIME utilizes a mutant of Escherichia coli lipoic acid ligase, LplA(W37V), which can catalyze the covalent ligation of a coumarin fluorophore onto a peptide recognition sequence called LAP1. The affinity between the ligase and LAP1 is tuned such that, when each is fused to a protein partner of interest, LplA(W37V) labels LAP1 with coumarin only when the protein partners to which they are fused bring them together. Coumarin labeling in the absence of such interaction is low or undetectable. Characterization of ID-PRIME in living mammalian cells shows that multiple protein-protein interactions can be imaged (FRB-FKBP, Fos-Jun, and neuroligin-PSD-95), with as little as 10 min of coumarin treatment. The signal intensity and detection sensitivity are similar to those of the widely used fluorescent protein complementation technique (BiFC) for PPI detection, without the disadvantage of irreversible complex trapping. ID-PRIME provides a powerful and complementary approach to existing methods for visualization of PPIs in living cells with spatial and temporal resolution.
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Affiliation(s)
- Sarah A Slavoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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53
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Cohen JD, Thompson S, Ting AY. Structure-guided engineering of a Pacific Blue fluorophore ligase for specific protein imaging in living cells. Biochemistry 2011; 50:8221-5. [PMID: 21859157 DOI: 10.1021/bi201037r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mutation of a gatekeeper residue, tryptophan 37, in E. coli lipoic acid ligase (LplA), expands substrate specificity such that unnatural probes much larger than lipoic acid can be recognized. This approach, however, has not been successful for anionic substrates. An example is the blue fluorophore Pacific Blue, which is isosteric to 7-hydroxycoumarin and yet not recognized by the latter's ligase ((W37V)LplA) or any tryptophan 37 point mutant. Here we report the results of a structure-guided, two-residue screening matrix to discover an LplA double mutant, (E20G/W37T)LplA, that ligates Pacific Blue as efficiently as (W37V)LplA ligates 7-hydroxycoumarin. The utility of this Pacific Blue ligase for specific labeling of recombinant proteins inside living cells, on the cell surface, and inside acidic endosomes is demonstrated.
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Affiliation(s)
- Justin D Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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54
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Ai HW, Shen W, Sagi A, Chen PR, Schultz PG. Probing protein-protein interactions with a genetically encoded photo-crosslinking amino acid. Chembiochem 2011; 12:1854-7. [PMID: 21678540 DOI: 10.1002/cbic.201100194] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 12/16/2022]
Affiliation(s)
- Hui-wang Ai
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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55
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Jin X, Uttamapinant C, Ting AY. Synthesis of 7-aminocoumarin by Buchwald-Hartwig cross coupling for specific protein labeling in living cells. Chembiochem 2011; 12:65-70. [PMID: 21154801 DOI: 10.1002/cbic.201000414] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Xin Jin
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge MA 02139, USA
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56
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Henriques R, Griffiths C, Hesper Rego E, Mhlanga MM. PALM and STORM: unlocking live-cell super-resolution. Biopolymers 2011; 95:322-31. [PMID: 21254001 DOI: 10.1002/bip.21586] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 01/06/2011] [Accepted: 01/06/2011] [Indexed: 12/11/2022]
Abstract
Live-cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super-resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live-cell imaging approaches have eluded super-resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super-resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization microscopy methods such as PALM and STORM to achieve this important goal.
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Affiliation(s)
- Ricardo Henriques
- Unidade de Biofisica e Expressão Genetica, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisboa, Portugal.
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57
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Liu LH, Yan M. Perfluorophenyl azides: new applications in surface functionalization and nanomaterial synthesis. Acc Chem Res 2010; 43:1434-43. [PMID: 20690606 PMCID: PMC2982936 DOI: 10.1021/ar100066t] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A major challenge in materials science is the ongoing search for coupling agents that are readily synthesized, capable of versatile chemistry, able to easily functionalize materials and surfaces, and efficient in covalently linking organic and inorganic entities. A decade ago, we began a research program investigating perfluorophenylazides (PFPA) as the coupling agents in surface functionalization and nanomaterial synthesis. The p-substituted PFPAs are attractive heterobifunctional coupling agents because of their two distinct and synthetically distinguishable reactive centers: (i) the fluorinated phenylazide, which is capable of forming stable covalent adducts, and (ii) the functional group R, which can be tailored through synthesis. Two approaches have been undertaken for material synthesis and surface functionalization. The first method involves synthesizing PFPA bearing the first molecule or material with a functional linker R and then attaching the resulting PFPA to the second material by activating the azido group. In the second approach, the material surface is first functionalized with PFPA via functional center R, and coupling of the second molecule or material is achieved with the surface azido groups. In this Account, we review the design and protocols of the two approaches, providing examples in which PFPA derivatives were successfully used in material surface functionalization, ligand conjugation, and the synthesis of hybrid nanomaterials. The methods developed have proved to be general and versatile, and they are applicable to a wide range of materials (especially those that lack reactive functional groups or are difficult to derivatize) and to various substrates of polymers, oxides, carbon materials, and metal films. The coupling chemistry can be initiated by light, heat, and electrons. Patterned structures can be generated by selectively activating the areas of interest. Furthermore, the process is easy to perform, and light activation occurs in minutes, greatly facilitating the efficiency of the reaction. PFPAs indeed demonstrate many benefits as versatile surface coupling agents and offer opportunities for further exploration.
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Affiliation(s)
- Li-Hong Liu
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207-0751
| | - Mingdi Yan
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207-0751
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58
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Wang J, Zhang W, Song W, Wang Y, Yu Z, Li J, Wu M, Wang L, Zang J, Lin Q. A biosynthetic route to photoclick chemistry on proteins. J Am Chem Soc 2010; 132:14812-8. [PMID: 20919707 PMCID: PMC2965590 DOI: 10.1021/ja104350y] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Light-induced chemical reactions exist in nature, regulating many important cellular and organismal functions, e.g., photosensing in prokaryotes and vision formation in mammals. Here, we report the genetic incorporation of a photoreactive unnatural amino acid, p-(2-tetrazole)phenylalanine (p-Tpa), into myoglobin site-specifically in E. coli by evolving an orthogonal tRNA/aminoacyl-tRNA synthetase pair and the use of p-Tpa as a bioorthogonal chemical "handle" for fluorescent labeling of p-Tpa-encoded myoglobin via the photoclick reaction. Moreover, we elucidated the structural basis for the biosynthetic incorporation of p-Tpa into proteins by solving the X-ray structure of p-Tpa-specific aminoacyl-tRNA synthetase in complex with p-Tpa. The genetic encoding of this photoreactive amino acid should make it possible in the future to photoregulate protein function in living systems.
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Affiliation(s)
- Jiangyun Wang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Zhang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjiao Song
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Yizhong Wang
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Jiasong Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Minhao Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Lin Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jianye Zang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA
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59
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Hinner MJ, Johnsson K. How to obtain labeled proteins and what to do with them. Curr Opin Biotechnol 2010; 21:766-76. [PMID: 21030243 DOI: 10.1016/j.copbio.2010.09.011] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/10/2010] [Accepted: 09/21/2010] [Indexed: 12/20/2022]
Abstract
We review new and established methods for the chemical modification of proteins in living cells and highlight recent applications. The review focuses on tag-mediated protein labeling methods, such as the tetracysteine tag and SNAP-tag, and new developments in this field such as intracellular labeling with lipoic acid ligase. Recent promising advances in the incorporation of unnatural amino acids into proteins are also briefly discussed. We describe new tools using tag-mediated labeling methods including the super-resolution microscopy of tagged proteins, the study of the interactions of proteins and protein domains, the subcellular targeting of synthetic ion sensors, and the generation of new semisynthetic metabolite sensors. We conclude with a view on necessary future developments, with one example being the selective labeling of non-tagged, native proteins in complex protein mixtures.
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Affiliation(s)
- Marlon J Hinner
- Institute of Chemical Sciences and Engineering, Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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60
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Dieterich DC. Chemical reporters for the illumination of protein and cell dynamics. Curr Opin Neurobiol 2010; 20:623-30. [PMID: 20650631 DOI: 10.1016/j.conb.2010.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/09/2010] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
Abstract
Fluorescent proteins have revolutionized cell biology and, therefore, our understanding of the complex molecular and cellular mechanisms that wire the brain together and enable its plasticity throughout life. The ability to visualize cell biological processes has inspired the development of alternative protein labeling strategies by both chemists and biologists. Among those approaches are the introduction of small bioorthogonal chemical reporters and new fluorescent probes by either genetic encoding or by utilizing the cell's own biosynthesis machinery in live cells. This review will highlight recent advances in approaches to track discrete proteins or whole subpopulations of a proteome including post-translational modifications with spatiotemporal resolution.
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Affiliation(s)
- Daniela C Dieterich
- Emmy Noether Research Group Neuralomics, Leibniz Institute for Neurobiology, Brenneckestr. 6, 39118 Magdeburg, Germany.
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61
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A fluorophore ligase for site-specific protein labeling inside living cells. Proc Natl Acad Sci U S A 2010; 107:10914-9. [PMID: 20534555 DOI: 10.1073/pnas.0914067107] [Citation(s) in RCA: 237] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Biological microscopy would benefit from smaller alternatives to green fluorescent protein for imaging specific proteins in living cells. Here we introduce PRIME (PRobe Incorporation Mediated by Enzymes), a method for fluorescent labeling of peptide-fused recombinant proteins in living cells with high specificity. PRIME uses an engineered fluorophore ligase, which is derived from the natural Escherichia coli enzyme lipoic acid ligase (LplA). Through structure-guided mutagenesis, we created a mutant ligase capable of recognizing a 7-hydroxycoumarin substrate and catalyzing its covalent conjugation to a transposable 13-amino acid peptide called LAP (LplA Acceptor Peptide). We showed that this fluorophore ligation occurs in cells in 10 min and that it is highly specific for LAP fusion proteins over all endogenous mammalian proteins. By genetically targeting the PRIME ligase to specific subcellular compartments, we were able to selectively label spatially distinct subsets of proteins, such as the surface pool of neurexin and the nuclear pool of actin.
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62
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Computational study on the ionization energies of benzyl azide and its methyl derivatives. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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63
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Park KD, Stables JP, Liu R, Kohn H. Proteomic searches comparing two (R)-lacosamide affinity baits: An electrophilic arylisothiocyanate and a photoactivated arylazide group. Org Biomol Chem 2010; 8:2803-13. [PMID: 20405068 DOI: 10.1039/c000987c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have advanced a novel strategy to search for lacosamide ((R)-1) targets in the brain proteome where protein binding is expected to be modest. Our approach used lacosamide agents containing affinity bait (AB) and chemical reporter (CR) units. The affinity bait moiety is designed to irreversibly react with the target, and the CR group permits protein detection and capture. In this study, we report the preparation and evaluation of (R)-N-(4-azido)benzyl 2-acetamido-3-(prop-2-ynyloxy)propionamide ((R)-3) and show that this compound exhibits potent anticonvulsant activities in the MES seizure model in rodents. We compared the utility of (R)-3 with its isostere, (R)-N-(4-isothiocyanato)benzyl 2-acetamido-3-(prop-2-ynyloxy)propionamide ((R)-2), in proteomic studies designed to identify potential (R)-1 targets. We showed that despite the two-fold improved anticonvulsant activity of (R)-3 compared with (R)-2, (R)-2 was superior in revealing potential binding targets in the mouse brain soluble proteome. The difference in these agents utility has been attributed to the reactivity of the affinity baits (i.e., (R)-2: aryl isothiocyanate moiety; (R)-3: photoactivated aryl azide intermediates) in the irreversible protein modification step, and we conclude that this factor is a critical determinant of successful target detection where ligand (drug) binding is modest. The utility of (R)-2 and (R)-3 in in situ proteome studies is explored.
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Affiliation(s)
- Ki Duk Park
- Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
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64
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Puthenveetil S, Liu DS, White KA, Thompson S, Ting AY. Yeast display evolution of a kinetically efficient 13-amino acid substrate for lipoic acid ligase. J Am Chem Soc 2010; 131:16430-8. [PMID: 19863063 DOI: 10.1021/ja904596f] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Escherichia coli lipoic acid ligase (LplA) catalyzes ATP-dependent covalent ligation of lipoic acid onto specific lysine side chains of three acceptor proteins involved in oxidative metabolism. Our lab has shown that LplA and engineered mutants can ligate useful small-molecule probes such as alkyl azides ( Nat. Biotechnol. 2007 , 25 , 1483 - 1487 ) and photo-cross-linkers ( Angew. Chem., Int. Ed. 2008 , 47 , 7018 - 7021 ) in place of lipoic acid, facilitating imaging and proteomic studies. Both to further our understanding of lipoic acid metabolism, and to improve LplA's utility as a biotechnological platform, we have engineered a novel 13-amino acid peptide substrate for LplA. LplA's natural protein substrates have a conserved beta-hairpin structure, a conformation that is difficult to recapitulate in a peptide, and thus we performed in vitro evolution to engineer the LplA peptide substrate, called "LplA Acceptor Peptide" (LAP). A approximately 10(7) library of LAP variants was displayed on the surface of yeast cells, labeled by LplA with either lipoic acid or bromoalkanoic acid, and the most efficiently labeled LAP clones were isolated by fluorescence activated cell sorting. Four rounds of evolution followed by additional rational mutagenesis produced a "LAP2" sequence with a k(cat)/K(m) of 0.99 muM(-1) min(-1), >70-fold better than our previous rationally designed 22-amino acid LAP1 sequence (Nat. Biotechnol. 2007, 25, 1483-1487), and only 8-fold worse than the k(cat)/K(m) values of natural lipoate and biotin acceptor proteins. The kinetic improvement over LAP1 allowed us to rapidly label cell surface peptide-fused receptors with quantum dots.
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Affiliation(s)
- Sujiet Puthenveetil
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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65
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Sadhu KK, Mizukami S, Watanabe S, Kikuchi K. Turn-on fluorescence switch involving aggregation and elimination processes for β-lactamase-tag. Chem Commun (Camb) 2010; 46:7403-5. [DOI: 10.1039/c0cc02432e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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66
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Chakraborty A, Wang D, Ebright YW, Ebright RH. Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy. Methods Enzymol 2010; 472:19-30. [PMID: 20580957 DOI: 10.1016/s0076-6879(10)72018-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe the synthesis of phosphine derivatives of three fluorescent probes that have a brightness and photostability suitable for single-molecule fluorescence spectroscopy and microscopy: Alexa488, Cy3B, and Alexa647. In addition, we describe procedures for use of these reagents in azide-specific, bioorthogonal labeling through Staudinger-Bertozzi ligation, as well as procedures for the quantitation of labeling specificity and labeling efficiency. The reagents and procedures of this report enable chemoselective, site-selective labeling of azide-containing biomolecules for single-molecule fluorescence spectroscopy and microscopy.
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Affiliation(s)
- Anirban Chakraborty
- Department of Chemistry and Chemical Biology, Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
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67
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Gautier A, Nakata E, Lukinavičius G, Tan KT, Johnsson K. Selective Cross-Linking of Interacting Proteins Using Self-Labeling Tags. J Am Chem Soc 2009; 131:17954-62. [DOI: 10.1021/ja907818q] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Arnaud Gautier
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Eiji Nakata
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Gražvydas Lukinavičius
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kui-Thong Tan
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kai Johnsson
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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68
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Lord SJ, Lee HLD, Samuel R, Weber R, Liu N, Conley NR, Thompson MA, Twieg RJ, Moerner WE. Azido push-pull fluorogens photoactivate to produce bright fluorescent labels. J Phys Chem B 2009; 114:14157-67. [PMID: 19860443 DOI: 10.1021/jp907080r] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Dark azido push-pull chromophores have the ability to be photoactivated to produce bright fluorescent labels suitable for single-molecule imaging. Upon illumination, the aryl azide functionality in the fluorogens participates in a photochemical conversion to an aryl amine, thus restoring charge-transfer absorption and fluorescence. Previously, we reported that one compound, DCDHF-V-P-azide, was photoactivatable. Here, we demonstrate that the azide-to-amine photoactivation process is generally applicable to a variety of push-pull chromophores, and we characterize the photophysical parameters including photoconversion quantum yield, photostability, and turn-on ratio. Azido push-pull fluorogens provide a new class of photoactivatable single-molecule probes for fluorescent labeling and super-resolution microscopy. Lastly, we demonstrate that photoactivated push-pull dyes can insert into bonds of nearby biomolecules, simultaneously forming a covalent bond and becoming fluorescent (fluorogenic photoaffinity labeling).
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Affiliation(s)
- Samuel J Lord
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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69
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Wang X, Liu LH, Ramström O, Yan M. Engineering nanomaterial surfaces for biomedical applications. Exp Biol Med (Maywood) 2009; 234:1128-39. [PMID: 19596820 PMCID: PMC4037294 DOI: 10.3181/0904-mr-134] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Nanomaterials, possessing unique physical and chemical properties, have attracted much interest and generated wide varieties of applications. Recent investigations of functionalized nanomaterials have expanded into the biological area, providing a versatile platform in biomedical applications such as biomolecular sensing, biological imaging, drug delivery and disease therapy. Bio-functions and bio-compatibility of nanomaterials are realized by introducing synthetic ligands or natural biomolecules onto nanomaterials, and combining ligand-receptor biological interactions with intrinsic nanomaterial properties. Common strategies of engineering nanomaterial surfaces involve physisorption or chemisorption of desired ligands. We developed a photochemically initiated surface coupling chemistry, bringing versatility and simplicity to nanomaterial functionalization. The method was applied to attach underivatized carbohydrates efficiently on gold and iron oxide nanoparticles, and the resulting glyconanoparticles were successfully used as a sensitive biosensing system probing specific interactions between carbohydrates and proteins as well as bacteria.
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Affiliation(s)
- Xin Wang
- Department of Chemistry, Portland State University, Portland, Oregon 97207-0751
| | - Li-Hong Liu
- Department of Chemistry, Portland State University, Portland, Oregon 97207-0751
| | - Olof Ramström
- Department of Chemistry, Portland State University, Portland, Oregon 97207-0751
- Department of Chemistry, KTH - Royal Institute of Technology, S-10044 Stockholm, Sweden
| | - Mingdi Yan
- Department of Chemistry, Portland State University, Portland, Oregon 97207-0751
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70
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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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71
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2338] [Impact Index Per Article: 155.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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72
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Sunbul M, Yin J. Site specific protein labeling by enzymatic posttranslational modification. Org Biomol Chem 2009; 7:3361-71. [DOI: 10.1039/b908687k] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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73
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Fernández-Suárez M, Ting AY. Fluorescent probes for super-resolution imaging in living cells. Nat Rev Mol Cell Biol 2008; 9:929-43. [PMID: 19002208 DOI: 10.1038/nrm2531] [Citation(s) in RCA: 891] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In 1873, Ernst Abbe discovered that features closer than approximately 200 nm cannot be resolved by lens-based light microscopy. In recent years, however, several new far-field super-resolution imaging techniques have broken this diffraction limit, producing, for example, video-rate movies of synaptic vesicles in living neurons with 62 nm spatial resolution. Current research is focused on further improving spatial resolution in an effort to reach the goal of video-rate imaging of live cells with molecular (1-5 nm) resolution. Here, we describe the contributions of fluorescent probes to far-field super-resolution imaging, focusing on fluorescent proteins and organic small-molecule fluorophores. We describe the features of existing super-resolution fluorophores and highlight areas of importance for future research and development.
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Affiliation(s)
- Marta Fernández-Suárez
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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