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Arora S, Mao C. Light-regulated RNA interference induced by p-hydroxyphenacyl-modified siRNA in mammalian cells. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:316-339. [PMID: 37700699 DOI: 10.1080/15257770.2023.2258171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023]
Abstract
siRNA is an important tool for modulating gene expression in current biomedical research. It would be highly desirable for siRNA to respond to an external stimulus. In this paper, we report a convenient, photolabile caging agent to regulate siRNA functions. 2-bromo-4'-hydroxyacetophenone (BHAP) can readily modify phosphorothioate backbones and inhibit siRNAs. Mild UV irradiation will cleave the modifying moiety to generate natural nucleic acid backbones, thus activating siRNA functions. Such modification is conveniently conducted in an aqueous solution with high efficiency and is cost-effective and scalable. This approach provides a convenient tool for the controlled regulation of gene expression by deploying minimal usage of complex organic synthesis for site-specific installation of the caging group to siRNA unlike previous reported works that required a series of intricate organic synthesis and cumbersome purification techniques to achieve similar aims. This study will open new doors for optochemical regulation of a variety of genes by pHP caging group in mammalian cell culture.
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Affiliation(s)
- Swati Arora
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
- Pharma Services Group, Patheon/Thermo Fisher Scientific, Florence, South Carolina, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
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2
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Adatia KK, Halbritter T, Reinfelds M, Michele A, Tran M, Laschat S, Heckel A, Tovar GEM, Southan A. Coumarin‐4‐ylmethyl‐ and p‐Hydroxyphenacyl‐Based Photoacid Generators with High Solubility in Aqueous Media: Synthesis, Stability and Photolysis. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.201900258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Karishma K. Adatia
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
| | - Thomas Halbritter
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
- Department of ChemistryUniversity of Iceland Dunhaga 3 107 Reykjavik Iceland
| | - Matiss Reinfelds
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Andre Michele
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Michael Tran
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Sabine Laschat
- Institute of Organic Chemistry IOCUniversity of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Günter E. M. Tovar
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB Nobelstr. 12 70569 Stuttgart Germany
| | - Alexander Southan
- Institute of Interfacial Process Engineering and Plasma Technology IGVPUniversity of Stuttgart Nobelstr. 12 70569 Stuttgart Germany
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3
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Auto-thiophosphorylation activity of Src tyrosine kinase. BMC BIOCHEMISTRY 2016; 17:13. [PMID: 27387461 PMCID: PMC4936181 DOI: 10.1186/s12858-016-0071-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 11/22/2022]
Abstract
Background Intermolecular autophosphorylation at Tyr416 is a conserved mechanism of activation among the members of the Src family of nonreceptor tyrosine kinases. Like several other tyrosine kinases, Src can catalyze the thiophosphorylation of peptide and protein substrates using ATPγS as a thiophosphodonor, although the efficiency of the reaction is low. Results Here, we have characterized the ability of Src to auto-thiophosphorylate. Auto-thiophosphorylation of Src at Tyr416 in the activation loop proceeds efficiently in the presence of Ni2+, resulting in kinase activation. Other tyrosine kinases (Ack1, Hck, and IGF1 receptor) also auto-thiophosphorylate in the presence of Ni2+. Tyr416-thiophosphorylated Src is resistant to dephosphorylation by PTP1B phosphatase. Conclusions Src and other tyrosine kinases catalyze auto-thiophosphorylation in the presence of Ni2+. Thiophosphorylation of Src occurs at Tyr416 in the activation loop, and results in enhanced kinase activity. Tyr416-thiophosphorylated Src could serve as a stable, persistently-activated mimic of Src. Electronic supplementary material The online version of this article (doi:10.1186/s12858-016-0071-z) contains supplementary material, which is available to authorized users.
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4
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Wang X, Feng M, Xiao L, Tong A, Xiang Y. Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme. ACS Chem Biol 2016; 11:444-51. [PMID: 26669486 DOI: 10.1021/acschembio.5b00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.
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Affiliation(s)
- Xiaoyan Wang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Mengli Feng
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
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5
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Markiewicz BN, Culik RM, Gai F. Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function. Sci China Chem 2014; 57:1615-1624. [PMID: 25722715 PMCID: PMC4337807 DOI: 10.1007/s11426-014-5225-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.
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Affiliation(s)
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, PA, 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, PA, 19104, USA
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6
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Senadheera SN, Yousef AL, Givens RS. Photorelease of phosphates: Mild methods for protecting phosphate derivatives. Beilstein J Org Chem 2014; 10:2038-54. [PMID: 25246963 PMCID: PMC4168878 DOI: 10.3762/bjoc.10.212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/07/2014] [Indexed: 12/17/2022] Open
Abstract
We have developed a new photoremovable protecting group for caging phosphates in the near UV. Diethyl 2-(4-hydroxy-1-naphthyl)-2-oxoethyl phosphate (14a) quantitatively releases diethyl phosphate upon irradiation in aq MeOH or aq MeCN at 350 nm, with quantum efficiencies ranging from 0.021 to 0.067 depending on the solvent composition. The deprotection reactions originate from the triplet excited state, are robust under ambient conditions and can be carried on to 100% conversion. Similar results were found with diethyl 2-(4-methoxy-1-naphthyl)-2-oxoethyl phosphate (14b), although it was significantly less efficient compared with 14a. A key step in the deprotection reaction in aq MeOH is considered to be a Favorskii rearrangement of the naphthyl ketone motif of 14a,b to naphthylacetate esters 25 and 26. Disruption of the ketone-naphthyl ring conjugation significantly shifts the photoproduct absorption away from the effective incident wavelength for decaging of 14, driving the reaction to completion. The Favorskii rearrangement does not occur in aqueous acetonitrile although diethyl phosphate is released. Other substitution patterns on the naphthyl or quinolin-5-yl core, such as the 2,6-naphthyl 10 or 8-benzyloxyquinolin-5-yl 24 platforms, also do not rearrange by aryl migration upon photolysis and, therefore, do not proceed to completion. The 2,6-naphthyl ketone platform instead remains intact whereas the quinolin-5-yl ketone fragments to a much more complex, highly absorbing reaction mixture that competes for the incident light.
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Affiliation(s)
| | - Abraham L Yousef
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, U.S.A
| | - Richard S Givens
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, U.S.A
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1238] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Givens RS, Rubina M, Wirz J. Applications of p-hydroxyphenacyl (pHP) and coumarin-4-ylmethyl photoremovable protecting groups. Photochem Photobiol Sci 2012; 11:472-88. [PMID: 22344608 PMCID: PMC3422890 DOI: 10.1039/c2pp05399c] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/20/2012] [Indexed: 12/12/2022]
Abstract
Most applications of photoremovable protecting groups have used o-nitrobenzyl compounds and their (often commercially available) derivatives that, however, have several disadvantages. The focus of this review is on applications of the more recently developed title compounds, which are especially well suited for time-resolved biochemical and physiological investigations, because they release the caged substrates in high yield within a few nanoseconds or less. Together, these two chromophores cover the action spectrum for photorelease from >700 nm to 250 nm.
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Affiliation(s)
- Richard S. Givens
- Department of Chemistry, University of Kansas, Kansas, USA; Tel: +1 785 864 3846
| | - Marina Rubina
- Department of Chemistry, University of Kansas, Kansas, USA; Tel: +1 785 864 1574
| | - Jakob Wirz
- Department of Chemistry, Klingelbergstrasse 80, CH-4056 Basel, Switzerland; Tel: +41 76 413 47 48
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10
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Givens RS, Stensrud K, Conrad PG, Yousef AL, Perera C, Senadheera SN, Heger D, Wirz J. p-Hydroxyphenacyl photoremovable protecting groups - Robust photochemistry despite substituent diversity. CAN J CHEM 2011; 89:364-384. [PMID: 24436496 PMCID: PMC3891043 DOI: 10.1139/v10-143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A broadly based investigation of the effects of a diverse array of substituents on the photochemical rearrangement of p-hydroxyphenacyl esters has demonstrated that common substituents such as F, MeO, CN, CO2R, CONH2, and CH3 have little effect on the rate and quantum efficiencies for the photo-Favorskii rearrangement and the release of the acid leaving group or on the lifetimes of the reactive triplet state. A decrease in the quantum yields across all substituents was observed for the release and rearrangement when the photolyses were carried out in buffered aqueous media at pHs that exceeded the ground-state pKa of the chromophore where the conjugate base is the predominant form. Otherwise, substituents have only a very modest effect on the photoreaction of these robust chromophores.
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Affiliation(s)
- Richard S. Givens
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Kenneth Stensrud
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Peter G. Conrad
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Abraham L. Yousef
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | - Chamani Perera
- Department of Chemistry, University of Kansas Lawrence, Lawrence, KS 66045, USA
| | | | - Dominik Heger
- Research Centre for Toxic Compounds in the Environment (RECETOX) and Department of Chemistry, Faculty of Science, Masaryk University, Kamenice3, 625 00 Brno, Czech Republic
| | - Jakob Wirz
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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11
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Kotzur N, Briand B, Beyermann M, Hagen V. Wavelength-Selective Photoactivatable Protecting Groups for Thiols. J Am Chem Soc 2009; 131:16927-31. [DOI: 10.1021/ja907287n] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nico Kotzur
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Benoît Briand
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Michael Beyermann
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Volker Hagen
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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12
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Priestman MA, Lawrence DS. Light-mediated remote control of signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:547-58. [PMID: 19765679 DOI: 10.1016/j.bbapap.2009.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/08/2009] [Indexed: 01/25/2023]
Abstract
Cell signaling networks display an extraordinary range of temporal and spatial plasticity. Our programmatic approach focuses on the construction of intracellular probes, including sensors, inhibitors, and functionally unique proteins that can be temporally and spatially controlled by the investigator even after they have entered the cell. We have designed and evaluated protein kinase sensors that furnish a fluorescent readout upon phosphorylation. In addition, since the sensors are inert (i.e., cannot be phosphorylated) until activated by light, they can be carried through the various stages of any given cell-based behavior without being consumed. Using this strategy, we have shown that PKCbeta is essential for nuclear envelope breakdown and thus the transition from prophase to metaphase in actively dividing cells. Photoactivatable proteins furnish the means to initiate cellular signaling pathways with a high degree of spatial and temporal control. We have used this approach to demonstrate that cofilin serves as a component of the steering apparatus of the cell. Finally, inhibitors are commonly used to assess the participation of specific enzymes in signaling pathways that control cellular behavior. We have constructed a photo-deactivatable inhibitor, an inhibitory species that can be switched off with light. In the absence of light, the target enzyme is inactive due to the presence of the potent inhibitory molecule. Upon photolysis, the inhibitory molecule is destroyed and enzymatic activity is released.
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Affiliation(s)
- Melanie A Priestman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Kenan Laboratories, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
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Stensrud K, Noh J, Kandler K, Wirz J, Heger D, Givens RS. Competing pathways in the photo-Favorskii rearrangement and release of esters: studies on fluorinated p-hydroxyphenacyl-caged GABA and glutamate phototriggers. J Org Chem 2009; 74:5219-27. [PMID: 19572582 PMCID: PMC3422889 DOI: 10.1021/jo900139h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three new trifluoromethylated p-hydroxyphenacyl (pHP)-caged gamma-aminobutyric acid (GABA) and glutamate (Glu) derivatives have been examined for their efficacy as photoremovable protecting groups in aqueous solution. Through the replacement of hydrogen with fluorine, e.g., a m-trifluoromethyl or a m-trifluoromethoxy versus m-methoxy substituents on the pHP chromophore, modest increases in the quantum yields for the release of amino acids GABA and glutamate as well as improved lipophilicity were realized. The pHP triplet undergoes a photo-Favorskii rearrangement with concomitant release of the amino acid substrate. Deprotonation competes with the rearrangement from the triplet excited state and yields the pHP conjugate base that, upon reprotonation, regenerates the starting ketoester, a chemically unproductive or "energy-wasting" process. When picosecond pump-probe spectroscopy is employed, GABA derivatives 2-5 are characterized by short triplet lifetimes, a manifestation of their rapid release of GABA. The bioavailability of released GABA at the GABA(A) receptor improved when the release took place from m-OCF3 (2) but decreased for m-CF3 (3) when compared with the parent pHP derivative. These studies demonstrate that pKa and lipophilicity exert significant but sometimes opposing influences on the photochemistry and biological activity of pHP phototriggers.
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Affiliation(s)
- Kenneth Stensrud
- Department of Chemistry,1251 Wescoe Hall Drive, University of Kansas, Lawrence, KS 66045
| | - Jihyun Noh
- Department of Otolaryngology, 3500 Terrace St., University of Pittsburgh, Pittsburgh, PA 15208
| | - Karl Kandler
- Department of Otolaryngology, 3500 Terrace St., University of Pittsburgh, Pittsburgh, PA 15208
| | - Jakob Wirz
- Departement Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Dominik Heger
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Richard S. Givens
- Department of Chemistry,1251 Wescoe Hall Drive, University of Kansas, Lawrence, KS 66045
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14
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Lee HM, Larson DR, Lawrence DS. Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds. ACS Chem Biol 2009; 4:409-27. [PMID: 19298086 DOI: 10.1021/cb900036s] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents; the scope and limitations associated with the instrumentation required for their application; and recent chemical and biological advances in this field.
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Affiliation(s)
- Hsien-Ming Lee
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Daniel R. Larson
- Department of Anatomy and Structural Biology, The Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - David S. Lawrence
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
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15
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Young DD, Lusic H, Lively MO, Yoder JA, Deiters A. Gene silencing in mammalian cells with light-activated antisense agents. Chembiochem 2009; 9:2937-40. [PMID: 19021142 DOI: 10.1002/cbic.200800627] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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Kawakami T, Cheng H, Hashiro S, Nomura Y, Tsukiji S, Furuta T, Nagamune T. A Caged Phosphopeptide‐Based Approach for Photochemical Activation of Kinases in Living Cells. Chembiochem 2008; 9:1583-6. [DOI: 10.1002/cbic.200800116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Givens RS, Heger D, Hellrung B, Kamdzhilov Y, Mac M, Conrad PG, Cope E, Lee JI, Mata-Segreda JF, Schowen RL, Wirz J. The photo-Favorskii reaction of p-hydroxyphenacyl compounds is initiated by water-assisted, adiabatic extrusion of a triplet biradical. J Am Chem Soc 2008; 130:3307-9. [PMID: 18290649 DOI: 10.1021/ja7109579] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard S Givens
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA.
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18
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Schultz C. Molecular tools for cell and systems biology. HFSP JOURNAL 2007; 1:230-48. [PMID: 19404424 DOI: 10.2976/1.2812442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 10/24/2007] [Indexed: 01/25/2023]
Abstract
The sequencing of the genomes of key organisms and the subsequent identification of genes merely leads us to the next real challenge in modern biology-revealing the precise functions of these genes. Further, detailed knowledge of how the products of these genes behave in space and time is required, including their interactions with other molecules. In order to tackle these considerable tasks, a large and continuously expanding toolbox is required to probe the functions of proteins on a cellular level. Here, the currently available tools are described and future developments are projected. There is no doubt that only the close interplay between the life science disciplines in addition to advances in engineering will be able to meet the challenge.
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Affiliation(s)
- Carsten Schultz
- Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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19
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Aemissegger A, Carrigan CN, Imperiali B. Caged O-phosphorothioyl amino acids as building blocks for Fmoc-based solid phase peptide synthesis. Tetrahedron 2007; 63:6185-6190. [PMID: 19543448 DOI: 10.1016/j.tet.2007.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The synthesis of 1-(2-nitrophenylethyl) caged O-phosphorothioylserine, -threonine and -tyrosine derivatives is reported. These amino acid building blocks can be directly incorporated into peptides by Fmoc-based solid phase synthesis as their pentafluorophenyl esters or as symmetric anhydrides. Upon irradiation with UV light, the thiophosphate group, representing a hydrolysis resistant phosphate analog, is revealed.
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Affiliation(s)
- Andreas Aemissegger
- Massachusetts Institute of Technology, Department of Chemistry, 18-590, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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20
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Abstract
The activity of light-activatable ("caged") compounds can be temporally and spatially controlled, thereby providing a means to interrogate intracellular biochemical pathways as a function of time and space. Nearly all caged peptides contain photocleavable groups positioned on the side chains of key residues. We describe an alternative active site targeted strategy that disrupts the interaction between the protein target (SH2 domain, kinase, and proteinase) and a critical amide NH moiety of the peptide probe.
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Abstract
Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Campus Box 8204, Raleigh, NC 27695, USA
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Ma C, Kwok WM, Chan WS, Du Y, Kan JTW, Toy PH, Phillips DL. Ultrafast Time-Resolved Transient Absorption and Resonance Raman Spectroscopy Study of the Photodeprotection and Rearrangement Reactions of p-Hydroxyphenacyl Caged Phosphates. J Am Chem Soc 2006; 128:2558-70. [PMID: 16492039 DOI: 10.1021/ja0532032] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics and mechanism of the photodeprotection and rearrangement reactions for the pHP phototrigger compounds p-hydroxyphenacyl diethyl phosphate (HPDP) and diphenyl phosphate (HPPP) were studied using transient absorption (TA) and picosecond time-resolved resonance Raman (ps-TR(3)) spectroscopy. TA spectroscopy was employed to detect the dynamics of the triplet precursor decay as well as to investigate the influence of the solvent and leaving group on the triplet quenching process. Ps-TR(3) spectroscopy was used to directly monitor the formation dynamics for the photosolvolytic rearrangement product and its solvent and leaving group dependence. The TA and TR(3) spectroscopy experiments were also used to characterize the structural and electronic properties of the triplet precursor to the HPDP and HPPP deprotection reactions. The solvent effect observed in conjunction with the leaving group dependence of the triplet decay dynamics are consistent with a concerted solvent assisted triplet cleavage through a heterolytic mechanism for the HPDP and HPPP photodeprotection process. Correlation of the dynamics between the deprotection and rearrangement processes reveals there is a consecutive mechanism and the involvement of an intermediate between the two reaction steps. The reaction rate of the deprotection and rearrangement steps and the influence of the solvent and leaving group were determined and evaluated based on kinetic modeling of the dynamical data obtained experimentally for HPDP and HPPP in H(2)O/MeCN mixed solvents with varying water concentration in the solvent system. A solvation complex with a contact ion pair character was proposed to be the intermediate involved in the deprotection and rearrangement pathway. The results here combined with our previous study on the photophysical events occurring on the early picosecond time scale (Ma; et al. J. Am. Chem. Soc. 2005, 127, 1463-1472) provide a real time overall mechanistic description for the photodeprotection and rearrangement reactions of pHP caged phosphate phototrigger compounds.
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Affiliation(s)
- Chensheng Ma
- Contribution from the Department of Chemistry, The University of Hong Kong, SAR, P R China
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Parker LL, Schilling AB, Kron SJ, Kent SBH. Optimizing thiophosphorylation in the presence of competing phosphorylation with MALDI-TOF-MS detection. J Proteome Res 2006; 4:1863-6. [PMID: 16212443 PMCID: PMC4568822 DOI: 10.1021/pr050150e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thiophosphorylation provides a metabolically stable, chemically reactive phosphorylation analogue for analyzing the phosphoproteome in vitro and in vivo. We developed a MALDI-TOF-MS based assay for optimizing thiophosphopeptide production by a kinase even in the presence of Mg(2+) and ATP. We found that Abl kinase thiophosphorylation rates can be "rescued" using Mn(2+) in the presence of Mg(2+). Under our ideal conditions, titration of Mn(2+) and ATPgammaS in the presence of Mg(2+) allowed relatively rapid, highly specific thiophosphorylation by Abl tyrosine kinase, both as purified enzyme and in complex cell extracts.
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Affiliation(s)
- Laurie L Parker
- Department of Biochemistry and Molecular Biology, University of Chicago, CIS 201, 929 E. 57 Street, Chicago, IL 60637, USA.
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Hahn ME, Muir TW. Photocontrol of Smad2, a multiphosphorylated cell-signaling protein, through caging of activating phosphoserines. Angew Chem Int Ed Engl 2005; 43:5800-3. [PMID: 15523718 DOI: 10.1002/anie.200461141] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michael E Hahn
- The Laboratory of Synthetic Protein Chemistry, The Rockefeller University, Box 223, 1230 York Avenue, New York, NY 10021, USA
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27
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Lawrence DS. The preparation and in vivo applications of caged peptides and proteins. Curr Opin Chem Biol 2005; 9:570-5. [PMID: 16182597 DOI: 10.1016/j.cbpa.2005.09.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 09/08/2005] [Indexed: 11/21/2022]
Abstract
Cellular behavior, such as mitosis and motility, are controlled by both when and where specific intracellular signaling pathways are activated in response to environmental cues. Analogous temporally and spatially controlled events occur throughout the lifetime of an organism (e.g. embryogenesis). Consequently, reagents that can be switched on (or off) at any time or at any place in a cell, a tissue, or a living animal, represent the means by which the biochemical basis of spatially and temporally sensitive biological behavior can be evaluated. This review summarizes recent advances in the design and synthesis of light-activated ('caged') peptides and proteins as well as the application of these caged reagents to unanswered questions in biology.
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Affiliation(s)
- David S Lawrence
- Department of Biochemistry, The Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA.
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005; 44:5713-7. [PMID: 16059958 DOI: 10.1002/anie.200501244] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jean-Philippe Pellois
- The Laboratory of Synthetic Protein Chemistry, The Rockefeller University, Box 223, 1230 York Avenue, New York, NY 10021, USA
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Pellois JP, Muir TW. A Ligation and Photorelease Strategy for the Temporal and Spatial Control of Protein Function in Living Cells. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501244] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Hahn ME, Muir TW. Photocontrol of Smad2, a Multiphosphorylated Cell-Signaling Protein, through Caging of Activating Phosphoserines. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461141] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Abstract
Expressed protein ligation (EPL) is a protein engineering approach that allows recombinant and synthetic polypeptides to be chemoselectively and regioselectively joined together. The approach makes the primary structure of most proteins accessible to the tools of synthetic organic chemistry, enabling the covalent structure of proteins to be modified in an unprecedented fashion. The ability to incorporate noncoded amino acids, biophysical probes, and stable isotopes into specific locations within proteins provides research tools to peer into the inner workings of these molecules. In this review I discuss the development of this technology, its broad application to biological systems, and its possible role in the area of proteomics.
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Affiliation(s)
- Tom W Muir
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
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p-Hydroxyphenacyl bromide as photoremoveable thiol label: a potential phototrigger for thiol-containing biomolecules. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)02194-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pelliccioli AP, Wirz J. Photoremovable protecting groups: reaction mechanisms and applications. Photochem Photobiol Sci 2002; 1:441-58. [PMID: 12659154 DOI: 10.1039/b200777k] [Citation(s) in RCA: 538] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolabile protecting groups enable biochemists to control the release of bioactive compounds in living tissue. 'Caged compounds' (photoactivatable bioagents) have become an important tool to study the events that follow chemical signalling in, e.g., cell biology and the neurosciences. The possibilities are by no means exhausted. Progress will depend on the development of photoremovable protecting groups that satisfy the diverse requirements of new applications--a challenging task for photochemists.
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Affiliation(s)
- Anna Paola Pelliccioli
- Institut für Physikalische Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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