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Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024; 25:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
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Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
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2
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Yuan Z, Liu X, Liu C, Zhang Y, Rao Y. Recent Advances in Rapid Synthesis of Non-proteinogenic Amino Acids from Proteinogenic Amino Acids Derivatives via Direct Photo-Mediated C-H Functionalization. Molecules 2020; 25:E5270. [PMID: 33198166 PMCID: PMC7696505 DOI: 10.3390/molecules25225270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022] Open
Abstract
Non-proteinogenic amino acids have attracted tremendous interest for their essential applications in the realm of biology and chemistry. Recently, rising C-H functionalization has been considered an alternative powerful method for the direct synthesis of non-proteinogenic amino acids. Meanwhile, photochemistry has become popular for its predominant advantages of mild conditions and conservation of energy. Therefore, C-H functionalization and photochemistry have been merged to synthesize diverse non-proteinogenic amino acids in a mild and environmentally friendly way. In this review, the recent developments in the photo-mediated C-H functionalization of proteinogenic amino acids derivatives for the rapid synthesis of versatile non-proteinogenic amino acids are presented. Moreover, postulated mechanisms are also described wherever needed.
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Affiliation(s)
- Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Xuanzhong Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Changmei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
| | - Yan Zhang
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China;
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.Y.); (X.L.); (C.L.)
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3
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Saha A, Duchambon P, Masson V, Loew D, Bombard S, Teulade-Fichou MP. Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes. Biochemistry 2020; 59:1261-1272. [PMID: 32191439 DOI: 10.1021/acs.biochem.9b01094] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We investigate herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite that adopt a parallel topology while differing in the length of the central loop (from nine nucleotides to one nucleotide). It is revealed that NCL strongly binds to long-loop (five to nine nucleotides) G4 while interacting weakly with the shorter variants (loop with fewer than three nucleotides). Photo-cross-linking experiments using 5-bromo-2'-deoxyuridine (BrU)-modified sequences further confirmed the loop-length dependency, thereby indicating that the WT-CEB25-L191 (nine-nucleotide loop) is the best G4 substrate. Quantitative proteomic analysis (LC-MS/MS) of the product(s) obtained by photo-cross-linking NCL to this sequence enabled the identification of one contact site corresponding to a 15-amino acid fragment located in helix α2 of RNA binding domain 2 (RBD2), which sheds light on the role of this structural element in G4-loop recognition. Then, the ability of a panel of benchmark G4 ligands to prevent the NCL-G4 interaction was explored. It was found that only the most potent ligand PhenDC3 can inhibit NCL binding, thereby suggesting that the terminal guanine quartet is also a strong determinant of G4 recognition, putatively through interaction with the RGG domain. This study describes the molecular mechanism by which NCL recognizes G4-containing long loops and leads to the proposal of a model implying a concerted action of RBD2 and RGG domains to achieve specific G4 recognition via a dual loop-quartet interaction.
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Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Vanessa Masson
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405 Orsay, France
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4
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Polevoda B, Joseph R, Friedman AE, Bennett RP, Greiner R, De Zoysa T, Stewart RA, Smith HC. DNA mutagenic activity and capacity for HIV-1 restriction of the cytidine deaminase APOBEC3G depend on whether DNA or RNA binds to tyrosine 315. J Biol Chem 2017; 292:8642-8656. [PMID: 28381554 DOI: 10.1074/jbc.m116.767889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
APOBEC3G (A3G) belongs to the AID/APOBEC protein family of cytidine deaminases (CDA) that bind to nucleic acids. A3G mutates the HIV genome by deamination of dC to dU, leading to accumulation of virus-inactivating mutations. Binding to cellular RNAs inhibits A3G binding to substrate single-stranded (ss) DNA and CDA activity. Bulk RNA and substrate ssDNA bind to the same three A3G tryptic peptides (amino acids 181-194, 314-320, and 345-374) that form parts of a continuously exposed protein surface extending from the catalytic domain in the C terminus of A3G to its N terminus. We show here that the A3G tyrosines 181 and 315 directly cross-linked ssDNA. Binding experiments showed that a Y315A mutation alone significantly reduced A3G binding to both ssDNA and RNA, whereas Y181A and Y182A mutations only moderately affected A3G nucleic acid binding. Consistent with these findings, the Y315A mutant exhibited little to no deaminase activity in an Escherichia coli DNA mutator reporter, whereas Y181A and Y182A mutants retained ∼50% of wild-type A3G activity. The Y315A mutant also showed a markedly reduced ability to assemble into viral particles and had reduced antiviral activity. In uninfected cells, the impaired RNA-binding capacity of Y315A was evident by a shift of A3G from high-molecular-mass ribonucleoprotein complexes to low-molecular-mass complexes. We conclude that Tyr-315 is essential for coordinating ssDNA interaction with or entry to the deaminase domain and hypothesize that RNA bound to Tyr-315 may be sufficient to competitively inhibit ssDNA deaminase-dependent antiviral activity.
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Affiliation(s)
- Bogdan Polevoda
- From the Departments of Biochemistry and Biophysics and.,Center for RNA Biology, and
| | | | | | | | | | | | | | - Harold C Smith
- From the Departments of Biochemistry and Biophysics and .,Center for RNA Biology, and.,OyaGen, Inc., Rochester, New York 14623.,Center for AIDS Research, University of Rochester Medical Center, Rochester, New York 14642 and
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5
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Krakowiak A, Kocoń-Rębowska B, Dolot R, Piotrzkowska D. New interactions between tumor suppressor Fhit protein and a nonhydrolyzable analog of its A P4 A substrate. FEBS Lett 2017; 591:548-559. [PMID: 28094435 DOI: 10.1002/1873-3468.12560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 11/06/2022]
Abstract
Fragile histidine triad protein (Fhit) is a protein which primarily hydrolyses dinucleoside polyphosphates. To investigate possible interactions between the protein and a substrate, we used a nonhydrolyzable phosphorothioate analog of Ap4 A, containing 5-bromo-2'-deoxyuridine instead of one adenosine residue. Photocrosslinking, followed by LC-MS experiments, determined a complex in which the probe was covalently linked to the NDSIYEELQK peptide (residues 110-119). The peptide was located within the 'disordered' region, which is invisible in the known crystal structures of Fhit. This invisible and flexible part seems to play a role in the stabilization of the Fhit-substrate complex, which may be important for its tumor suppressor activity.
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Affiliation(s)
- Agnieszka Krakowiak
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Beata Kocoń-Rębowska
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Rafał Dolot
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Danuta Piotrzkowska
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
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6
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Dai X, Song D, Liu K, Su H. Photoinduced C—I bond homolysis of 5-iodouracil: A singlet predissociation pathway. J Chem Phys 2017; 146:025103. [DOI: 10.1063/1.4973650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Xiaojuan Dai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunhui Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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7
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Seamon KJ, Bumpus NN, Stivers JT. Single-Stranded Nucleic Acids Bind to the Tetramer Interface of SAMHD1 and Prevent Formation of the Catalytic Homotetramer. Biochemistry 2016; 55:6087-6099. [PMID: 27775344 DOI: 10.1021/acs.biochem.6b00986] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sterile alpha motif and HD domain protein 1 (SAMHD1) is a unique enzyme that plays important roles in nucleic acid metabolism, viral restriction, and the pathogenesis of autoimmune diseases and cancer. Although much attention has been focused on its dNTP triphosphohydrolase activity in viral restriction and disease, SAMHD1 also binds to single-stranded RNA and DNA. Here we utilize a UV cross-linking method using 5-bromodeoxyuridine-substituted oligonucleotides coupled with high-resolution mass spectrometry to identify the binding site for single-stranded nucleic acids (ssNAs) on SAMHD1. Mapping cross-linked amino acids on the surface of existing crystal structures demonstrated that the ssNA binding site lies largely along the dimer-dimer interface, sterically blocking the formation of the homotetramer required for dNTPase activity. Surprisingly, the disordered C-terminus of SAMHD1 (residues 583-626) was also implicated in ssNA binding. An interaction between this region and ssNA was confirmed in binding studies using the purified SAMHD1 583-626 peptide. Despite a recent report that SAMHD1 possesses polyribonucleotide phosphorylase activity, we did not detect any such activity in the presence of inorganic phosphate, indicating that nucleic acid binding is unrelated to this proposed activity. These data suggest an antagonistic regulatory mechanism in which the mutually exclusive oligomeric state requirements for ssNA binding and dNTP hydrolase activity modulate these two functions of SAMHD1 within the cell.
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Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine , 725 North Wolfe Street, WBSB 314, Baltimore, Maryland 21205, United States
| | - Namandjé N Bumpus
- Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins University School of Medicine , 725 North Wolfe Street, Biophysics 307, Baltimore, Maryland 21205, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine , 725 North Wolfe Street, WBSB 314, Baltimore, Maryland 21205, United States
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8
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The excluded DNA strand is SEW important for hexameric helicase unwinding. Methods 2016; 108:79-91. [DOI: 10.1016/j.ymeth.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 02/04/2023] Open
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9
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Chen K, Lu Z, Wang X, Fu Y, Luo GZ, Liu N, Han D, Dominissini D, Dai Q, Pan T, He C. High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410647] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Chen K, Lu Z, Wang X, Fu Y, Luo GZ, Liu N, Han D, Dominissini D, Dai Q, Pan T, He C. High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing. Angew Chem Int Ed Engl 2014; 54:1587-90. [PMID: 25491922 DOI: 10.1002/anie.201410647] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 11/08/2022]
Abstract
N(6) -methyladenosine (m(6) A) is an abundant internal modification in eukaryotic mRNA and plays regulatory roles in mRNA metabolism. However, methods to precisely locate the m(6) A modification remain limited. We present here a photo-crosslinking-assisted m(6) A sequencing strategy (PA-m(6) A-seq) to more accurately define sites with m(6) A modification. Using this strategy, we obtained a high-resolution map of m(6) A in a human transcriptome. The map resembles the general distribution pattern observed previously, and reveals new m(6) A sites at base resolution. Our results provide insight into the relationship between the methylation regions and the binding sites of RNA-binding proteins.
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Affiliation(s)
- Kai Chen
- Department of Chemistry, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637 (USA) http://he-group.uchicago.edu
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11
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12
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Norris CL, Meisenheimer KM, Koch TH. Mechanistic Studies Relevant to Bromouridine-Enhanced Nucleoprotein Photocrosslinking: Possible Involvement of an Excited Tyrosine Residue of the Protein. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1997.tb08546.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Kanevskii IE, Kuznetsova SA. Synthesis of reactive nucleic acid analogues and their application for the study of structure and functions of biopolymers. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1998v067n07abeh000394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Ciesielska B, Łukaszewicz A, Celewicz L, Maciejewski A, Kubicki J. Method of determination of emission properties of very weakly emitting species ensuring elimination of emission of impurities. APPLIED SPECTROSCOPY 2007; 61:102-9. [PMID: 17311723 DOI: 10.1366/000370207779701389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This paper describes a new type of spectrofluorimeter, composed of a high-performance liquid chromatography (HPLC) system directly connected to a fluorescence detector and an absorption photodiode array detector, designed for studying the emission of weakly emitting species. Procedures for measurements of emission spectra (ES), emission excitation spectra (EES), and quantum yields of emission (PhiE) for very weakly emitting systems (PhiE>or=10(-7)) have been proposed. The original methodical solution allows verification of whether the emission observed comes solely from the compound studied (and not from its impurities) or from some photochemical or thermal process taking place during measurements. Thanks to the use of this new type of spectrofluorimeter, it is possible to establish with a high probability that the dependence of the shape and position of the ES on the excitation wavelength and the differences between EES and absorptance spectra are due to photophysical and/or photochemical properties of the compound studied and not due to the presence of emitting impurities. An especially interesting application of this method is to study the emission of species whose very weak emission is related to a very short lifetime as well as a low radiative rate constant. It is particularly suitable to the study of the emission properties of flexible molecules that can occur in a few conformers of different absorption and emission properties. The performance of the method is illustrated by the results of the emission studies carried out for Nalpha-acetyl-2-(uracil-5-yl)-L-tryptophan N-ethylamide.
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Affiliation(s)
- Barbara Ciesielska
- Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
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15
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Coman MM, Jin M, Ceapa R, Finkelstein J, O'Donnell M, Chait BT, Hingorani MM. Dual functions, clamp opening and primer-template recognition, define a key clamp loader subunit. J Mol Biol 2004; 342:1457-69. [PMID: 15364574 PMCID: PMC2849281 DOI: 10.1016/j.jmb.2004.07.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2004] [Revised: 07/27/2004] [Accepted: 07/27/2004] [Indexed: 10/26/2022]
Abstract
Clamp loader proteins catalyze assembly of circular sliding clamps on DNA to enable processive DNA replication. During the reaction, the clamp loader binds primer-template DNA and positions it in the center of a clamp to form a topological link between the two. Clamp loaders are multi-protein complexes, such as the five protein Escherichia coli, Saccharomyces cerevisiae, and human clamp loaders, and the two protein Pyrococcus furiosus and Methanobacterium thermoautotrophicum clamp loaders, and thus far the site(s) responsible for binding and selecting primer-template DNA as the target for clamp assembly remain unknown. To address this issue, we analyzed the interaction between the E.coli gamma complex clamp loader and DNA using UV-induced protein-DNA cross-linking and mass spectrometry. The results show that the delta subunit in the gamma complex makes close contact with the primer-template junction. Tryptophan 279 in the delta C-terminal domain lies near the 3'-OH primer end and may play a key role in primer-template recognition. Previous studies have shown that delta also binds and opens the beta clamp (hydrophobic residues in the N-terminal domain of delta contact beta. The clamp-binding and DNA-binding sites on delta appear positioned for facile entry of primer-template into the center of the clamp and exit of the template strand from the complex. A similar analysis of the S.cerevisiae RFC complex suggests that the dual functionality observed for delta in the gamma complex may be true also for clamp loaders from other organisms.
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Affiliation(s)
- Maria Magdalena Coman
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Mi Jin
- Rockefeller University, New York, NY 10021, USA
| | - Razvan Ceapa
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Jeff Finkelstein
- Rockefeller University, New York, NY 10021, USA
- Howard Hughes Medical Institute, New York, NY 10021 USA
| | - Michael O'Donnell
- Rockefeller University, New York, NY 10021, USA
- Howard Hughes Medical Institute, New York, NY 10021 USA
| | | | - Manju M. Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- Corresponding author:
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16
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Koch TH, Smith D, Tabacman E, Zichi DA. Kinetic analysis of site-specific photoaptamer-protein cross-linking. J Mol Biol 2004; 336:1159-73. [PMID: 15037076 DOI: 10.1016/j.jmb.2004.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 12/29/2003] [Accepted: 01/05/2004] [Indexed: 10/26/2022]
Abstract
ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.
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Affiliation(s)
- Tad H Koch
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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17
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Sanderson JM, Whelan EJ. Characterisation of the interactions of aromatic amino acids with diacetyl phosphatidylcholine. Phys Chem Chem Phys 2004. [DOI: 10.1039/b312184d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Abstract
The potential of photoaptamers as proteomic probes was investigated. Photoaptamers are defined as aptamers that bear photocross-linking functionality, in this report, 5-bromo-2'-deoxyuridine. A key question regarding the use of photoaptamer probes is the specificity of the cross-linking reaction. The specificity of three photoaptamers was explored by comparing their reactions with target proteins and non-target proteins. The range of target/non-target specificity varies from 100- to >10(6)-fold with most values >10(4)-fold. The contributions of the initial binding step and the photocross-linking step were evaluated for each reaction. Photocross-linking never degraded specificity and significantly increased aptamer specificity in some cases. The application of photoaptamer technology to proteomics was investigated in microarray format. Immobilized anti-human immunodeficiency virus-gp120 aptamer was able to detect subnanomolar concentrations of target protein in 5% human serum. The levels of sensitivity and specificity displayed by photoaptamers, combined with other advantageous properties of aptamers, should facilitate development of protein chip technology.
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Affiliation(s)
- Drew Smith
- SomaLogic, Inc, Boulder, Colorado 80301, USA.
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19
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Steen H, Jensen ON. Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. MASS SPECTROMETRY REVIEWS 2002; 21:163-182. [PMID: 12476441 DOI: 10.1002/mas.10024] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Photochemical cross-linking is a commonly used method for studying the molecular details of protein-nucleic acid interactions. Photochemical cross-linking aids in defining nucleic acid binding sites of proteins via subsequent identification of cross-linked protein domains and amino acid residues. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross-linking sites in proteins. The present review of the field describes a number of MS-based approaches for the characterization of cross-linked protein-nucleic acid complexes and for sequencing of peptide-nucleic acid heteroconjugates. The combination of photochemical cross-linking and MS provides a fast screening method to gain insights into the overall structure and formation of protein-oligonucleotide complexes. Because the analytical methods are continuously refined and protein structural data are rapidly accumulating in databases, we envision that many protein-nucleic acid assemblies will be initially characterized by combinations of cross-linking methods, MS, and computational molecular modeling.
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Affiliation(s)
- Hanno Steen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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20
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Steen H, Petersen J, Mann M, Jensen ON. Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA. Protein Sci 2001; 10:1989-2001. [PMID: 11567090 PMCID: PMC2374209 DOI: 10.1110/ps.07601] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Protein-nucleic acid complexes are commonly studied by photochemical cross-linking. UV-induced cross-linking of protein to nucleic acid may be followed by structural analysis of the conjugated protein to localize the cross-linked amino acids and thereby identify the nucleic acid binding site. Mass spectrometry is becoming increasingly popular for characterization of purified peptide-nucleic acid heteroconjugates derived from UV cross-linked protein-nucleic acid complexes. The efficiency of mass spectrometry-based methods is, however, hampered by the contrasting physico-chemical properties of nucleic acid and peptide entities present in such heteroconjugates. Sample preparation of the peptide-nucleic acid heteroconjugates is, therefore, a crucial step in any mass spectrometry-based analytical procedure. This study demonstrates the performance of four different MS-based strategies to characterize E. coli single-stranded DNA binding protein (SSB) that was UV-cross-linked to a 5-iodouracil containing DNA oligomer. Two methods were optimized to circumvent the need for standard liquid chromatography and gel electrophoresis, thereby dramatically increasing the overall sensitivity of the analysis. Enzymatic degradation of protein and oligonucleotide was combined with miniaturized sample preparation methods for enrichment and desalting of cross-linked peptide-nucleic acid heteroconjugates from complex mixtures prior to mass spectrometric analysis. Detailed characterization of the peptidic component of two different peptide-DNA heteroconjugates was accomplished by matrix-assisted laser desorption/ionization mass spectrometry and allowed assignment of tryptophan-54 and tryptophan-88 as candidate cross-linked residues. Sequencing of those peptide-DNA heteroconjugates by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry identified tryptophan-54 and tryptophan-88 as the sites of cross-linking. Although the UV-cross-linking yield of the protein-DNA complex did not exceed 15%, less than 100 pmole of SSB protein was required for detailed structural analysis by mass spectrometry.
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Affiliation(s)
- H Steen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark/Odense University, DK-5230 Odense M, Denmark
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21
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Meisenheimer KM, Meisenheimer PL, Koch TH. Nucleoprotein photo-cross-linking using halopyrimidine-substituted RNAs. Methods Enzymol 2001; 318:88-104. [PMID: 10889982 DOI: 10.1016/s0076-6879(00)18046-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- K M Meisenheimer
- Department of Chemistry, Angelo State University, San Angelo, Texas 76909, USA
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22
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Abstract
High sensitivity and specificity of two modified ssDNA aptamers capable of photocross-linking recombinant human basic fibroblast growth factor (bFGF((155))) were demonstrated. The aptamers were identified through a novel, covalent, in vitro selection methodology called photochemical systematic evolution of ligands by exponential enrichment (PhotoSELEX). The aptamers exhibited high sensitivity for bFGF((155)) comparable with commercially available ELISA monoclonal antibodies with an absolute sensitivity of at least 0.058 ppt bFGF((155)) under prevailing test conditions. The aptamers exquisitely distinguished bFGF((155)) from consanguine proteins, vascular endothelial growth factor (VEGF) and platelet derived growth factor (PDGF). A commercially viable diagnostic system incorporating PhotoSELEX-evolved aptamers capable of simultaneous quantification of a large number of analyte molecules is also described. Such a system benefits from covalent bonding of aptamer to target protein allowing vigorous washing with denaturants to improve signal to noise.
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Affiliation(s)
- M C Golden
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
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23
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Golden MC, Resing KA, Collins BD, Willis MC, Koch TH. Mass spectral characterization of a protein-nucleic acid photocrosslink. Protein Sci 1999; 8:2806-12. [PMID: 10631998 PMCID: PMC2144224 DOI: 10.1110/ps.8.12.2806] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A photocrosslink between basic fibroblast growth factor (bFGF155) and a high affinity ssDNA oligonucleotide was characterized by positive ion electrospray ionization mass spectrometry (ESIMS). The DNA was a 61-mer oligonucleotide photoaptamer bearing seven bromodeoxyuridines, identified by in vitro selection. Specific photocrosslinking of the protein to the oligonucleotide was achieved by 308 nm XeCl excimer laser excitation. The cross-linked protein nucleic acid complex was proteolyzed with trypsin. The resulting peptide crosslink was purified by PAGE, eluted, and digested by snake venom phosphodiesterase/alkaline phosphatase. Comparison of the oligonucleotide vs. the degraded peptide crosslink by high performance liquid chromatography coupled to an electrospray ionization triple quadrupole mass spectrometer showed a single ion unique to the crosslinked material. Sequencing by collision induced dissociation (MS/MS) on a triple quadrupole mass spectrometer revealed that this ion was the nonapeptide TGQYKLGSK (residues 130-138) crosslinked to a dinucleotide at Tyr133. The MS/MS spectrum indicated sequential fragmentation of the oligonucleotide to uracil covalently attached to the nonapeptide followed by fragmentation of the peptide bonds. Tyr133 is located within the heparin binding pocket, suggesting that the in vitro selection targeted this negative ion binding region of bFGF155.
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Affiliation(s)
- M C Golden
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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24
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Revers F, Cario M, Cao TL, Cazenave C. Detection of proteins binding to short RNA.DNA hybrids or short antisense oligonucleotides in Xenopus laevis oocytes and human macrophage cell extracts by photoaffinity radiolabeling. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:317-31. [PMID: 10463076 DOI: 10.1089/oli.1.1999.9.317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using a 12 base pair RNA.DNA hybrid, substituted with bromouracil on either the RNA or DNA strand, we have detected by photoaffinity radiolabeling a limited set of proteins able to bind to RNA.DNA hybrids in both Xenopus oocyte extracts and human macrophage extracts. Resulting patterns of crosslinked proteins were highly dependent on the strand (DNA or RNA) that was substituted. With one exception, none of the proteins investigated in competition experiments was found to be absolutely specific for RNA.DNA hybrids, as at least one other nucleic acid, either single-stranded DNA or single-stranded RNA, was found to compete efficiently. None of the proteins detected in this assay correspond to the size expected for RNases H. Using the same methodology, we have detected proteins that bind to short oligodeoxyribonucleotides. Although we have essentially detected in Xenopus oocytes one prominent protein of approximately 75 kDa, corresponding to replication protein A (RPA) whatever the oligonucleotide used, the patterns obtained with extracts of human macrophages were more complex and dependent on the oligonucleotide used. If a protein corresponding to RPA was observed most of the time, other crosslinks of similar or sometimes higher intensity were also detected. Interestingly, among these, one protein of 35 kDa appears paradoxically to bind and crosslink to a dodecamer but not to an octadecamer containing the same sequence placed either at its 3'-end or 5'-end.
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Affiliation(s)
- F Revers
- Laboratoire de Biophysique Moléculaire, INSERM U386, Université Victor Segalen Bordeaux II, France
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25
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Connor DA, Falick AM, Shetlar MD. UV Light-induced Cross-linking of Nucleosides, Nucleotides and a Dinucleotide to the Carboxy-terminal Heptad Repeat Peptide of RNA Polymerase II as Studied by Mass Spectrometry. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb03244.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Photochemical reactions of 5-fluorouracil and 5-fluoro-2′-deoxyuridine with Nα-acetyl-L-tryptophan N-ethylamide in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1998. [DOI: 10.1016/s1011-1344(98)00090-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Bromination of pyrimidines using bromide and monoperoxysulfate: A competition study between cytidine, uridine and thymidine. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00512-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Meisenheimer KM, Koch TH. Photocross-linking of nucleic acids to associated proteins. Crit Rev Biochem Mol Biol 1997; 32:101-40. [PMID: 9145285 DOI: 10.3109/10409239709108550] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.
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Affiliation(s)
- K M Meisenheimer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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29
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Norris CL, Meisenheimer PL, Koch TH. Mechanistic Studies of the 5-Iodouracil Chromophore Relevant to Its Use in Nucleoprotein Photo-Cross-Linking. J Am Chem Soc 1996. [DOI: 10.1021/ja9607852] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Celewicz L. Photochemical reactions of 5-bromocytosine and its N-1-substituted derivatives with in aqueous solution. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1995. [DOI: 10.1016/1011-1344(95)07176-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Görner H. Free radical chain mechanism in the acetone-sensitized photolysis of 5-bromouracil and derivatives in alcohol-water mixtures. J Photochem Photobiol A Chem 1995. [DOI: 10.1016/1010-6030(95)04048-k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Willis MC, LeCuyer KA, Meisenheimer KM, Uhlenbeck OC, Koch TH. An RNA-protein contact determined by 5-bromouridine substitution, photocrosslinking and sequencing. Nucleic Acids Res 1994; 22:4947-52. [PMID: 7800485 PMCID: PMC523761 DOI: 10.1093/nar/22.23.4947] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
An analogue of the replicase translational operator of bacteriophage R17, that contains a 5-bromouridine at position -5 (RNA 1), complexes with a dimer of the coat protein and photocrosslinks to the coat protein in high yield upon excitation at 308 nm with a xenon chloride excimer laser. Tryptic digestion of the crosslinked nucleoprotein complex followed by Edman degradation of the tryptic fragment bearing the RNA indicates crosslinking to tyrosine 85 of the coat protein. A control experiment with a Tyr 85 to Ser 85 variant coat protein showed binding but no photocrosslinking at saturating protein concentration. This is consistent with the observation from model compound studies of preferential photocrosslinking of BrU to the electron rich aromatic amino acids tryptophan, tyrosine, and histidine with 308 nm excitation.
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Affiliation(s)
- M C Willis
- Department of Chemistry, University of Colorado, Boulder 80309-0215
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33
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Wower J, Rosen KV, Hixson SS, Zimmermann RA. Recombinant photoreactive tRNA molecules as probes for cross-linking studies. Biochimie 1994; 76:1235-46. [PMID: 7538327 DOI: 10.1016/0300-9084(94)90054-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Photoreactive tRNA derivatives have been used extensively for investigating the interaction of tRNA molecules with their ligands and substrates. Recombinant RNA technology facilitates the construction of such tRNA probes through site-specific incorporation of photoreactive nucleosides. The general strategy involves preparation of suitable tRNA fragments and their ligation either to a photoreactive nucleotide or to each other. tRNA fragments can be prepared by site-specific cleavage of native tRNAs, or synthesized by enzymatic and chemical means. A number of photoreactive nucleosides suitable for incorporation into tRNA are presently available. Joining of tRNA fragments is accomplished either by RNA ligase or by DNA ligase in the presence of a DNA splint. The application of this methodology to the study of tRNA binding sites on the ribosome is discussed, and a model of the tRNA-ribosome complex is presented.
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Affiliation(s)
- J Wower
- Department of Biochemistry, University of Massachusetts, Amherst 01003, USA
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34
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Acetone-sensitized photolysis of 5-iodouracil and 5-iodouridine in aqueous solution in the presence of alcohols: free radical chain mechanism. J Photochem Photobiol A Chem 1993. [DOI: 10.1016/1010-6030(93)80015-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Katouzian-Safadi M, Laine B, Chartier F, Cremet JY, Belaiche D, Sautiere P, Charlier M. Determination of the DNA-interacting region of the archaebacterial chromosomal protein MC1. Photocrosslinks with 5-bromouracil-substituted DNA. Nucleic Acids Res 1991; 19:4937-41. [PMID: 1923761 PMCID: PMC328793 DOI: 10.1093/nar/19.18.4937] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protein MC1 is the major chromosomal protein in methanosarcinaceae. Using photochemical crosslinking on 5-bromouracil-substituted DNA, we identified the region of the protein that interacts with it. This region is located in the C-terminal part of the polypeptide chain, and the crosslinked amino-acids are in the region 74-86. Tryptophan 74 is one of the amino-acids crosslinked to DNA.
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36
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Gott JM, Willis MC, Koch TH, Uhlenbeck OC. A specific, UV-induced RNA-protein cross-link using 5-bromouridine-substituted RNA. Biochemistry 1991; 30:6290-5. [PMID: 1711897 DOI: 10.1021/bi00239a030] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The well-characterized RNA binding site of the bacteriophage R17 coat protein has been used to investigate the cross-linking of protein to 5-bromouridine (BrU)-substituted RNA using medium-wavelength UV light. We have demonstrated a specific RNA-protein cross-link and identified the site on the RNA of protein attachment. Formation of the covalent complex is dependent upon the presence of BrU at position -5 of the RNA and specific binding of the RNA by coat protein. The amount of cross-linking increases with time and depends on the light source and conditions used. Irradiations using a broad-spectrum UV transilluminator (peak at 312 nm) or monochromatic XeCl excimer laser (308 nm) gave levels of cross-linking exceeding 20 and 50%, respectively. The quantum yield of photo-cross-linking, determined with 308-nm excitation, was 0.003. While little strand breakage or debromination of the RNA occurred, significant protein photodamage was observed.
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Affiliation(s)
- J M Gott
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215
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37
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Shetlar MD, Rose RB, Hom K, Shaw AA. Ring opening photoreactions of 5-bromouracil and 5-bromo-2'-deoxyuridine with selected alkylamines. Photochem Photobiol 1991; 53:595-609. [PMID: 1881960 DOI: 10.1111/j.1751-1097.1991.tb08486.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several studies in the literature indicate that histones (lysine rich proteins found associated with DNA in eukaryotic chromatin), as well as poly-L-lysine, can be photocross-linked by ultraviolet (UV) light to DNA in which 5-bromo-2'-deoxyuridine has been substituted for thymidine. To gain some insight into the possible nature of this cross-linking, we have studied the photoreactions occurring in deoxygenated aqueous solutions containing 5-bromouracil (I) (BrUra) or 5-bromo-2'-deoxyuridine (III) (BrdUrd) and ethylamine, a lysine side chain analog. In the case of I this reaction produced the ring opened compound N-(N'-ethylcarbamoyl)-3-amino-2-bromoacrylamide (Ia). A small amount of N-(N'-ethylcarbamoyl)-3-ethylamino-2-bromoacrylamide (Ic) was also isolated. It was found that purified Ia, standing in the presence of ethylamine, was gradually converted to Ic in a dark reaction. The beta and alpha anomers of N-(N'-ethylcarbamoyl)-3-(2'deoxyribofuranos-1'-yl) amino-2-bromoacrylamide (IIIa and IIIb respectively) were isolated as products in the photoreaction of III with ethylamine; the alpha anomer was produced in a dark reaction from the beta anomer. The identity of these anomers was established by comparison of their proton NMR spectra with those of the four corresponding alpha and beta furanosyl and pyranosyl isomeric nucleosides of thymine, which are presented in the Appendix. A study was also made of the reaction of I with methylamine; a ring opened product analogous to Ia, viz. N-(N'-methylcarbamoyl)-3-amino-2-bromoacrylamide (IIa) was formed. A similar study with 5-bromo-1-methyluracil produced N-(N'-methylcarbamoyl)-3-methylamino-2-bromoacrylamide (IIc) as a product. Likewise, the reaction of 5-chlorouracil with ethylamine was studied and N-(N'-ethylcarbamoyl)-3-amino-2-chloroacrylamide (Ie), which is analogous in structure to Ia, was found to be produced. Structural identifications were made through use of UV spectroscopy, high resolution 1H-NMR spectroscopy, mass spectrometry and, in the case of Ia and IIa, 13C-NMR spectroscopy. In the BrUra and BrdUrd reaction systems, described above, dehalogenation reactions accounted for a major portion of the products. The yields of ring opened products, determined at pH 10, ranged from a high of 10.3% in the BrUra-ethylamine system to a low of 1.7% in the MeBrUra-methylamine system.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- M D Shetlar
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143
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38
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Katouzian-Safadi M, Blazy B, Charlier M. Photochemical cross-linking of the cyclic adenosine 3',5' monophosphate receptor protein to Escherichia coli 5-bromouracil-substituted DNA. Role of the effectors. Photochem Photobiol 1991; 53:611-6. [PMID: 1652772 DOI: 10.1111/j.1751-1097.1991.tb08487.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic AMP receptor protein (CRP) is a regulatory protein implicated in the transcription of several operons in Escherichia coli. Its activity is modulated by effectors, such as cAMP or cGMP, which could induce (or not) structural changes in the protein, and activate (or not) the transcription. CRP can bind non-specifically to DNA, and we investigated the photocross-linking of the protein to E. coli 5-bromouracil-substituted DNA, in the absence and in the presence of effectors. The photochemistry of the protein alone, under the conditions used for the cross-linking reaction, was studied. We show that tryptophyl residues are more photoreactive than tyrosyl ones. Photocross-linking of the protein implicates only one of the two subunits, and the rate of the reaction is not modified upon cAMP binding. Binding of cGMP reduces the rate of photocross-linking by a factor of two. These new results show that the protein in the CRP-cGMP complex behaves differently from the free protein.
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39
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KATOUZIAN-SAFADI MEHRNAZ, BLAZY BERNADETTE, CHARLIER MICHEL. PHOTOCHEMICAL CROSS-LINKING OF THE CYCLIC ADENOSINE 3', 5'MONOPHOSPHATE RECEPTOR PROTEIN TO Escherichia coli 5-BROMOURACIL-SUBSTITUTED DNA. ROLE OF THE EFFECTORS. Photochem Photobiol 1991. [DOI: 10.1111/j.1751-1097.1991.tb08916.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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41
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Celewicz L. Photochemical coupling of 5-bromo-1,3-dimethyluracil and its 6-alkyl derivatives to 3-methylindole and N alpha-acetyl-L-tryptophan methyl ester. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1989; 3:565-74. [PMID: 2507761 DOI: 10.1016/1011-1344(89)80080-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photochemical reactions between 5-bromo-1,3-dimethyluracils and 3-substituted indoles in acetone solution were studied. Irradiation (lambda greater than 290 nm) of 5-bromo-1,3-dimethyluracil (1) and N alpha-acetyl-L-tryptophan methyl ester (2) yields, in addition to 5-(2-indolyl)uracil (3), a new photoadduct 5-(7-indolyl)uracil (4). 5-Bromo-1,3-dimethyluracils with 6-alkyl substituents irradiated in the presence of 2 give the 5-(2-indolyl)uracil-type photoadducts exclusively.
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Affiliation(s)
- L Celewicz
- Adam Mickiewicz University, Faculty of Chemistry, Poznan, Poland
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42
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Dietz TM, Koch TH. Photochemical reduction of 5-bromouracil by cysteine derivatives and coupling of 5-bromouracil to cystine derivatives. Photochem Photobiol 1989; 49:121-9. [PMID: 2710822 DOI: 10.1111/j.1751-1097.1989.tb04085.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Irradiation of pH 7, aqueous solutions of 5-bromouracil (BU) in the presence of cysteine peptide-like derivatives at 308 nm using a XeCl excimer laser yielded initial formation of only uracil (U) and the corresponding cystine derivative. Continued irradiation yielded an S-uracilylcysteinyl adduct as well as additional U and cystine derivative. Similar irradiation of a solution of BU and a cystine derivative yielded initial formation of U and the S-uracilylcysteinyl adduct. Formation of these products as well as secondary products of uracil photochemistry was observed upon irradiation of the respective solutions with 254 nm light. With 308 nm laser excitation, U-Cys adduct formation and reduction of BU to U are proposed to occur via initial electron transfer from the disulfide of the cystine derivative to triplet BU. The quantum yield of BU destruction with 308 nm excitation in the presence of cystine derivative is 1.1 X 10(-3). Reaction of triplet BU with the cysteine derivative does not yield U-Cys adduct but U and cystine derivative. A possible byproduct of reduction of triplet BU to U by a cysteinyl residue in a protein BU-DNA complex is a sulphenyl bromide which might yield a protein-DNA crosslink via nucleophilic substitution on sulfur by a nucleophilic site in DNA.
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