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Feng H, Lu XJ, Maji S, Liu L, Ustianenko D, Rudnick ND, Zhang C. Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes. Nat Commun 2024; 15:2279. [PMID: 38480694 PMCID: PMC10937933 DOI: 10.1038/s41467-024-46429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
UV-crosslinking of protein and RNA in direct contacts has been widely used to study protein-RNA complexes while our understanding of the photo-crosslinking mechanisms remains poor. This knowledge gap is due to the challenge of precisely mapping the crosslink sites in protein and RNA simultaneously in their native sequence and structural contexts. Here we systematically analyze protein-RNA interactions and photo-crosslinking by bridging crosslinked nucleotides and amino acids mapped using different assays with protein-RNA complex structures. We developed a computational method PxR3D-map which reliably predicts crosslink sites using structural information characterizing protein-RNA interaction interfaces. Analysis of the informative features revealed that photo-crosslinking is facilitated by base stacking with not only aromatic residues, but also dipeptide bonds that involve glycine, and distinct mechanisms are utilized by different RNA-binding domains. Our work suggests protein-RNA photo-crosslinking is highly selective in the cellular environment, which can guide data interpretation and further technology development for UV-crosslinking-based assays.
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Affiliation(s)
- Huijuan Feng
- Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Suvrajit Maji
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Linxi Liu
- Department of Statistics, Columbia University, New York, NY, 10027, USA
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA
| | - Noam D Rudnick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, 10032, USA.
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Brief Funct Genomics 2019; 17:96-103. [PMID: 29126220 DOI: 10.1093/bfgp/elx038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine antisense oligonucleotide hybridization with enrichment of RNA from cross-linked chromatin extracts. These techniques have provided insight into lncRNA localization and the interactions of lncRNAs with protein to better understand biological roles of lncRNAs. Here, we review the core principles of hybridization capture methods, focusing on the three most commonly used protocols: capture hybridization analysis of RNA targets (CHART), chromatin isolation by RNA purification (ChIRP) and RNA affinity purification (RAP). We highlight the general principles of these techniques and discuss how differences in experimental procedures present distinct challenges to help researchers using these protocols or, more generally, interpreting the results of hybridization capture experiments.
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A novel combined RNA-protein interaction analysis distinguishes HIV-1 Gag protein binding sites from structural change in the viral RNA leader. Sci Rep 2015; 5:14369. [PMID: 26449409 PMCID: PMC4598872 DOI: 10.1038/srep14369] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/20/2015] [Indexed: 01/26/2023] Open
Abstract
RNA-protein interactions govern many viral and host cell processes. Conventional 'footprinting' to examine RNA-protein complex formation often cannot distinguish between sites of RNA-protein interaction and sites of RNA structural remodelling. We have developed a novel technique combining photo crosslinking with RNA 2' hydroxyl reactivity ('SHAPE') that achieves rapid and hitherto unachievable resolution of both RNA structural changes and the sites of protein interaction within an RNA-protein complex. 'XL-SHAPE' was validated using well-characterized viral RNA-protein interactions: HIV-1 Tat/TAR and bacteriophage MS2 RNA/Coat Binding Protein. It was then used to map HIV-1 Gag protein interactions on 2D and 3D models of the viral RNA leader. Distinct Gag binding sites were identified on exposed RNA surfaces corresponding to regions identified by mutagenesis as important for genome packaging. This widely applicable technique has revealed a first view of the stoichiometry and structure of the initial complex formed when HIV captures its genome.
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Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RHJ, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods 2015; 89:138-48. [PMID: 26071038 DOI: 10.1016/j.ymeth.2015.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/19/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleoprotein (RNP) complexes play important roles in the cell by mediating basic cellular processes, including gene expression and its regulation. Understanding the molecular details of these processes requires the identification and characterization of protein-RNA interactions. Over the years various approaches have been used to investigate these interactions, including computational analyses to look for RNA binding domains, gel-shift mobility assays on recombinant and mutant proteins as well as co-crystallization and NMR studies for structure elucidation. Here we report a more specialized and direct approach using UV-induced cross-linking coupled with mass spectrometry. This approach permits the identification of cross-linked peptides and RNA moieties and can also pin-point exact RNA contact sites within the protein. The power of this method is illustrated by the application to different single- and multi-subunit RNP complexes belonging to the prokaryotic adaptive immune system, CRISPR-Cas (CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated). In particular, we identified the RNA-binding sites within three Cas7 protein homologs and mapped the cross-linking results to reveal structurally conserved Cas7 - RNA binding interfaces. These results demonstrate the strong potential of UV-induced cross-linking coupled with mass spectrometry analysis to identify RNA interaction sites on the RNA binding proteins.
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Affiliation(s)
- Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ajla Hrle
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Katharina Kramer
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Timo Sachsenberg
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Elena Conti
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
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Shetlar MD, Chung J. Ring-opening photoreactions of 5-methylcytosine with 3-mercaptopropionic acid and other thiols. Photochem Photobiol 2013; 89:878-83. [PMID: 23410521 DOI: 10.1111/php.12058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/11/2013] [Indexed: 11/30/2022]
Abstract
The photoproducts from reaction of thymine with cysteine, an amino acid containing a sulfhydryl group, have been studied in detail, whereas results of less extensive studies have been reported for the uracil-cysteine system. However, products arising from corresponding reactions of cytosine and related compounds with compounds containing a sulfhydryl group have not been similarly studied. We report here the results of our study of the photoreaction of 5-methylcytosine (5MeCyt), a minor base occurring in mammalian DNA, with 3-mercaptopropionic acid (3MP), a model compound for cysteine. We found that this reaction proceeds at pH 7 to yield N-(N'-(2'-carboxyethyl)thiocarbamoyl)-3-amino-2-methylacrylamidine (Ia) as a primary photoproduct. A secondary thermal product, identified as 3-(2'-carboxyethylthio)-2-methylacrylamidine (IIa), appears if photoreacted solution is allowed to stand for appreciable times prior to workup; this latter compound is formed via an intermediate product. Heating of purified Ia at 100°C or standing at lower temperatures produces 3-amino-2-methylacrylamidine (IId); similarly, irradiation of Ia with UVB light in aqueous solution converts it into IId. Results from exploratory studies suggest that 5MeCyt similarly reacts with other thiols (2-mercaptoethanol, 2-mercaptoacetic acid) to form analogs of Ia and IIa. Other preliminary results suggest that 5-methyl-2'-deoxycytidine and 1,5-dimethylcytosine photoreact with 3MP to form compounds similar to Ia.
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Affiliation(s)
- Martin D Shetlar
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
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Shetlar MD, Chung J, Hom K. Photoinduced ring opening reactions and subsequent thermal ring closure reactions in the thymine–ammonia system and related systems. Photochem Photobiol Sci 2010; 9:1228-43. [PMID: 20714675 DOI: 10.1039/c0pp00144a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Martin D Shetlar
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143-0446, USA.
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Hom K, Strahan G, Shetlar MD. Ring Opening Photoreactions of Cytosine and Uracil with Ethylamine. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0710243ropoca2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
The photochemical reactions of cytosine (Cyt) and uracil (Ura) with ethylamine, an analog of the side chain of the amino acid lysine, have been studied. After irradiation of Cyt in aqueous ethylamine at lambda = 254 nm, N-(N'-ethylcarbamoyl)-3-aminoacrylamidine (Ia) and N-(N'-ethylcarbamoyl)-3-ethylaminoacrylamidine (Ib) were isolated as products, while irradiation of Ura gave N-(N'-ethylcarbamoyl)-3-aminoacrylamide (IIa) and N-(N'-ethylcarbamoyl)-3-ethylaminoacrylamide (IIb) as products. Studies in which Ia and IIa were incubated with ethylamine at various pH values indicate that Ib and IIb are secondary products produced via thermal reactions of Ia and IIa with ethylamine. Heating of Ia and Ib leads to ring closure with the resultant formation of 1-ethylcytosine; small amounts of 1-ethyluracil are also produced. Heating of IIa and IIb produces 1-ethyluracil as the sole product. Spectroscopic properties were determined for each of these opened ring products, as well as for N-(N'-ethylcarbamoyl)-3-amino-2-methylacrylamidine (III) and N-(N'-ethylcarbamoyl)-3-amino-2-methylacrylamide (IV). Quantum yield measurements showed that Ia was formed with a phi of 1.6 x 10(-4) at pH 9.8, while phi for formation of IIa was 7.2 x 10(-4) at pH 11.5. A profile of the relative quantum yield for formation of Ia, determined as a function of pH, showed that the maximum quantum yield occurs at around pH 9.5; the analogous profile for IIa shows a maximum quantum yield at pH 11.3 and above. Acetone sensitization does not produce Ia in the Cyt-ethylamine system, which indicates that the known triplet state of Cyt is not involved in reactions leading to this opened ring product.
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Affiliation(s)
- K Hom
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, 994143-0446, USA
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11
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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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Islam N, Ali R. Formation of thymine-lysine and cytosine-lysine adducts in DNA-lysine photoconjugate. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1995; 27:109-15. [PMID: 7714671 DOI: 10.1016/1011-1344(94)07062-s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Lysine was covalently conjugated to calf thymus DNA by irradiation with UV light (wavelength, 253.7 nm). The results showed monofunctional covalent photobinding of lysine molecules with bases in DNA. Only the epsilon-amino group of lysine participated in the photoconjugation reaction. Thymine and cytosine were modified by 60% and 25% respectively. The kinetics of the DNA-lysine photoreaction showed that one lysine molecule was in the photobound state per 10, 6, 5 and 4 nucleotide base pairs of DNA on irradiation for 20, 30 40 and 60 min respectively.
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Affiliation(s)
- N Islam
- Department of Biochemistry, Faculty of Medicine, A.M.U., Aligarh, India
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Kubasek WL, Spann D, Hockensmith JW. Laser cross-linking of proteins to nucleic acids: photodegradation and alternative photoproducts of the bacteriophage T4 gene 32 protein. Photochem Photobiol 1993; 58:1-10. [PMID: 8378427 DOI: 10.1111/j.1751-1097.1993.tb04895.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Pulsed laser cross-linking provides a means of introducing a covalent bond between proteins and the nucleic acids to which they are bound. This rapid cross-linking effectively traps the equilibrium that exists at the moment of irradiation and thus allows examination of the protein-nucleic acid interactions that existed. Laser irradiation may also induce photodestruction of protein and we have used the bacteriophage T4 gene 32 protein to investigate this phenomenon. Our results show that both nonspecific and specific photoproducts can occur, specifically at wavelengths where the peptide backbone of proteins is known to absorb. These results demonstrate that nonspecific photodegradation can be correlated with the formation of a specific photodegradation product. The formation of this product was monitored to show that product yield is nonlinearly dependent on laser power and wavelength. We have also investigated an unexpected photoproduct whose formation is dependent on the length of the polynucleotide to which the gene 32 protein binds and that further demonstrates the complexities of analyzing protein-nucleic acid interactions through the use of UV laser cross-linking. These data provide essential information for the establishment of appropriate conditions for future studies that use UV cross-linking of protein-nucleic acid complexes.
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Affiliation(s)
- W L Kubasek
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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Hockensmith J, Kubasek W, Vorachek W, von Hippel P. Laser cross-linking of proteins to nucleic acids. I. Examining physical parameters of protein-nucleic acid complexes. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)82314-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Hockensmith JW, Kubasek WL, Vorachek WR, Evertsz EM, von Hippel PH. Laser cross-linking of protein-nucleic acid complexes. Methods Enzymol 1991; 208:211-36. [PMID: 1779835 DOI: 10.1016/0076-6879(91)08015-a] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Budowsky EI, Abdurashidova GG. Polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:1-65. [PMID: 2475887 DOI: 10.1016/s0079-6603(08)60694-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Dorwin EL, Shaw AA, Hom K, Bethel P, Sheltar MD. Photoexchange products of cytosine and 5-methylcytosine with N alpha-acetyl-L-lysine and L-lysine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1988; 2:265-78. [PMID: 3149993 DOI: 10.1016/1011-1344(88)80009-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The photoinduced exchange reactions of cytosine (Ia) and 5-methylcytosine (IIa) with N alpha-acetyl-L-lysine, a derivative of the common amino acid L-lysine, were studied. These reactions of Ia and IIa at pH 7.5 produce, respectively, 2-N-acetylamino-6-(1-cytosinyl)hexanoic acid (Ib) and 2-N-acetylamino-6-(1-(5-methylcytosinyl]hexanoic acid (IIb) as major final products. In addition, small amounts of the corresponding deamination products were formed in the 5-methylcytosine-N alpha-acetyl-L-lysine and cytosine-N alpha-acetyl-L-lysine systems, namely 2-N-acetylamino-6-(1-thyminyl)-hexanoic acid and 2-N-acetylamino-6-(1-uracilyl)hexanoic acid. The compounds Ib and IIb were deacetylated by acid hydrolysis to yield the corresponding lysine products: 2-amino-6-(1-cytosinyl)hexanoic acid (Ic) and 2-amino-6-(1-(5-methylcytosinyl]hexanoic acid (IIc). The compound Ic was identified as a product in the photoreaction of cytosine with L-lysine at near neutral pH, while IIc is found as a product in the corresponding reaction of 5-methylcytosine. The occurrence of the above photoexchange reactions at pH values near those found in physiological systems could have biological implications; in particular, our observations suggest that cytosine and 5-methylcytosine residues, contained in DNA, might react with the epsilon-amino groups of lysine residues in proteins upon UV irradiation of nucleosomes and other DNA-protein complexes under physiological conditions.
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Affiliation(s)
- E L Dorwin
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143
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Shetlar MD, Hom K, Distefano S, Ekpenyong K, Yang J. Photochemical reactions of cytosine and 5-methylcytosine with methylamine and n-butylamine. Photochem Photobiol 1988; 47:779-86. [PMID: 3217431 DOI: 10.1111/j.1751-1097.1988.tb01659.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Hockensmith JW, Kubasek WL, Vorachek WR, von Hippel PH. Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35677-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Peak MJ, Peak JG, Jones CA. Different (direct and indirect) mechanisms for the induction of DNA-protein crosslinks in human cells by far- and near-ultraviolet radiations (290 and 405 nm). Photochem Photobiol 1985; 42:141-6. [PMID: 4048296 DOI: 10.1111/j.1751-1097.1985.tb01552.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Cadet J, Voituriez L, Grand A, Hruska FE, Vigny P, Kan LS. Recent aspects of the photochemistry of nucleic acids and related model compounds. Biochimie 1985; 67:277-92. [PMID: 3929843 DOI: 10.1016/s0300-9084(85)80070-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This survey focuses on recent developments in the far ultraviolet photochemistry of nucleic acids and related model compounds. The photoproducts discussed are the cyclobutidipyrimidines, the pyrimidine-pyrimidone adducts, the purine-pyrimidine adducts and the addition products of amino acids to pyrimidine bases. The specific aspects of the high-intensity laser photochemistry of nucleic acid components are also briefly reviewed.
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Shetlar MD, Taylor JA, Hom K. Photochemical exchange reactions of thymine, uracil and their nucleosides with selected amino acids. Photochem Photobiol 1984; 40:299-308. [PMID: 6484001 DOI: 10.1111/j.1751-1097.1984.tb04591.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Shetlar MD, Carbone J, Steady E, Hom K. Photochemical addition of amino acids and peptides to polyuridylic acid. Photochem Photobiol 1984; 39:141-4. [PMID: 6709720 DOI: 10.1111/j.1751-1097.1984.tb03419.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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