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Abstract
Genome integrity is constantly challenged by endogenous or exogenous genotoxic agents, which can give rise to various DNA adducts. After metabolic activation, tobacco-specific nitrosamines N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) can lead to pyridyloxobutylphosphotriesters (POB-PTEs) in DNA. Here, we synthesized oligodeoxyribonucleotides containing a site-specifically inserted SP- or RP-POB-PTE flanked by two thymidines, and we examined the impact that these lesions have on DNA replication in Escherichia coli cells. We found that these two lesions are not strong impediments to DNA replication, and their replicative bypass is not modulated by genetic depletion of the three SOS-induced DNA polymerases or Ada protein. In addition, neither SP- nor RP-POB-PTEs was mutagenic in E. coli cells. Together, our study unveiled, for the first time, the influence of tobacco-specific nitrosamine-induced POB-PTE lesions on DNA replication in vivo.
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Taoka M, Yamauchi Y, Nobe Y, Masaki S, Nakayama H, Ishikawa H, Takahashi N, Isobe T. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes. Nucleic Acids Res 2010; 37:e140. [PMID: 19740761 PMCID: PMC2790879 DOI: 10.1093/nar/gkp732] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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Zhou C, Pathmasiri W, Honcharenko D, Chatterjee S, Barman J, Chattopadhyaya J. High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions. CAN J CHEM 2007. [DOI: 10.1139/v07-025] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During the F–-promoted deprotection of the oligo–RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is formed as a by-product. The TVS formed has been shown to react with the exocyclic amino functions of adenosine (A), guanosine (G), and cytidine (C) of the fully deprotected oligo–RNA to give undesirable adducts, which are then purified by HPLC and unambiguously characterized by 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) NMR and mass spectroscopic analysis. The relative nucleophilic reactivities of the nucleobases toward TVS have been found to be the following: N6–A > N4–C > N2–G > > N3–U. This reactivity of TVS toward RNA nucleobases to give various Michael adducts could, however, be suppressed by using various amines as scavengers. Among all these amines, morpholine and piperidine are the most efficient scavenger for TVS, which gave highly pure oligo–RNA even in the crude form and can be used directly in RNA chemical biology studies.Key words: RNA synthesis, RNA alkylation, p-tolyl vinyl sulphone, Michael addition.
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Reactivity of lithium trimethylsilyldiazomethane and diazomethane toward the 5,6-double bond of uracil and uridine derivatives. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)00402-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hedayatullah M, Roger A. Synthèse de pyrimidines et purines adamantylées par alkylation régiosélective directe, en catalyse par transfert de phase. J Heterocycl Chem 1989. [DOI: 10.1002/jhet.5570260434] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Arendes J, Zahn RK, Müller WE. Size determination of poly(A) after in vitro methylation with radioactive dimethyl sulfate. Anal Biochem 1980; 101:488-93. [PMID: 7362044 DOI: 10.1016/0003-2697(80)90218-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Engel J, von Hippel P. Effects of methylation on the stability of nucleic acid conformations. Studies at the polymer level. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38193-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Gaubatz J, Cutler RG. Hybridization of ribosomal RNA labeled to high specific radioactivity with dimethyl sulfate. Biochemistry 1975; 14:760-5. [PMID: 1115771 DOI: 10.1021/bi00675a018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RNA radioactively methylated with dimethyl sulfate has the advantage of relatively low background noise level when utilized in DNA saturation hybridization employing the membrane filter technique. In addition, the RNA can be methylated with either 3H- or 14C-labeled methyl groups. However, the low specific radioactivity usually obtained with dimethyl sulfate has limited the use of this labeling technique. We describe a detailed characterization of the methylation of rRNA with dimethyl sulfate giving specific radioactivities on the order 10-5 cpm/mug. Kinetics and optimum conditions for the methylation reaction of rRNA were studied. The methylation did not cause excessive degradation of RNA in neutral aqueous solution, and the methyl derivative of RNA was stable under normal hybridization conditions. Specific radioactivitiy of the methylated RNA was found to be a linear function of the product of RNA concentration and specific radioactivity of the dimethyl sulfate in the reaction mixture at a constant incubation time. The methylated bases of the RNA lowered the thermal stability of the DNA-RNA hybrids by 1 degree in Tm per 1.6 per cent methylated RNA bases. rRNA gene dosage values using high specific radioactive methylated RNA were found to be 81 and 180 genes/haploid genome, respectively. Dissociation constants of the hybridization reaction ranged from 0.90 times 10-10 to 2.37 times 10-10 M.
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Powers DM, Holley RW. Selective chemical methylation of yeast alanine transfer RNA. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 287:456-64. [PMID: 4345028 DOI: 10.1016/0005-2787(72)90289-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Bannon P, Verly W. Alkylation of phosphates and stability of phosphate triesters in DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 31:103-11. [PMID: 4344908 DOI: 10.1111/j.1432-1033.1972.tb02506.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Rhaese HJ, Freese E. Chemical analysis of DNA alterations. IV. Reactions of oligodeoxynucleotides with monofunctional alkylating agents leading to backbone breakage. BIOCHIMICA ET BIOPHYSICA ACTA 1969; 190:418-33. [PMID: 5351277 DOI: 10.1016/0005-2787(69)90091-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Leng M, Pochon F, Michelson A. Photochimie des polynucléotides II. Étude de la luminescence à température ordinaire de mononucléotides et dinucléotides. ACTA ACUST UNITED AC 1968. [DOI: 10.1016/0005-2787(68)90042-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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The isolation, analysis and chemical reactions of deoxyribonucleic acid [DNA]—III. The chemical reactions of DNA. Eur Polym J 1968. [DOI: 10.1016/0014-3057(68)90006-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pochon F, Michelson AM. Polynucleotides. IX. Methylation of nucleic acids, homopolynucleotides and complexes. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 149:99-106. [PMID: 5625710 DOI: 10.1016/0005-2787(67)90694-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Smith KD, Armstrong JL, McCarthy BJ. The introduction of radioisotopes into RNA by methylation in vitro. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 142:323-30. [PMID: 4861434 DOI: 10.1016/0005-2787(67)90615-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Griffin BE, Haines JA, Reese CB. The methylation of adenylyl-(3'-5')-uridine and uridylyl-(3'-5')-adenosine with diazomethane. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 142:536-8. [PMID: 6054275 DOI: 10.1016/0005-2787(67)90634-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Brimacombe RL. The secondary structure of N-methylated derivatives of polycytidylic acid. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 142:24-34. [PMID: 6048842 DOI: 10.1016/0005-2787(67)90512-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Ludlum DB. Reaction of nitrogen mustard with synthetic polynucleotides. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 142:282-4. [PMID: 6048846 DOI: 10.1016/0005-2787(67)90540-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Follmann H, Wieker HJ, Witzel H. [On the mechanism of the ribonuclease reaction. 2. The pre-ordering in the substrate as the accelerating factor in cinucleoside phosphates and analagous compounds]. EUROPEAN JOURNAL OF BIOCHEMISTRY 1967; 1:243-250. [PMID: 6061957 DOI: 10.1111/j.1432-1033.1967.tb00068.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Holy A, Scheit KH. On the methylation of dinucleoside phosphates with diazomethane. BIOCHIMICA ET BIOPHYSICA ACTA 1966; 123:430-1. [PMID: 5967259 DOI: 10.1016/0005-2787(66)90298-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Lawley PD. Effects of some chemical mutagens and carcinogens on nucleic acids. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1966; 5:89-131. [PMID: 5337700 DOI: 10.1016/s0079-6603(08)60232-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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