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Dudley E, Tuytten R, Bond A, Lemière F, Brenton AG, Esmans EL, Newton RP. Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:3075-85. [PMID: 16206154 DOI: 10.1002/rcm.2151] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Many nucleosides and their modified forms have been studied by mass spectrometry elaborating the detailed fragmentation pathways under MS2 and MS(n) conditions. Although the C-nucleoside pseudouridine has been fragmented and studied briefly, usually amongst many other nucleosides, it has not been investigated to the same extent as other nucleosides. In this report a number of different mass spectrometric techniques are applied to obtain a fuller picture of pseudouridine fragmentation. At the same time this study is used to compare different tandem mass spectrometric techniques, including a novel methodology utilising a quadrupole time-of-flight (Q-ToF) instrument for MS(n) analysis comparable with that available with an ion trap mass spectrometer.
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Affiliation(s)
- Edward Dudley
- Biomolecular Analysis Mass Spectrometry (BAMS) Facility, Grove Building, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK.
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Saha M, Kresbach GM, Giese RW, Annan RS, Vouros P. Preparation and mass spectral characterization of pentafluorobenzyl derivatives of alkyl and hydroxyalkyl-nucleobase DNA adducts. BIOMEDICAL & ENVIRONMENTAL MASS SPECTROMETRY 1989; 18:958-72. [PMID: 2620157 DOI: 10.1002/bms.1200181103] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pentafluorobenzyl (PFBz) derivatives of the following nucleobases were prepared: cytosine, 5-methylcytosine, O2-methylcytosine, O2-ethylthymine, O4-ethylthymine, 5-hydroxymethyluracil, N6-methyladenine, O6-methylguanine, O6-hydroxyethylguanine and O6-hydroxyethylpurine. 13C nuclear magnetic resonance was diagnostic for O- versus N-attachment of the PFBz moiety: the resonance of the methylene carbon appeared in the range 29.15-42.13 ppm for NCH2C6F5, and 58.45-69.01 for OCH2C6F5. Considerable structural information was provided by mass spectrometry with ionization by electron impact. All of the derivatives were detected with high sensitivity and specificity by gas chromatography with detection by electron capture negative ion mass spectrometry, reflecting not only their chemical and physical stability, but also their strong tendency to form a structurally diagnostic anion, [M - PFBz]-, in high yield under these ionization conditions. PFBz derivatives are therefore attractive forms of alkyl-substituted nucleobases for analysis by mass spectrometry.
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Affiliation(s)
- M Saha
- Department of Medicinal Chemistry, Northeastern University, Boston, Massachusetts
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Schubert EM, Schram KH, Glennon RA. Mass spectrometry of modified nucleic acid bases and nucleosides. 2. Class II mesoionic nucleosides and bases derived from thiazolo[3,2-a]pyrimidine-5,7-diones. J Heterocycl Chem 1985. [DOI: 10.1002/jhet.5570220357] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Michie PD, Johnson BM. Competitive electron impact induced methylene imine elimination from methyl- and dimethylaminoN-heterocycles. 1—substituted melamines. ACTA ACUST UNITED AC 1983. [DOI: 10.1002/oms.1210180505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Liehr JG, Weise CL, Wise DS, Townsend LB, Crain PF, Milne G, Mccloskey JA. Mass spectrometry of nucleoside derivatives. Seleno analogs of purine and pyrimidine bases and nucleosides. J Heterocycl Chem 1979. [DOI: 10.1002/jhet.5570160634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cory HT, Yamaizumi K, Smith DL, Knowles DR, Broom AD, Mccloskey JA. Characterization of blocked nucleosides by mass spectrometry. Benzyl derivatives. J Heterocycl Chem 1979. [DOI: 10.1002/jhet.5570160336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Lawrence F, Richou M, Vedel M, Farrugia G, Blanchard P, Robert-Gero M. Identification of some metabolic products of 5' -deoxy-5' -S-isobutylthioadenosine, an inhibitor of virus-induced cell transformation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 87:257-63. [PMID: 208841 DOI: 10.1111/j.1432-1033.1978.tb12374.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
5' -Deoxy-5' -S-isobutylthioadenosine (iBuS)5' Ado has been shown to be rapidly degraded to 5-deoxy-5-S-isobutylthioribose and adenine in procaryotes. In chick embryo fibroblasts there are two metabolic pathways for (iBuS)5' Ado degradation: (a) oxidative deamination into 5' -deoxy-5'-S-isobutylthioinosine (the main product) and (b) hydrolysis into 5-deoxy-5-S-isobutylthioribose plus adenine. The latter reaction is not due to bacterial contamination, since the same results were obtained under sterile conditions and in chick embryo fibroblasts in culture. The inhibition of the virus-induced cell transformation reported by us previously was due to (iBuS)5' Ado rather than to the main metabolic product of this molecule in chick embryo fibroblasts.
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Jeffrey AM, Blobstein SH, Weinstein IB, Beland FA, Harvey RG, Kasai H, Nakanishi K. Structure of 7,12-dimethylbenz(a)anthracene-guanosine adducts. Proc Natl Acad Sci U S A 1976; 73:2311-5. [PMID: 821053 PMCID: PMC430543 DOI: 10.1073/pnas.73.7.2311] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Arene oxides have been proposed as the reactive intermediates in the process of carcinogenesis induced by polycyclic aromatic hydrocarbons. The present study defines the structures of four guanosine adducts formed by the reaction of 7,12-dimethylbenz[a]anthracene-5,6-oxide with polyguanylic acid. The modified polymer was hydrolyzed to nucleotides and the hydrophobic guanosine adducts separated from unmodified guanosine by LH-20 column chromatograhy. The adducts were further resolved into four components (I-IV) by reverse phase high pressure liquid chromatography. Analysis of the ultraviolet, circular dichroism, mass, and proton magnetic resonance spectra of these compounds, or their acetate and free base derivatives, indicates that in all four compounds the aromatic hydrocarbon is present on the 2 amino group of guanine. Compounds I and IV, and II and III constitute diastereoisomeric pairs, respectively. In the I and IV pair, the adducts result from addition at the 6 position of the original dimethylbenz[a]anthracene oxide, whereas in the II and III pair, the addition occurs at the 5 position. Indirect evidence suggests that trans opening of the oxide occurred in all cases but this remains to be established.
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Kasai H, Oashi Z, Harada F, Nishimura S, Oppenheimer NJ, Crain PF, Liehr JG, von Minden DL, McCloskey JA. Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine. Biochemistry 1975; 14:4198-208. [PMID: 1101947 DOI: 10.1021/bi00690a008] [Citation(s) in RCA: 161] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The structure of the unknown modified nucleoside Q, which is present in the first position of the anticodons of Escherichia coli tRNA Tyr, tRNA His, tRNA Asn, tRNA Asp, is proposed to be 7-(4,5-cis-dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine (1). The structure of Q was deduced by means of its uv absorption, mass spectrometry, proton magnetic resonance spectroscopy, and studies of its chemical reactivity. The structure of Q is unique since it is a derivative of 7-deazaguanosine having cyclopentenediol in the side chain at the C-7 position. This is the first example of purine skeleton modification in a nucleoside from tRNA.
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Liehr JG, von Minden DL, Hattox SE, McCloskey JA. Characterization of cytosine nucleosides by mass spectrometry. BIOMEDICAL MASS SPECTROMETRY 1974; 1:281-5. [PMID: 4441623 DOI: 10.1002/bms.1200010413] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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12
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Ohashi Z, Maeda M, McCloskey JA, Nishimura S. 3-(3-Amino-3-carboxypropyl)uridine: a novel modified nucleoside isolated from Escherichia coli phenylalanine transfer ribonucleic acid. Biochemistry 1974; 13:2620-5. [PMID: 4598734 DOI: 10.1021/bi00709a023] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Szczepanik PA. The mass spectra of some 5′-alkul substituted 5′-thioadenosine trimethylsilyl derivatives. ACTA ACUST UNITED AC 1974. [DOI: 10.1002/oms.1210090616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Quilliam MA, Ogilvie KK, Westmore JB. Separation and characterization of isomeric substituted nucleosides by gas chromatography and mass spectrometry. BIOMEDICAL MASS SPECTROMETRY 1974; 1:78-9. [PMID: 4547982 DOI: 10.1002/bms.1200010116] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Wildenauer D, Gross HJ. Methyldeficient mammalian 4s RNA: evidence for L-ethionine-induced inhibition of N6-dimethyladenosine synthesis in rat liver tRNA. Nucleic Acids Res 1974; 1:279-88. [PMID: 4414662 PMCID: PMC343346 DOI: 10.1093/nar/1.2.279] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The nucleotide composition of 4s RNA from livers of rats fed with a diet containing 0.3% D-ethionine was found to be identical with that from untreated animals. In contrast, one single modified nucleotide was absent in 4s RNA from livers of rats fed with a 0.3% L-ethionine diet. The minor nucleo=tide was also absent in liver 4s RNA from rats fed with a 0.3% L-ethionine diet followed by ten days of normal food. It was identified after dephosphorylation by ultraviolet absorption spectra, cochromatography with authentic material and mass spectra as N(6)-dimethyladenosine. It is concluded that S-adenosylethionine, the primary product of L-ethionine in the liver, causes strong and selective inhibition of the specific RNA-methylase responsible for adenosine to N(6)-dimethyl=adenosine methylation in rat liver 4s RNA. Compared to the strong inhibition of N(6)-dimethyladenosine formation described here, L-ethionine-dependent ethylation of liver 4s RNA is far less efficient. The quantitation of l-methyladenosine, ribothymidine and 3'-terminal adenosine in this 4s RNA as well as its aminoacid acceptor activity is typical for tRNA; hence it may be concluded that N(6)-dimethyladenosine is a component of rat liver tRNA. This may demonstrate the first evidence for the existence of specifically methyl-deficient mammalian tRNA. A possible correlation between the activity of L-ethionine as a liver carcinogen and its ability to induce the formation of methyl-deficient tRNA by selectively inhibiting the synthesis of N(6)-dimethyladenosine on the tRNA level in the same organ is discussed.
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Parker RB, Simmonds HA, Jones AS, Snedden W. The use of high resolution mass spectrometry to study purine metabolism in pigs. Biochem Pharmacol 1973; 22:2869-74. [PMID: 4761556 DOI: 10.1016/0006-2952(73)90153-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Von Minden DL, Stillwell RN, Koenig WA, Lyman KJ, McCloskey JA. Mass spectrometry of 7-methylpurine nucleosides: studies of a characteristic oxygen incorporation reaction that occurs during trimethylsilylation. Anal Biochem 1972; 50:110-21. [PMID: 5080722 DOI: 10.1016/0003-2697(72)90491-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Westmore JB, Lin DCK, Ogilvie KK, Wayborn H, Berestiansky J. The study and characterization of nucleosides by mass spectrometry—I: The mass spectra of pyrimidine 2,2′-anhydronucleosides and their derivatives. ACTA ACUST UNITED AC 1972. [DOI: 10.1002/oms.1210061110] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hecht SM, McDonald JJ. Mass spectra of some 6-substituted ureidopurines and N 6 -acyladenines. Anal Biochem 1972; 47:157-73. [PMID: 5031108 DOI: 10.1016/0003-2697(72)90289-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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König WA, Zech K, Uhmann R, Voelter W. [Mass spectrometry of adenosine analogues]. CHEMISCHE BERICHTE 1972; 105:262-72. [PMID: 4646249 DOI: 10.1002/cber.19721050128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Koenig WA, Smith LC, Crain PF, McCloskey JA. Mass spectrometry of trifluoroacetyl derivatives of nucleosides and hydrolysates of deoxyribonucleic acid. Biochemistry 1971; 10:3968-79. [PMID: 4334285 DOI: 10.1021/bi00797a026] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Wilson MS, Dzidic I, McCloskey JA. Chemical ionization mass spectrometry of nucleosides. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 240:623-6. [PMID: 5315932 DOI: 10.1016/0005-2787(71)90722-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Howlett HA, Johnson MW, Trim AR, Eagles J, Self R. Mass spectral analysis of modified ribonucleosides obtained by degradation of 14 alkali-stable dinucleotides isolated from yeast ribonucleic acid. Anal Biochem 1971; 39:429-40. [PMID: 5555471 DOI: 10.1016/0003-2697(71)90433-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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