Mass spectra of nucleoside components of tRNA

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

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.

Preparation and mass spectral characterization of pentafluorobenzyl derivatives of alkyl and hydroxyalkyl-nucleobase DNA adducts

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.

Identification of some metabolic products of 5' -deoxy-5' -S-isobutylthioadenosine, an inhibitor of virus-induced cell transformation

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.

Structure of 7,12-dimethylbenz(a)anthracene-guanosine adducts

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.

Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine

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.

Methyldeficient mammalian 4s RNA: evidence for L-ethionine-induced inhibition of N6-dimethyladenosine synthesis in rat liver tRNA

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.