Mass spectrometry of 7-methylpurine nucleosides: studies of a characteristic oxygen incorporation reaction that occurs during trimethylsilylation

Artifacts in trimethylsilyl derivatization reactions and ways to avoid them

Trimethylsilyl derivatives are routinely employed in gas chromatography to increase the volatility and stability of organic compounds containing active hydrogens. Normally only the desired derivative is formed when organic compounds are derivatized with common silylation reagents. However, some compounds form additional unexpected derivatives or by-products (artifacts). Artifact formation leads to multiple peaks for the same compound or unexpected components in the gas chromatographic analysis of mixtures. This review includes silylation artifacts identified in our laboratory by mass spectrometry during the last 20 years and references to those found in the literature. Also, means of avoiding artifact formation are discussed in detail.

Urinary nucleosides

The methods of analysis, origins, and clinical significance of urinary nucleosides are reviewed through 1997. Structures, chromatographic and mass spectral data and references to the clinical literature are presented for each of the 57 nucleosides currently identified in normal and pathogenic human urine samples. Data from the HPLC separation and GC/MS analysis of 37 individual HPLC fractions are presented and discussed. Methods, including sample preparation techniques, used for the analysis of urinary nucleosides including GC, HPLC, GC/MS, HPLC/MS and immunoassays are compared and the advantages and limitations of each method described. The conclusion is drawn that the urinary nucleosides do serve as biomarkers of cancer and other diseases, but analytical methods need further improvement if clinical decisions are to be made based on the levels of nucleosides in human urine.

Structure determination of a new fluorescent tricyclic nucleoside from archaebacterial tRNA

A highly fluorescent nucleoside was detected in enzymatic digests of the extremely thermophilic archaebacterium Sulfolobus solfataricus by combined liquid chromatography-mass spectrometry (LC/MS). Following isolation, the structure was determined primarily by mass spectrometry, to be 3-(beta-D-ribofuranosyl)-4,9-dihydro-4,6,7-trimethyl-9-oxoimidazo[ 1, 2-a]purine (mimG), a new derivative of the Y (wye) nucleoside. The structural assignment was verified by comparison of the base released by acid hydrolysis with the corresponding synthetic base, using mass spectrometry, chromatography, and UV absorption and fluorescence properties. Nucleoside mimG was also detected by LC/MS in hydrolysates of the thermophiles Thermoproteus neutrophilus and Pyrodictium occultum. These results constitute the first finding of a member of the hypermodified Y family of nucleosides in archaebacteria.

Replacement of aromatic fluorine by a methoxy group during reaction with methyl iodide in N,N-dimethylformamide solvent

The DNA base uracil was derivatized with pentafluorobenzoyl chloride, followed by methylation with methyl iodide in the presence of N,N-dimethylformamide (DMF). In addition to a 3-pentafluorobenzoyl-1-methyl derivative of uracil, GC/MS analysis of the reaction mixture revealed the formation of an unusual product, whose molecular weight was 12 U higher than that of the prior derivative. This unexpected product has been identified as the 3-(para-methoxytetrafluorobenzoyl)-1-methyl derivative of uracil. Isotopic labeling and related experiments have revealed that the DMF solvent contributes the oxygen atom of the methoxy group that replaces the para fluorine atom. This work allowed a single derivative to be obtained for the methylation reaction by changing the solvent to acetonitrile.

Identification of nucleosides in hydrolysates of transfer RNA by high-resolution mass spectrometry

High-resolution mass spectrometry has been investigated as a technique for identification of modified nucleosides in unfractionated hydrolysates of transfer RNA. The method is based on recognition of predetermined sets of exact mass values which are characteristic of individual nucleoside components. Mass spectra are photographically recorded in a non-time-resolved fashion, so that differing rates of nucleoside vaporization are of no consequence. Experimental parameters of sensitivity, spectrometer resolution and rates of vaporization were studied. Under typical conditions, 1-4 micrograms of tRNA are hydrolyzed, converted to volatile trimethylsilyl derivatives, and mass spectra of the resulting mixture recorded during 3 min at resolution 20 000; 75-100% of the minor nucleosides are usually identified in a single recording. The method is complementary to conventional methods of identification which rely on chromatographic mobilities, and can in principle be generally applied to recognition of biologically or chemically modified bases in nucleic acid.

The effects of heating rate and sample size on the direct exposure/chemical ionization mass spectra of some biological conjugates

A direct exposure probe has been used to obtain mass spectra of underivatized guanosine, deoxyguanosine, sucrose and the p-nitrophenyl-beta-D-glucuronide. In all cases, a protonated molecular ion is produced with good relative abundance. The effects of heating rate and sample size on the production of the [MH]+ ION ARE EXAMINED IN DETAIL FROM TOTAL ION ANd single ion currents produced during rapid, repetitive scanning of the spectra after probe insertion. From this data we conclude that protonated molecular ions are produced as a result of the enhanced volatility of neutral molecules on the probe surface, followed by chemical ionization, and not by surface ionization.

Characterization of N6, O2-dimethyladenosine from nuclear RNA of Novikoff hepatoma

A modified nucleoside was isolated from low molecular weight nuclear RNA of Novikoff hepatoma, the nucleotide sequence of which was reported earlier. The structure of this novel nucleoside was shown to be N6, O2'-dimethyladenosine (m6Am) by mass spectrometry of its trimethylsilyl derivative and by comparison with the mass spectra of N6- and O-2' monmethyl model compounds. The complete characterization was carried out using 0.04 A260 units (2 microgram) of m6Am.