Analysis of base composition of RNA and DNA hydrolysates by gas-liquid chromatography

Instrumental analysis of RNA modifications

Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.

Ultrasensitive and simultaneous determination of RNA modified nucleotides by sheathless interfaced capillary electrophoresis-tandem mass spectrometry

A label-free ultrasensitive determination of eight RNA modified nucleotides simultaneously was first established based on a sheathless capillary electrophoresis-tandem mass spectrometry system. This system performed well using only 500 pg-5 ng practical RNA samples, and a downward trend of most target nucleotides in HCT 116 cells was observed with the increase of nickel concentration.

Quantitative gas chromatography mass spectrometric analysis of 2′-deoxyinosine in tissue DNA

Several studies examining DNA deamination have published levels of 2'-deoxyinosine that illustrated a large variation between studies. Most of them are the result of artifactual DNA deamination that occurs during the process of sample preparation, particularly acid hydrolysis. This protocol for measurement of 2'-deoxyinosine describes the use of nuclease P1 and alkaline phosphatase to achieve release of nucleosides from DNA, followed by HPLC prepurification with subsequent gas chromatography-mass spectrometry analysis of the nucleosides. It has been used in the measurement of the levels of 2'-deoxyinosine in DNA of commercial sources and DNA from cells and animal tissues, and gives values ranging from 3 to 7 2'-deoxyinosine per 10(6) 2-deoxyadenosine. This protocol should take approximately 7 days to complete.

Potential artifacts in the measurement of DNA deamination

Attack on DNA by some reactive nitrogen species results in deamination of adenine and guanine, leading to the formation of hypoxanthine and xanthine, respectively. Published levels of these products in cellular DNA have varied widely. Although these two deamination products are often measured by GC-MS analysis, the procedure of acid hydrolysis to release DNA bases for derivatization poses a risk of artifactual deamination of the DNA. In this study, we demonstrated the artifactual formation of these two deamination products during acid hydrolysis and hence developed a method for detecting and measuring 2'-deoxyinosine, the nucleoside of hypoxanthine. Our assay for 2'-deoxyinosine employs nuclease P1 and alkaline phosphatase to achieve release of the nucleosides from DNA, followed by HPLC prepurification with subsequent GC-MS analysis of the nucleosides. This assay detected an increase in the levels of 2'-deoxyinosine in DNA when commercial salmon testis DNA was treated with nitrous acid. We also used it to measure levels in various rat tissues of both normal and endotoxin-treated rats, but could not find increased 2'-deoxyinosine formation in tissues even though *NO production was substantially increased.

[Determination of individual purine and pyrimidine bases in carbohydrate-rich food]

The following method was developed for the qualitative and quantitative determination of purine and pyrimidine bases in carbohydrate rich food: The bases were liberated from nucleic acids, nucleotides or nucleosides by acid hydrolysis in a pressure digestion vessel. A complete liberation without losses of purine bases occurs upon hydrolysis for 15 min at 240 degrees C with trifluoroacetic and formic acids (1+1; V + V), pyrimidine bases need 45 min at 240 degrees C. The products arising from side reactions (such as hydroxymethylfurfural from hexoses and furfural from pentoses) could be removed from the hydrolysate by extraction with dichlormethane. The liberated bases could be separated upon stepwise elution by cation exchange chromatography. They were detected and determined by UV-measurements, continuously monitoring at lambda = 260 nm, and integrating electronically. The evaluation was carried out by a method with internal standard.

Determination of uracil and thymine and their nucleosides and nucleotides in picomole amounts by gas chromatography mass spectrometry selected ion monitoring

A stable isotope dilution method is presented by which uracil (Ura) and thymine (Thy) can be determined with high precision and sensitivity at the picomole level utilizing stable isotope dilution and gas chromatography electron impact mass spectrometry in the selected ion monitoring mode. [15N2]Ura and [2H3]Thy served as internal standards. The molecular ions as well as the [M-CH3]+ ion fragments of silylated Ura and Thy (Ura-TMS and Thy-TMS) were suitable for the assay which provides evidence of specificity, if identical results are obtained at both ions. Nucleosides and nucleotides of Ura and Thy were determined following quantitative hydrolysis in 6 N HCl at 180 degrees C for two hours. Other hydrolysis procedures did not give satisfactory results. Levels of free Ura and Thy were measured in human and rat plasma after solvent extraction with a sensitivity of 20-40 pm ml-1 demonstrating ready applicability of the assay method to biological samples. The potential physiological role of circulating Ura and Thy is discussed.

Separation of amino acids and peptides on non-polar stationary phases by high-performance liquid chromatography

Microparticulate non-polar stationary phases, such as octadecyl-silica offer a rapid and efficient means for the separation of peptides and amino acids by high-performance liquid chromatography. Retention is attributed to hydrophobic interaction between the solutes and the hydrocarbonaceous functions covalently bound to the stationary phase surface. Consequently the species are eluted in the order of increasing hydrophobicity. Various peptide mixtures were analyzed by using gradient elution with increasing acetonitrile concentration in the eluent and monitoring the column effluent at 200 or 210 nm with an UV detector. The separation of angiotensins and enzymic digest of polypeptides illustrates the speed of the method which can be used to assay the purity of peptide hormones such as alpha-melanotropin and gramicidin or to analyze the composition of reaction mixtures involving peptides. The efficiency of the method is superior to that obtained on the conventionally used ion-exchanger columns, except for hydrophilic amino acids and peptides that are poorly retarded. Nevertheless, with a suitable ionic surfactant in the mobile phase, non-polar stationary phases can be used for the separation of these species as well.

Separation of alkyl derivatives of uracil by solvophobic adsorption chromatography on spheron

Derivatives of such related substances as cytosine, uracil, thymine, 6-methyl-uracil, 5-ethyluracil, 5-propyluracil, 5-isopropyluracil, 5-cyclopropyluracil, 5-allyluracil, 5,6-trimethyleneuracil, 6-cyclopropyluracil, 5-cyclobutyluracil and 5-tert-butyluracil have been separated on a column of Spheron P-300. Retention on the column was found to depend on the size of the non-polar part of the molecule. The chromatographic behaviour is analyzed according to the theory of solvophobic chromatography.

Isocratic separation of some purine nucleotide, nucleoside, and base metabolites from biological extracts by high-performance liquid chromatography

Separation of ATP, ADP, AMP, adenine, adenosine, cAMP, ITP, IDP, IMP, hypoxanthine, inosine, cIMP, the guanine series, NAD, NADPH, xanthine, 3-methylxanthine, theobromine, theophylline, and caffeine was accomplished using high-performance liquid chromatography with a microparticulate reversed-phase column. Under isocratic conditions all compounds could be eluted with reasonable resolution and retention time. Quantitation by peak height for several of the compounds was used to the 10-ng level.

Gas-liquid chromatographic analysis of trimethylsilyl derivatives of pyrimidine and purine bases and nucleosides

A systematic study of basic nucleic acid components and their biologically significant derivatives has been carried out. The optimum silylation conditions have been found and the chromatographic behaviour of the trimethylsilyl derivatives formed has been studied. Relations between the gas chromatographic behaviour and the structure of the substances analyzed were investigated on the basis of the retention indices measured on two stationary phases of different polarity. The relative molar responses were determined for the quantitative determination of the substances. The results make possible the determination of biologically active substances in pharmaceuticals.

Determination of trimethylsilyl methylated nucleic acid bases in urine by gas-liquid chromatography

A method for the determination of the urinary excretion level of methylated nucleic acid bases by gas-liquid chromatography (GLC) has been developed. A clean-up procedure prior to GLC analysis consisted of hydrolysis, filtration, charcoal adsorption, and anion exchange. Studies to determine optimum derivatization conditions for conversion of the methylated bases to their trimethylsilyl derivatives and to evaluate GLC parameters and columns to obtain the best separation were conducted. Application of the method was shown by determining the excretion levels of methylated bases in urine of normal controls and of patients with various types of malignancy.

High-resolution liquid chromatographic analysis of methylated purine and pyrimidine bases in transfer RNA

Methylated and major purine and pyrimidine bases were separated and quantified by high-resolution liquid chromatography after hydrolyzing transfer ribonucleic acids (tRNAs). Separation was accomplished by eluting the hydrolyzed samples from an anion-exchange column with a concentration gradient of ammonium acetate at pH 9.2. Isolated sample of tRNA were hydrolyzed to the free bases with a trifluoroacetic acid-formic acid mixture of 200 degrees. Detection limits of 100-200 ng/ml were measured for the methylated bases; analytical data are reported for ten methylated bases plus the four major bases of calf liver and rat liver tRNA.