Sequence analysis of oligodeoxyribonucleotides by mass spectrometry

Mass spectral studies of probe pyrolysis products of intact oligoribonucleotides

Pyrolysis of underivatized homogeneous oligoribonucleotides in the source of a mass spectrometer leads to production of simple mass spectra which resemble the spectra of the bases themselves. It is proposed that pyrolysis occurs by hydrogen transfer to the base moiety followed by elimination of the neutral base. Ionization by electron impact gives rise to the observed spectra. Mixed oligoribonucleotides pyrolyze readily to give spectra of adenine and uracil, but evidence for the presence of guanine and cytosine in mixed polymers and native RNA's is difficult to obtain presumably because of their low vapor pressure. The method may be useful for detection of modified bases in tRNA and for studies of temperature effects on RNA pyrolysis.

Detection and identification of minor nucleotides in intact deoxyribonucleic acids by mass spectrometry

A mass spectral method is described for the detection and identification of unusual nucleotide residues present in DNAs. Analysis by this method of intact, underivatized DNA from salmon sperm, calf thymus, mouse L-cells, wheat germ, M. lysodeikticus, E. Coli, and the bacteriophages 0X-174, fd, and lamda, yields diagnostic ions for the four common components of DNA as well as characteristic ions for 5-methyldeoxycytidine residues. The spectrum from T2 DNA contains ions indicative of 5-hydroxymethyldeoxycytidine and 5-methyldoxycytidine components but no ions corresponding to deoxycytidine residues. The DNAs of phages fd and 0X-174 also display ion products indicative of N6-methyldeoxyadenosine residues. Additional series of ions in the spectra of all four bacteriophage DNAs suggest the presence of 5-substituted deoxyuridine residues. The detection method exhibits considerable sensitivity in that amounts of DNA as low as 0.01 A260nm units can be used in the analysis, and thus, the procedure should prove of some value in the detection and location of modified components in specific regions of the various genomes by analysis of the appropriate endonuclease restriction fragments.