Sequence analysis of oligodeoxyribonucleotides by mass spectrometry. 1. Dinucleoside monophosphates

The base components of underivatized oligodeoxynucleotides can be determined qualitatively by mass-spectral analysis at the nanogram level. The thermal and electron-impact conditions of the spectrometer allow the cleavage of the phosphodiester bonds of the oligonucleotide chain, resulting in fragments (I), whose mass identifies the base, and other fragments (II), which contain the purine or pyrimidine base plus portions of the deoxyribose and the phosphate moieties. A study of 16 dinucleoside monophosphates indicates that the relative intensities of the m/e values of the type II fragments are significantly and reproducibly different for sequence isomers. From the complex spectra of dinucleoside monophosphates, specific ions for each mono-nucleotide residue have been selected which reveal the location (5' or 3' terminus) of the bases in the dinucleoside monophosphate. These ions appear in spectra of deoxyribonucleic acid fragments as well as in model compounds. A simple computer program has been devised which utilizes ion ratio values to determine sequence. The method is applicable to oligonucleotides of longer length.