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.

The products of the reaction between [Pt(dien)Cl]Cl and salmon sperm DNA have been purified and their structures determined. [Pt(dien)Cl]Cl binds at the N7 position of guanine for levels of fixation below 0.1 platinum per DNA base. Above this level of binding, [Pt(dien)Cl]Cl also reacts at the N7 position of adenine. 1,7-[Pt(dien)]2Ade was observed when more than 0.3 platinum per base were bound to the DNA. Platination at the N7 position of guanosine, unlike alkylation, stabilized the glycosyl linkage and did not lead to fission of the imidazole ring at high pH.

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The mass spectra of derivatives of uridine, adenosine, cytidine and guanosine are recorded. Derivatization techniques include permethylation, acetylation, trifiuoroacetylation, trimethylsilylation and the synthesis of 2',3'-O-isopropylidenes and 2',3'-0-phenylboronic esters. Sequential derivatization by a selective combination of some of these procedures results in nucleosides which are blocked with a characteristic group at the cis 1,2 diol position, and, which contain other substituent groups that enhance the volatility of the compound. The specific substitution at the cis-glycol region has been shown to be particularly useful in asymmetrically derivatizing dinucleoside phosphates since certain fragment ions from their mass spectra indicate the sequence of the two nucleoside components. Sequence isomers such as adenylyl-(3'-5')-uridine and uridylyl-(3'-5')-adenosine can be unambiguously distinguished.