Studies on the distribution of oligodeoxynucleotide charge states in the gas phase by ion spray mass spectrometry

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Abstract
The naturally occurring purine and pyrimidine heterocycles found in nucleic acids differ significantly in their basicity. To investigate whether such differences may provide useful mass spectrometric information about nucleic acid sequence and/or composition, the distribution of charge states in a series of oligodeoxynucleotide gas‐phase ions was studied by ion spray mass spectrometry (MS). Hexadeoxynucleotides of adenosine, cytidine, guanosine and thymidine were evaluated over the pH range 2.6–7.0 using negative‐ion MS. A significant reduction in the maximum charge state was noted for d(pA)6, d(pC)6 and d(G)6 at low pH, while the maximum charge state observed for d(pT)6 was independent of pH. These effects displayed a good correlation with the pKa values of the respective nucleoside bases. The findings suggest that charge‐state reduction probably resulted from internal charge neutrazation by gas‐phase protonation of the nucleoside base.