A comprehensive study of the low energy collision-induced dissociation of dinucleoside monophosphates

Abstract

The dissociation reactions of protonated and deprotonated molecular ions from the 12 possible hetero-dinucleotides in both the 2′-deoxyribonucleotide and ribonucleotide series have been studied using tandem mass spectrometry with collisional activation in the low energy (21–72 eV, E LAB)_translational energy range. Gas-phase model structures for both MH + and (M—H) − ions are considered which take into account the need for tertiary structural stabilization through intramolecular hydrogen bonding, and charge delocalization by proton or hydrogen atom sharing. These structures serve as initial models to demonstrate the types of stabilizing features which are likely to exist in large gas-phase polynucleotide ions, and in the present study to effectively rationalize formation of the observed dissociation products of dinucleotides. It is proposed that dissociation reactions of positive ions are influenced by a tertiary structure in which the proton of ionization is shared by the heterocyclic bases. In negative ions, the charge is delocalized through the phosphate oxygens, stabilized by interactions with the 3′-terminus base and (in ribonucleotides) by 2′-OH. The resulting mass spectra are readily interpreted in terms of dinucleotide structure, including sequence, and the presence or absence of ribose methylation.