Gas-phase hydrogen/deuterium exchange of dinucleotides and 5′-monophosphate dinucleotides in a quadrupole ion trap

Abstract

Gas-phase hydrogen/deuterium (H/D) exchange reactions of four deprotonated dinucleotides (dAA, dAG, dGA, dGG) and their 5′-monophosphate analogs (5′-dAA, 5′-dAG, 5′-dGA, 5′-dGG) with D 2O were performed in a quadrupole ion trap mass spectrometer. Significant differences in the rates and extents of exchange were found when the 5′-hydroxyl group of the dinucleotides was replaced by a phosphate functionality. Extensive and nucleobase-dependent exchange occurred for the deprotonated 5′-monophosphate dinucleotides, whereas the dinucleotides all exhibited essentially the same limited exchange. Results for the isomeric 5′-monophosphates, 5′-dAG and 5′-dGA, were remarkably different, indicating that the H/D exchange reaction was sequence dependent. An elaborate array of computations was performed to investigate the gas-phase structures of the ions individually and also as participants in ion-molecule complexes with D 2O. Integration of the experimental and theoretical results supports a relay exchange mechanism and suggests that the exchange behavior depends highly on the identity and sequence of the nucleobases as well as their ability to interact with the deprotonation site. Finally, a shuttling mechanism is proposed to possibly account for the bimodal H/D exchange behavior observed for deprotonated 5′P-dGA. In this case, hydrogen bonding between the nucleobases in concert with interaction from the deuterating agent creates an ion-molecule complex in which hydrogen and deuterium atoms may be shuttled amongst the hydrogen-bonded participants.