Partecipation of the Nucleobases in the Regioselective Backbone Fragmentation of Nucleic Acid. A Molecular Dynamics and Tandem Mass Spectrometric Investigation on a Model Dinucleoside Phosphotriester

The anions (I-III) obtained from O-methyl 5'-O-(5'-deoxythymidine) 3'- O-(2',3'-dideoxyuridine) phosphate by the competitive removal of the 3-N-H protons of the nucleobases and of the methyl group from the phosphotriester bond, assume in the gas phase stable conformations as a function of their charge site. The mass-analyzed ion kinetic energy (MIKE) spectra of I and III show that the regioselective backbone cleavage of the internucleotidic linkage is controlled by the 2'-H proton transfer to the nucleobase within the 5'-end nucleoside. Similar pathways are taken by species II when the nucleobase is eliminated as neutral from the 5'-end nucleoside.