Gas-Phase Dissociation of Oligoribonucleotides and their Analogs Studied by Electrospray Ionization Tandem Mass Spectrometry

In contrast to the dissociation of DNA, dissociation of RNA was found to be independent of nucleobase loss and it is characterized by cleavage of the 5′-PO bond, resulting in the formation of c- and their complementary y-type ions. To evaluate the influence of different 2′-substituents, several modified tetraribonucleotides were analyzed. Oligoribonucleotides incorporating a 2′-methoxy-ribose or a 2′-fluoro-ribose show fragmentation that does not exhibit any preferred dissociation pathway because all different types of fragment ions are generated with comparable abundance. To analyze the role of the nucleobases in the fragmentation of the phosphodiester backbone, an oligonucleotide lacking the nucleobase at one position has been studied. Experiments indicated that the dissociation mechanism of RNA is not influenced by the nucleobase, thus, supporting a mechanism where dissociation is initiated by formation of an intramolecular cyclic transition state with the 2′-hydroxyl proton bridged to the 5′-phosphate oxygen.