Structural and Energetic Effects of O2′-Ribose Methylation of Protonated Pyrimidine Nucleosides

The 2 '-substituents distinguish DNA from RNA nucleosides. 2 '-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2 '-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2 '-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2 '-O-methylated pyrimidine nucleosides, [Nuom+H](+), were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2 '-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H](+) and [Nuo+H](+), yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H](+) < [Nuo+H](+) < [Nuom+H](+). The slightly altered structures help explain the stabilization induced by 2 '-O-methylation of the pyrimidine nucleosides.