Conformations and N-glycosidic bond stabilities of sodium cationized 2′-deoxycytidine and cytidine: Solution conformation of [Cyd + Na]+ is preserved upon ESI

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with metal cations. In order to determine the effects of sodium cationization on the structures of 2′-deoxycytidine and cytidine, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides, [dCyd+Na]+ and [Cyd+Na]+, are measured using the FELIX free electron laser and an OPO/OPA laser system. Energy-resolved collision-induced dissociation (ER-CID) experiments for the protonated and sodium cationized forms of the cytosine nucleosides are performed using a Bruker amaZon ETD quadrupole ion trap mass spectrometer (QIT MS) to evaluate the relative propensities of protons and sodium cations for activating the glycosidic bonds of the cytosine nucleosides. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of [dCyd + Na]+ and [Cyd + Na]+. For both cytosine nucleosides, theory suggests that tridentate binding of Na+ to the O2, O4′ and O5′ atoms of the cytosine nucleobase and sugar moiety is the most stable binding mode. However, comparison of the measured IRMPD action spectrum and computed linear IR spectra suggests that anti oriented bidentate conformers of [Cyd + Na]+ are predominantly populated in the experiments. The 2′-hydroxyl substituent of Cyd stabilizes the anti oriented bidentate conformers of [Cyd + Na]+, and enables formation of a 2′OH⋯3′OH hydrogen-bonding interaction. The 2′-hydroxyl substituent is found to stabilize the glycosidic bond of Cyd vs. that of dCyd for both the protonated and sodium cationized cytosine nucleosides. Compared to protonation, sodium cationization activates the N-glycosidic bond less effectively.