Gas-Phase Conformations and N‑Glycosidic Bond Stabilities of Sodium Cationized 2′-Deoxyguanosine and Guanosine: Sodium Cations Preferentially Bind to the Guanine Residue
journal contributionposted on 2017-03-29, 00:00 authored by Y. Zhu, L. A. Hamlow, C. C. He, J. K. Lee, J. Gao, G. Berden, J. Oomens, M. T. Rodgers
2′-Deoxyguanosine (dGuo) and guanosine (Guo) are fundamental building blocks of DNA and RNA nucleic acids. In order to understand the effects of sodium cationization on the gas-phase conformations and stabilities of dGuo and Guo, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and complementary electronic structure calculations are performed. The measured IRMPD spectra of [dGuo+Na]+ and [Guo+Na]+ are compared to calculated IR spectra predicted for the stable low-energy structures computed for these species to determine the most favorable sodium cation binding sites, identify the structures populated in the experiments, and elucidate the influence of the 2′-hydroxyl substituent on the structures and IRMPD spectral features. These results are compared with those from a previous IRMPD study of the protonated guanine nucleosides to elucidate the differences between sodium cationization and protonation on structure. Energy-resolved collision-induced dissociation (ER-CID) experiments and survival yield analyses of protonated and sodium cationized dGuo and Guo are performed to compare the effects of these cations toward activating the N-glycosidic bonds of these nucleosides. For both [dGuo+Na]+ and [Guo+Na]+, the gas-phase structures populated in the experiments are found to involve bidentate binding of the sodium cation to the O6 and N7 atoms of guanine, forming a 5-membered chelation ring, with guanine found in both anti and syn orientations and C2′-endo (2T3 or 3T2) puckering of the sugar. The ER-CID results, IRMPD yields and the computed C1′–N9 bond lengths indicate that sodium cationization activates the N-glycosidic bond less effectively than protonation for both dGuo and Guo. The 2′-hydroxyl substituent of Guo is found to impact the preferred structures very little except that it enables a 2′OH···3′OH hydrogen bond to be formed, and stabilizes the N-glycosidic bond relative to that of dGuo in both the sodium cationized and protonated complexes.
Read the peer-reviewed publication
sodium cationization activatesOHER-CIDN 7 atomssodium cationizationprotonated guanine nucleosidessodium cationized dGuoDNAIRMPDEnergy-resolved collision-induced dissociation5- membered chelation ringSodium Cations Preferentially Bindsodium cation binding sitesaction spectroscopy experimentsRNA3 T 22 T 3N-glycosidic bondIR