Effects of sodium cationization versus protonation on the conformations and N-glycosidic bond stabilities of sodium cationized Urd and dUrd: solution conformation of [Urd+Na]+ is preserved upon ESI.
Effects of sodium cationization versus protonation on the conformations and N-glycosidic bond stabilities of sodium cationized Urd and dUrd: solution conformation of [Urd+Na]+ is preserved upon ESI.
复制标题
钠阳离子化与质子化对钠阳离子化 Urd 和 dUrd 的构象和 N-糖苷键稳定性的影响：[Urd Na] 的溶液构象在 ESI 上得以保留。
DOI：
--
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
M. Rodgers
中科院分区：
文献类型：
--
作者：
Y. Zhu;H. Roy;N. A. Cunningham;S. Strobehn;J. Gao;M. U. Munshi;G. Berden;J. Oomens;M. Rodgers
尿苷 (Urd) 是 RNA 天然存在的嘧啶核苷之一。 2'-脱氧尿苷 (dUrd) 是 Urd 的天然修饰形式，但不是典型的 DNA 核苷之一。为了了解钠阳离子化对 Urd 和 dUrd 构象和能量的影响，进行了红外多光子解离 (IRMPD) 作用光谱实验和密度泛函理论 (DFT) 计算。通过将计算的 [Urd+Na]+ 和 [dUrd+Na]+ 的红外光谱与测量的 IMPD 光谱进行比较，确定了实验中存在的稳定的低能构象异构体。 [Urd+Na]+ 的反向二齿 O2 和 O2' 结合构象异构体是实验中占据的主要构象异构体，而 [dUrd+Na]+ 的顺向三齿 O2、O4' 和 O5' 结合构象异构体在实验中占主导地位。 Urd 的 2'-羟基取代基可稳定 [Urd+Na]+ 的反定向 O2 结合构象异构体。 [Urd+Na]+ 和 [dUrd+Na]+ 复合物涉及核碱基的少量互变异构形式，测量的 IRMPD 和计算的 IR 光谱之间存在显着差异，这表明实验中没有填充任何物质。基于能量分辨碰撞诱导解离 (ER-CID) 实验的存活率分析表明，质子化和钠阳离子化 Urd 和 dUrd 的相对稳定性遵循以下顺序：[dUrd+H]+ < [Urd+H]+ < [dUrd+Na]+ < [Urd+Na]+。与钠阳离子化尿苷核苷的 Urd 相比，2'-脱氧修饰被发现削弱了 dUrd 的糖苷键。
Uridine (Urd) is one of the naturally occurring pyrimidine nucleosides of RNA. 2'-Deoxyuridine (dUrd) is a naturally occurring modified form of Urd, but is not one of the canonical DNA nucleosides. In order to understand the effects of sodium cationization on the conformations and energetics of Urd and dUrd, infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and density functional theory (DFT) calculations are performed. By comparing the calculated IR spectra of [Urd+Na]+ and [dUrd+Na]+ with the measured IRMPD spectra, the stable low-energy conformers populated in the experiments are determined. Anti oriented bidentate O2 and O2' binding conformers of [Urd+Na]+ are the dominant conformers populated in the experiments, whereas syn oriented tridentate O2, O4', and O5' binding conformers of [dUrd+Na]+ are dominantly populated in the experiments. The 2'-hydroxyl substituent of Urd stabilizes the anti oriented O2 binding conformers of [Urd+Na]+. Significant differences between the measured IRMPD and calculated IR spectra for complexes of [Urd+Na]+ and [dUrd+Na]+ involving minor tautomeric forms of the nucleobase make it obvious that none are populated in the experiments. Survival yield analyses based on energy-resolved collision-induced dissociation (ER-CID) experiments suggest that the relative stabilities of protonated and sodium cationized Urd and dUrd follow the order: [dUrd+H]+ < [Urd+H]+ < [dUrd+Na]+ < [Urd+Na]+. The 2'-deoxy modification is found to weaken the glycosidic bond of dUrd versus that of Urd for the sodium cationized uridine nucleosides.