Department of Chemistry-027, University of California, Riverside, CA 92521-0403, USA.
Biochemistry. 2012 Aug 14;51(32):6458-62. doi: 10.1021/bi300797q. Epub 2012 Jul 31.
B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) density functional theory calculations were employed to explore the kinetics and thermodynamics of gas-phase N-glycosidic bond cleavage induced by nucleophilic attack of C1' with a hydroxide ion in 5-substituted 2'-deoxycytidines. The results showed that, among the 5-substituted 2'-deoxycytidine derivatives examined [XdC, where X = H (dC), CH(3) (medC), CH(2)OH (hmdC), CHO (fmdC), COOH (cadC), F (FdC), or Br (BrdC)], fmdC and cadC exhibited the lowest energy barrier and largest exothermicity for N-glycosidic bond cleavage. These results paralleled previously reported nucleobase excision activities of human thymine DNA glycosylase (hTDG) toward duplex DNA substrates harboring a thymine and 5-substituted cytosine derivatives when paired with a guanine. Our study suggests that the inherent chemistry associated with the nucleophilic cleavage of N-glycosidic bond constitutes a major factor contributing to the selectivity of hTDG toward 5-substituted dC derivatives. These findings provided novel insights into the role of TDG in active cytosine demethylation.
采用 B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d)密度泛函理论计算方法，研究了在 5 位取代的 2'-脱氧胞嘧啶核苷中，C1'上的亲核进攻与氢氧根离子诱导的 N-糖苷键断裂的反应动力学和热力学。结果表明，在所研究的 5 位取代的 2'-脱氧胞嘧啶核苷衍生物[XdC，其中 X = H (dC)、CH(3) (medC)、CH(2)OH (hmdC)、CHO (fmdC)、COOH (cadC)、F (FdC)或 Br (BrdC)]中，fmdC 和 cadC 表现出最低的 N-糖苷键断裂能垒和最大的放热。这些结果与先前报道的人类胸腺嘧啶 DNA 糖基化酶（hTDG）对含有胸腺嘧啶和 5 位取代胞嘧啶核苷的双链 DNA 底物的核碱基切除活性相平行，当与鸟嘌呤配对时。我们的研究表明，N-糖苷键亲核断裂所涉及的固有化学性质是 hTDG 对 5 位取代 dC 衍生物选择性的主要因素。这些发现为 TDG 在活性胞嘧啶去甲基化中的作用提供了新的见解。
