Reactivity of damaged pyrimidines: formation of a Schiff base intermediate at the glycosidic bond of saturated dihydrouridine.
Reactivity of damaged pyrimidines: formation of a Schiff base intermediate at the glycosidic bond of saturated dihydrouridine.
复制标题
受损嘧啶的反应性：在饱和二氢尿苷的糖苷键上形成席夫碱中间体。
DOI：
10.1021/ja512435j
复制
发表时间：
2015
影响因子：
15
通讯作者：
Li,Lei
中科院分区：
文献类型：
--
作者：
Jian,Yajun;Lin,Gengjie;Chomicz,Lidia;Li,Lei
DNA糖基化酶催化碱基切除修复（BER）途径的第一步。这些酶用于去糖基化的化学作用主要被认为是氧碳正离子的化学作用，例如，C1 '-N1键直接断裂，产生氧碳正离子中间体。在这里，我们目前的机制研究揭示了2′-脱氧核糖异构化和随后的去糖基化过程中的两个嘧啶损伤：5，6-二氢-2 ′-脱氧尿苷（dHdU）和5，6-二氢胸苷（dHT），形成通过电离辐射损伤2′-脱氧胞苷和胸苷，在缺氧条件下。这两个损伤的酸或热处理导致产生两对分别含有吡喃糖和呋喃糖的C1′差向异构体，表明这两个损伤都有利于C1′-O 4 ′键的断裂，从而在N-糖苷键处产生Schiff碱中间体。这样的席夫碱中间体被捕获，其特征在于无论是钯催化氢化或硫醇介导的加成反应。相反，在未受损的2′-脱氧尿苷和胸苷中，在高温下的反应导致核碱基的释放，最有可能通过传统的氧碳正离子途径。DFT计算进一步支持了实验结果，表明如果嘧啶环的完整性得以保持，则氧碳正离子中间体负责去糖基化过程，而如果C5-C6键饱和，则优选席夫碱中间体。目前，oxocarbenium离子途径被认为是唯一负责BER酶的去糖基化，但我们的研究结果表明，一个替代的席夫碱机制，这可能是负责饱和嘧啶损伤的修复。
DNA glycosylases catalyze the first step of the base excision repair (BER) pathway. The chemistry used by these enzymes for deglycosylation has been largely considered as the chemistry of the oxocarbenium ion, e.g., direct rupture of the C1′–N1 bond resulting in an oxocarbenium ion intermediate. Here we present mechanistic studies revealing the 2′-deoxyribose isomerization and subsequent deglycosylation processes in two pyrimidine lesions: 5,6-dihydro-2′-deoxyuridine (dHdU) and 5,6-dihydrothymidine (dHT), formed via ionizing radiation damage to 2′-deoxycytidine and thymidine, respectively, under anoxic conditions. Acid or heat treatment of these two lesions leads to the production of two pairs of C1′ epimers containing a pyranose and a furanose, respectively, indicating that both lesions favor the rupture of the C1′–O4′ bond, resulting in a Schiff base intermediate at the N-glycosidic bond. Such a Schiff base intermediate was trapped and characterized by either Pd-catalyzed hydrogenation or thiol-mediated addition reaction. In contrast, in undamaged 2′-deoxyuridine and thymidine, reactions at elevated temperatures lead to the release of nucleobases most likely via the traditional oxocarbenium ion pathway. DFT calculations further support the experimental findings, suggesting that the oxocarbenium ion intermediate is responsible for the deglycosylation process if the integrity of the pyrimidine ring is maintained, while the Schiff base intermediate is preferred if the C5C6 bond is saturated. Currently, the oxocarbenium ion pathway is indicated to be solely responsible for the deglycosylation in BER enzymes, however our results suggest an alternative Schiff base mechanism which may be responsible for the repair of saturated pyrimidine damages.