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Sequential electron transfer governs the UV-induced self-repair of DNA photolesions†
Chemical Science ( IF 7.6 ) Pub Date : 2018-02-22 00:00:00 , DOI: 10.1039/c8sc00024g Rafał Szabla 1, 2 , Holger Kruse 2 , Petr Stadlbauer 2, 3 , Jiří Šponer 2 , Andrzej L Sobolewski 1
Chemical Science ( IF 7.6 ) Pub Date : 2018-02-22 00:00:00 , DOI: 10.1039/c8sc00024g Rafał Szabla 1, 2 , Holger Kruse 2 , Petr Stadlbauer 2, 3 , Jiří Šponer 2 , Andrzej L Sobolewski 1
Affiliation
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Cyclobutane pyrimidine dimers (CpDs) are among the most common DNA lesions occurring due to the interaction with ultraviolet light. While photolyases have been well known as external factors repairing CpDs, the intrinsic self-repairing capabilities of the GAT![[double bond, length as m-dash]](https://www.rsc.org/images/entities/char_e001.gif)
T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the TT dimer. Consequently, the molecular mechanism of GATT self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S1 potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S1/S0 state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
中文翻译：
顺序电子转移控制着紫外线诱导的 DNA 光损伤自我修复†
环丁烷嘧啶二聚体 (CpD) 是由于与紫外线相互作用而发生的最常见的 DNA 损伤之一。虽然光解酶作为修复 CpD 的外部因素而广为人知，但 GATT DNA 序列的内在自我修复能力直到最近才被发现，并且在很大程度上仍不清楚。在这里，我们通过涉及二阶 [ADC(2)] 方法的代数图解构造的 MD 模拟和 QM/MM 计算来阐明这种自我修复过程的机械细节。我们表明，鸟嘌呤的局部 UV 激发之后可能会发生多达三个后续电子转移，当负电荷驻留在 T T 二聚体上时，这可能最终实现有效的 CpD 开环。因此，GAT的分子机制T 自修复可以设想为沿着 S 1势能表面的斜率下坡发生的顺序电子转移 (SET)。尽管 SET 机制的一般特征在所研究的两个堆叠构象体中都保留了，但我们对不同 S 1 /S 0状态交叉的优化揭示了可能影响其自我修复效率的微小差异。我们预计，对其他 DNA 寡聚体中 SET 过程的可用性和效率的评估可能暗示其他序列表现出相似的光化学性质。由于太古代缺乏外部修复因子，在地球上生物分子起源的背景下，这种探索将特别引人入胜。
更新日期：2018-02-22
T DNA sequence were discovered only recently and are still largely obscure. Here, we elucidate the mechanistic details of this self-repair process by means of MD simulations and QM/MM computations involving the algebraic diagrammatic construction to the second order [ADC(2)] method. We show that local UV-excitation of guanine may be followed by up to three subsequent electron transfers, which may eventually enable efficient CpD ring opening when the negative charge resides on the TT dimer. Consequently, the molecular mechanism of GATT self-repair can be envisaged as sequential electron transfer (SET) occurring downhill along the slope of the S1 potential energy surface. Even though the general features of the SET mechanism are retained in both of the studied stacked conformers, our optimizations of different S1/S0 state crossings revealed minor differences which could influence their self-repair efficiencies. We expect that such assessment of the availability and efficiency of the SET process in other DNA oligomers could hint towards other sequences exhibiting similar photochemical properties. Such explorations will be particularly fascinating in the context of the origins of biomolecules on Earth, owing to the lack of external repairing factors in the Archean age.
中文翻译：
顺序电子转移控制着紫外线诱导的 DNA 光损伤自我修复†
环丁烷嘧啶二聚体 (CpD) 是由于与紫外线相互作用而发生的最常见的 DNA 损伤之一。虽然光解酶作为修复 CpD 的外部因素而广为人知，但 GAT
T DNA 序列的内在自我修复能力直到最近才被发现，并且在很大程度上仍不清楚。在这里，我们通过涉及二阶 [ADC(2)] 方法的代数图解构造的 MD 模拟和 QM/MM 计算来阐明这种自我修复过程的机械细节。我们表明，鸟嘌呤的局部 UV 激发之后可能会发生多达三个后续电子转移，当负电荷驻留在 T T 二聚体上时，这可能最终实现有效的 CpD 开环。因此，GAT的分子机制T 自修复可以设想为沿着 S 1势能表面的斜率下坡发生的顺序电子转移 (SET)。尽管 SET 机制的一般特征在所研究的两个堆叠构象体中都保留了，但我们对不同 S 1 /S 0状态交叉的优化揭示了可能影响其自我修复效率的微小差异。我们预计，对其他 DNA 寡聚体中 SET 过程的可用性和效率的评估可能暗示其他序列表现出相似的光化学性质。由于太古代缺乏外部修复因子，在地球上生物分子起源的背景下，这种探索将特别引人入胜。
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