氢消除诱导DNA双链断裂的反应性分子动力学模拟
Reactive Molecular Dynamics Simulation on DNA Double Strand Breaks Induced by Hydrogen Elimination
AI总结：
本研究提出瘢痕模型，通过反应力场分子动力学模拟探究氚β衰变致氢消除引发的端粒DNA双链断裂机制，明确了双链断裂需两条链均有邻近分布的足量瘢痕的必要条件。
摘要：
我们提出了一种瘢痕模型，用于复现氚β衰变为氦的效应对端粒DNA造成损伤时双链断裂的发生机制。在该瘢痕模型中，连接戊糖与磷酸的5'碳上键合的两个氢原子被移除。我们针对由16个碱基对（32个核苷酸）组成的端粒DNA开展了10组基于反应力场的分子动力学模拟。结果显示，瘢痕数量超过24个的结构中观察到了双链断裂（DSBs）；瘢痕数量为16个的案例中仅观察到单链断裂（SSB）。此外，在仅单链存在瘢痕的{16, 0}和{0, 16}案例中，单链断裂仅发生在有瘢痕的链上；而在{16, 8}和{8, 16}案例中则发生了双链断裂。因此我们得出结论，双链断裂需满足以下必要条件：（i）L链和R链上都必须出现瘢痕；（ii）必须有大量（24个及以上）瘢痕在彼此邻近的位置产生。
英文摘要：
We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $β$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the pent saccharides and phosphate are removed. Molecular dynamics simulations using the reactive force field are carried out for 10 cases for the telomeric DNA consisting of 16 base pairs (32 nucleotides). It results in double-strand breaks (DSBs) being observed for structures with more than 24 scars. For 16 scar cases, only single-strand breaks (SSB) are observed. Moreover, in the case of $\left\{16, 0 \right\}$ and $\left\{ 0, 16 \right\},$ where only one of the strands had scars, SSB occurs only in the scarred strand. Secondly, in the $\left\{16, 8 \right\}$ and $\left\{ 8, 16 \right\}$ cases, DSBs occurs. Therefore, we conclude that the following conditions are necessary for DSBs:(i) Scars must occur on both the L and R strands. (ii) A large number of scars (24 or more) must occur in close proximity to each other.
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