How repair proteins identify DNA damage in the nucleosome

The DNA base-excision repair (BER) pathway shares the second part of its enzymatic chain with the single-strand break (SSB) repair pathway. BER is initiated by a glycosylase, such as UDG, while SSBR is initiated by the multifunctional enzyme PARP1. The very early steps in the identification of the DNA damage are crucial to the correct initiation of the repair chains, and become even more complex when considering the realistic environment of damage to the DNA in the nucleosome. We performed molecular dynamics computer simulations of the interaction between the glycosylase UDG and a mutated uracil (as resulting from oxidative deamination of cytosine), and between the Zn1-Zn2 fragment of PARP1 and a simulated SSB. The model system is a whole nucleosome in which DNA damage is inserted at various typical positions along the 145-bp sequence. It is shown that damage recognition by the enzymes requires very strict conditions, unlikely to be matched by pure random search along the DNA. We propose that mechanical deformation of the DNA around the defective sites may help signaling the presence of the defect, accelerating the search process.

DNA碱基切除修复（base-excision repair, BER）通路与单链断裂（single-strand break, SSB）修复通路共享其酶促级联反应的第二阶段。BER由糖苷酶（glycosylase）启动，例如尿嘧啶DNA糖苷酶（uracil-DNA glycosylase, UDG），而单链断裂修复（single-strand break repair, SSBR）则由多功能酶PARP1启动。DNA损伤识别的极早期步骤对于修复级联的正确启动至关重要，而当考虑核小体中DNA损伤的真实生理环境时，这一过程会变得更为复杂。我们开展了分子动力学计算机模拟，分别针对糖苷酶UDG与胞嘧啶氧化脱氨产生的突变尿嘧啶之间的相互作用，以及PARP1的Zn1-Zn2结构域与模拟单链断裂损伤之间的相互作用。本研究的模型系统为完整核小体，其中DNA损伤被插入至145 bp序列的多个典型位置。研究表明，酶对损伤的识别需要极为严苛的条件，难以通过沿DNA的纯随机搜索达成。我们提出，缺陷位点周围的DNA机械变形可能有助于传递损伤存在的信号，进而加速损伤识别的搜索过程。