Zou Yue, Shell Steven M, Utzat Christopher D, Luo Charlie, Yang Zhengguan, Geacintov Nicholas E, Basu Ashis K
Department of Biochemistry and Molecular Biology, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614, USA.
Biochemistry. 2003 Nov 4;42(43):12654-61. doi: 10.1021/bi034446e.
DNA damage recognition of nucleotide excision repair (NER) in Escherichia coli is achieved by at least two steps. In the first step, a helical distortion is recognized, which leads to a strand opening at the lesion site. The second step involves the recognition of the type of chemical modification in the single-stranded region of DNA during the processing of the lesions by UvrABC. In the current work, by comparing the efficiencies of UvrABC incision of several types of different DNA adducts, we show that the size and position of the strand opening are dependent on the type of DNA adducts. Optimal incision efficiency for the C8-guanine adducts of 2-aminofluorene (AF) and N-acetyl-2-aminofluorene (AAF) was observed in a bubble of three mismatched nucleotides, whereas the same for C8-guanine adduct of 1-nitropyrene and N(2)-guanine adducts of benzo[a]pyrene diol epoxide (BPDE) was noted in a bubble of six mismatched nucleotides. This suggests that the size of the aromatic ring system of the adduct might influence the extent and number of bases associated with the opened strand region catalyzed by UvrABC. We also showed that the incision efficiency of the AF or AAF adduct was affected by the neighboring DNA sequence context, which, in turn, was the result of differential binding of UvrA to the substrates. The sequence context effect on both incision and binding disappeared when a bubble structure of three bases was introduced at the adduct site. We therefore propose that these effects relate to the initial step of damage recognition of DNA structural distortion. The structure-function relationships in the recognition of the DNA lesions, based on our results, have been discussed.
大肠杆菌中核苷酸切除修复（NER）的DNA损伤识别至少通过两个步骤实现。第一步，识别螺旋扭曲，这会导致损伤位点处的链打开。第二步涉及在UvrABC处理损伤过程中识别DNA单链区域中的化学修饰类型。在当前的工作中，通过比较几种不同DNA加合物的UvrABC切割效率，我们表明链打开的大小和位置取决于DNA加合物的类型。在三个错配核苷酸的气泡中观察到2-氨基芴（AF）和N-乙酰-2-氨基芴（AAF）的C8-鸟嘌呤加合物的最佳切割效率，而在六个错配核苷酸的气泡中注意到1-硝基芘的C8-鸟嘌呤加合物和苯并[a]芘二醇环氧化物（BPDE）的N（2）-鸟嘌呤加合物的最佳切割效率。这表明加合物的芳香环系统大小可能会影响由UvrABC催化的与开放链区域相关的碱基数量和范围。我们还表明，AF或AAF加合物的切割效率受相邻DNA序列上下文的影响，而这又是UvrA与底物差异结合的结果。当在加合物位点引入三个碱基的气泡结构时，序列上下文对切割和结合的影响都消失了。因此，我们提出这些影响与DNA结构扭曲损伤识别的初始步骤有关。基于我们的结果，已讨论了DNA损伤识别中的结构-功能关系。
