The Nucleotide Excision Repair (NER) mechanism removes a wide spectrum of structurally different lesions that critically depend on the binding of the DNA damage sensing NER factor XPC-RAD23B (XPC) to the lesions. The bulky mutagenic benzo[a]pyrene diol epoxide metabolite-derived cis- and trans-B[a]P-dG lesions (G*) adopt base-displaced intercalative (cis) or minor groove (trans) conformations in fully paired DNA duplexes with the canonical C opposite G* (G*:C duplexes). While XPC has a high affinity for binding to these DNA lesions in fully complementary double-stranded DNA, we show here that deleting only the C in the complementary strand opposite the lesion G* embedded in 50-mer duplexes, fully abrogates XPC binding. Accurate values of XPC dissociation constants (K_D) were determined by employing an excess of unmodified DNA as a competitor; this approach eliminated the binding and accumulation of multiple XPC molecules to the same DNA duplexes, a phenomenon that prevented the accurate estimation of XPC binding affinities in previous studies. Surprisingly, a detailed comparison of XPC dissociation constants K_D of unmodified and lesion-containing G*:Del complexes, showed that the K_D values were −2.5–3.6 times greater in the case of G*:Del than in the unmodified G:Del and fully base-paired G:C duplexes. The origins of this unexpected XPC lesion avoidance effect is attributed to the intercalation of the bulky, planar B[a]P aromatic ring system between adjacent DNA bases that thermodynamically stabilize the G*:Del duplexes. The strong lesion-base stacking interactions associated with the absence of the partner base, prevent the DNA structural distortions needed for the binding of the BHD2 and BHD3 β−hairpins of XPC to the deletion duplexes, thus accounting for the loss of XPC binding and the known NER-resistance of G*:Del duplexes.

核苷酸切除修复 (NER) 机制可去除多种结构不同的病变，这些病变主要取决于 DNA 损伤感应 NER 因子 XPC-RAD23B (XPC) 与病变的结合。大体积诱变苯并[ a ]芘二醇环氧化物代谢物衍生的顺式和反式-B[ a ]P-dG损伤（G*）在完全配对的DNA双链体中采用碱基置换的插入（顺式）或小沟（反式）构象规范 C 与 G* 相反（G*:C 双链体）。虽然 XPC 对完全互补的双链 DNA 中的这些 DNA 损伤具有高亲和力，但我们在此表明​​，仅删除与 50 聚体双链体中嵌入的损伤 G* 相对的互补链中的 C，即可完全消除 XPC 结合。 XPC 解离常数 ( _KD ) 的准确值是通过使用过量的未修饰 DNA 作为竞争剂来确定的；这种方法消除了多个 XPC 分子与相同 DNA 双链体的结合和积累，这种现象阻碍了先前研究中 XPC 结合亲和力的准确估计。令人惊讶的是，对未修饰和含有损伤的 G*:Del 复合物的 XPC 解离常数_KD的详细比较表明，G*:Del 的_KD值比未修饰的 G 大 -2.5–3.6 倍： Del 和完全碱基配对的 G:C 双链体。这种意想不到的 XPC 损伤避免效应的起源归因于相邻 DNA 碱基之间插入的大体积平面 B[ a ]P 芳香环系统，可热力学稳定 G*:Del 双链体。 与伴侣碱基缺失相关的强损伤碱基堆积相互作用，防止了 XPC 的 BHD2 和 BHD3 β-发夹与缺失双链体结合所需的 DNA 结构扭曲，从而解释了 XPC 结合的损失和已知 G*:Del 双链体的 NER 抗性。