DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N²-2′-deoxyguanosine (N²-dG) and N⁶-2′-deoxyadenosine (N⁶-dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligodeoxynucleotides containing a structural analogue (LdG) of lucidin-N²-dG DNA adduct and determined the crystal structures of DNA polymerase (pol) κ in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol η, pol ι, pol κ, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in translesion DNA synthesis. Our results demonstrate that pol κ efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol η, pol ι is compromised to different extents. Rev1 retains its ability to incorporate dCTP opposite the lesion albeit with decreased efficiency. Two ternary crystal structures of pol κ illustrate that the LdG adduct is accommodated by pol κ at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol κ allows the adducted DNA to adopt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.

中文翻译：

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人类DNA聚合酶κ克服露蛋白素引起的DNA损伤而无错复制DNA的机制

DNA损伤影响遗传信息流，对人类疾病和衰老具有重大影响。Lucidin-3- O - primeveroside（LuP）是存在于茜草根中的蒽醌衍生物，已被用作着色剂和食品添加剂。LuP可以代谢转化为遗传毒性化合物lucidin，随后形成lucidin特异性的N ² -2'-脱氧鸟苷（N ² -dG）和N ⁶ -2'-脱氧腺苷（N ⁶-dA）DNA加合物。Lucidin在啮齿动物中具有致突变性和致癌性，但对人类的致癌风险却很低。为了了解人体中低水平的lucidin致癌性的分子机制，我们使用含有lucidin- N ²的结构类似物（LdG）的位点特异性修饰的寡脱氧核苷酸进行了DNA复制分析-dG DNA加合物，并确定了带有LdG的DNA和传入核苷酸与DNA聚合酶（pol）κ的晶体结构。我们在用LdG复制DNA的过程中检查了四个人类pols（polη，polι，polκ和Rev1）的效率和准确性。这些pols是跨病变DNA合成的关键角色。我们的结果表明，polκ有效且准确地复制通过LdG加合物，而polη，polη的DNA复制受到不同程度的损害。Rev1保留了将dCTP掺入病灶对面的能力，尽管效率有所降低。polκ的两个三元晶体结构说明，在插入和病变扩展步骤中，polκ可以在酶活性位点容纳LdG加合物。polκ独特的开放活性位点使加合物的DNA可以采用标准B形式进行准确的DNA复制。总的来说，这些生化和结构数据提供了对人体中低风险的lucidin致癌风险的机械见解。