南京大学陈加余团队利用化学蛋白质组学分析，揭示了与内源性三联体DNA相互作用的内源性蛋白质的结合和功能多样性。相关研究成果于2024年9月2日发表在《自然—化学》。

当第三条DNA链包裹在DNA的主槽上时形成的三重DNA结构，是关键的分子调节因子和基因组威胁。然而，控制三链DNA动力学的调控网络仍然知之甚少。

该文中，研究人员通过活细胞中的化学蛋白质组学分析，揭示了与三链DNA相互作用的蛋白质的结合和功能库。开发了一种对三链DNA表现出特殊特异性的化学探针。通过采用共结合介导的邻近捕获策略，丰富了用于定量蛋白质组学分析的三链DNA相互作用体。

这使得能够鉴定与三链DNA相互作用的蛋白质的完整列表，其特征是在天然染色质环境中具有不同的结合特性和调节机制。作为证明，研究人员验证了DDX3X是一种ATP非依赖性的三链DNA解旋酶，可以解开5′悬垂的底物以防止DNA损伤。

总的来说，研究结果为探索三链DNA的生物学和翻译潜力提供了宝贵的资源。

附：英文原文

Title: Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA

Author: Xu, Hongzhan, Ye, Jing, Zhang, Kui-Xing, Hu, Qingxi, Cui, Tongxiao, Tong, Chong, Wang, Mengqi, Geng, Huichao, Shui, Kun-Ming, Sun, Yan, Wang, Jian, Hou, Xiaomeng, Zhang, Kai, Xie, Ran, Yin, Yafei, Chen, Nan, Chen, Jia-Yu

Issue&Volume: 2024-09-02

Abstract: Triplex DNA structures, formed when a third DNA strand wraps around the major groove of DNA, are key molecular regulators and genomic threats. However, the regulatory network governing triplex DNA dynamics remains poorly understood. Here we reveal the binding and functional repertoire of proteins that interact with triplex DNA through chemoproteomic profiling in living cells. We develop a chemical probe that exhibits exceptional specificity towards triplex DNA. By employing a co-binding-mediated proximity capture strategy, we enrich triplex DNA interactome for quantitative proteomics analysis. This enables the identification of a comprehensive list of proteins that interact with triplex DNA, characterized by diverse binding properties and regulatory mechanisms in their native chromatin context. As a demonstration, we validate DDX3X as an ATP-independent triplex DNA helicase to unwind substrates with a 5′ overhang to prevent DNA damage. Overall, our study provides a valuable resource for exploring the biology and translational potential of triplex DNA.

DOI: 10.1038/s41557-024-01609-7

Source: https://www.nature.com/articles/s41557-024-01609-7