2. Academic Validation
  3. Chemoproteomic profiling unveils binding and functional diversity of endogenous proteins that interact with endogenous triplex DNA

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

  • Nat Chem. 2024 Sep 2. doi: 10.1038/s41557-024-01609-7.
Hongzhan Xu # 1,  Jing Ye # 1,  Kui-Xing Zhang # 1,  Qingxi Hu 1,  Tongxiao Cui 2,  Chong Tong 3,  Mengqi Wang 1,  Huichao Geng 1,  Kun-Ming Shui 1,  Yan Sun 1,  Jian Wang 1,  Xiaomeng Hou 4,  Kai Zhang 1,  Ran Xie 2,  Yafei Yin 3,  Nan Chen 4,  Jia-Yu Chen 5 6
Affiliations

Affiliations

  • 1 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China.
  • 2 State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
  • 3 Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
  • 4 ChomiX Biotech (Nanjing) Co. Ltd., Nanjing, China.
  • 5 State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Department of Neurology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China. jiayuchen@nju.edu.cn.
  • 6 Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, China. jiayuchen@nju.edu.cn.
  • # Contributed equally.
PMID: 39223307 DOI: 10.1038/s41557-024-01609-7
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.

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