Photocatalytic proximity labeling for the identification of G-quadruplex DNA-interacting proteins

Abstract

DNA–protein interactions play an essential role in fundamental cellular biological processes. Herein, we report a photocatalytic proximity labeling approach for the broad screening of G-quadruplex (G4)-interacting proteins (G4IPs) using human telomere G4 DNA modified with a photocatalyst (Ruthenium complex or BODIPY). We confirmed efficient labeling of unwinding protein 1 (UP1), a model of G4-interacting protein, with 1-methyl-4-arylurazole (MAUra) as a labeling reagent under blue light irradiation. We applied this labeling approach to nuclear extract proteins and identified labeled proteins using quantitative proteomics analysis. Numerous unknown G4 binding protein candidates were identified. Notably, the hexokinase-1 (HK1) protein was identified as a G4IP, and its selective binding toward G4 DNA was confirmed. This finding could be used to highlight the essential subcellular G4-mediated functions of HK1. The proposed labeling approach is a promising tool for investigating the protein interactions of the higher-order structural motifs and functional nucleic acids. Protein–nucleic acid interactions are pivotal in regulating cellular processes, yet identifying weakly bound proteins remains challenging. Here, the authors introduce a photocatalyst-modified DNA G-quadruplex approach for precise profiling of G4-interacting proteins, revealing insights into their roles in biological processes and advancing our understanding of nucleic acid regulation.