Development of Nuclear-Targeted Photoaffinity Probes with Cleavable Disulfide Bonds for Enhancing Selectivity in hPTM Interactome Profiling

Cell-penetrating, nuclear-targeted histone photoaffinity probes enable histone post-translational modification (hPTM) interactome profiling in native cells, yet noncleavable cell-penetrating peptides (e.g., cyclic polyarginine cell-penetrating peptide, cR10) induce interference due to their high positive charge. Herein, via facile synthesis, we developed novel nuclear-targeted histone photoaffinity probes with intracellularly cleavable cR10-disulfide linkages, targeting H3K4me3/H3K14la. In vitro labeling and proteomic assays demonstrated significantly improved binding selectivity for reader proteins and drastically reduced false-positive signals following cR10 cleavage.