Programmable DNA Origami-Based Protease Device for Precise and Direct Proteins Degradation

Targeted protein degradation as a therapeutic modality leverages cellular proteolytic pathways to specifically eliminate disease-associated proteins. However, the dependence on endogenous pathways limited its further development in safety and universality. We fabricate a DNA origami-based protease device (DOPD) for extracellular direct degradation of tumor-associated proteins by regulating the activity of the protease. The DOPD features a six-helix bundle structure with a dual-functional architecture: an inner catalytic layer assembling proteases and trap strands and an outer shielding layer decorated with poly(lactic-co-glycolic acid) to limit the protease activity. By incorporating a pH-sensitive switch and a recognition module, this system enables direct protein degradation by inducing proximity between target proteins and proteases. We demonstrate that this system specifically degrades nucleolin and PD-L1 on tumor cells under acidic conditions, exerting direct cytotoxicity on tumor cells and alleviating immunosuppression in immune cells. As a proof of concept, DOPD-mediated tumor immunotherapy was validated in a xenograft mouse model, underscoring its potential as a programmable platform for precise protein degradation.