GA: The targeted degradation of proteins through the proteasome pathway is achieved by utilizing the programmability of DNA, known as DNA-Proteolysis targeting chimera. This approach involves the construction of two DNA strands conjugated with separate ligands: one for interacting with E3 ligase and another for targeting the protein of interest.

Proteolysis targeting chimera (PROTAC) technology holds great promise as a protein degradation modality in therapeutic development. However, there remain challenges, including complex chemical synthesis and linker screening. To address this, a proof-of-concept of a new modularized method by constructing DNA-PROTAC is presented by identifying the valid BRD4 and Sirt2 DNA-PROTACs. These findings may provide new approaches for linker design and ligand screening for PROTACs. Herein, a ligand modularization strategy is proposed that leverages the programmability of DNA to modulate the design and construction of PROTAC molecules to facilitate the programmatic discovery of new PROTAC molecules. The bromodomain-containing protein 4 (BRD4) is selected as a target for degradation to verify the effectiveness of DNA-PROTACs. The kinetics of BRD4 degradation were assessed by performing time-course experiments in HeLa cells. In addition, to evaluate the feasibility of the DNA-PROTAC strategy for degradation of other proteins, the silent mating type information regulation 2 homolog−2 (Sirt2) is selected as the degradation target. The design and synthesis procedures of BRD4 and Sirt2 DNA-PROTACs and their mechanisms of action, are systematically introduced, and the results may provide a new method for linker design and ligand screening of PROTACs.