DNA-Programmable Protein Degradation: Dynamic Control of Proteolysis-Targeting Chimera Activity via DNA Hybridization and Strand Displacement.

Targeted protein degradation is a powerful therapeutic approach: expanding the druggable proteome, providing enhanced selectivity, and having the ability to overcome conventional resistance mechanisms. A major class of such molecules is proteolysis-targeting chimeras (PROTACs). PROTACs are catalytic heterobifunctional small molecules that simultaneously bind a protein of interest (POI) and an E3 ligase. And thus, PROTACs induce a proximity-dependent ubiquitination of the POI and its subsequent degradation by the ubiquitin-proteasome system. While PROTACs have successfully transitioned from academia to industry, increasing awareness of off-target effects and related toxicities highlights the urgent need for precise control mechanisms over activity. Achieving this level of control, however, remains challenging, with traditional chemistries. DNA nanotechnology, with its unparalleled programmability and structural versatility, presents a powerful tool for achieving such control. Here, we report the design and characterization of oligonucleotide-linked PROTACs (OligoPROTACs). These constructs comprise PROTAC warheads covalently linked to separate complementary DNA strands, brought together in space via DNA hybridization. OligoPROTACs are able to degrade the POI in a distance-dependent manner. Furthermore, we demonstrate the first instance of a dynamic off-switch mechanism for PROTAC activity, enabled by toehold-mediated strand displacement using a third DNA strand. This work highlights the potential of DNA nanotechnology combined with the clinical emergence of nucleic acid therapeutics to enhance the safety and functionality of PROTAC systems, paving the way for more refined and translatable therapeutic strategies.