A Simple Proton-Driven Allosteric Aptamer Nanorobot for Receptor Tyrosine Kinase Degradation and Behavior Modulation in Cancer Cells

Abstract The aptamer-based strategy for selective protein degradation demonstrates broad application prospects in the field of biomedicine, particularly holding significant therapeutic potential for tumors and other protein dysregulation-related diseases. However, it faces substantial challenges due to on-target off-tumor effects arising from nonspecific expression of target proteins. To address this issue efficiently, we report here a pH-responsive allosteric DNA nanorobot (named A/I) that enhances the precision of aptamer-mediated target protein degradation through tumor microenvironment-specific activation. The allosteric nanorobot is comprised of two modules: the recognition module (A-strand) and the response module (I-strand). To be specific, the A-strand integrates both target recognition and degradation-inducing capabilities, while the I-strand blocks the recognition sites of the A-strand through complementary base pairing and confers pH sensitivity. Under physiological pH conditions, the A/I nanorobot exists stably in the form of a double-stranded structure. When the acidic tumor microenvironment is encountered, the pH-triggered conformational change of the I-strand induces the duplex disassembly, releasing the A-strand, which can specifically bind to the target protein and subsequently induce its degradation. Our findings demonstrate that the activatable allosteric nanorobot achieves targeted protein degradation, significantly inhibiting the proliferative and migratory abilities of tumor cells. In general, the activatable allosteric nanorobot has innovatively overcome the bottleneck of insufficient selectivity in traditional aptamer-based protein degradation strategies, providing a molecular tool for precision tumor therapy technologies. In addition, the allosteric nanorobot features a simple design and enables specific degradation of diverse target proteins by flexible replacement of the recognition module, demonstrating significant potential for constructing a universal protein precise degradation platform.