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Some diseases, including certain types of cancer, Pompe disease, Alzheimer’s, Parkinson’s, and Huntington’s disease, are often treated by targeting lysosomes. These cellular organelles play a crucial role in various processes, such as regulating cell death. Our study demonstrates that, depending on the surface modification of DNA nanostructures, concentration, and exposure time, we can regulate the lysosomal response and set conditions leading either to the activation of the immune response or to controlled killing of cancer cells.