Logic‐Gated Molecular Machines Encapsulate Environment‐Responsive DNA Actuators for Tunable Cellular Lysosome Interference

Intracellular DNA nanoassemblies have proven to potently induce organelle dysfunction and cell death, while their scale-dependent capacity of cellular interference remains undefined. To address it, here we engineer a logic-gated lysosome-targeted molecular machine that encapsulates ATP-driven DNA actuators, which can assemble into different-scaled nanoarchitectures in response to lysosomal microenvironments. Such a design enables the programmable DNA nanoassembly and tunable lysosome interference, straightforwardly visualized by atomic force microscopy (AFM) and bio-transmission electron microscopy (bio-TEM), respectively, showing that larger DNA assemblies promote stronger membrane permeabilization and greater cytotoxicity. It evidences the pronounced scale-dependent lysosome interference and clues how to rationally design DNA nanoassemblies for cell regulation. We further investigate the primary pathway of programmed cell death induced by DNA nanoassemblies, which reveals the cathepsin-mediated caspase-independent lysosomal cell death, alongside a minor caspase-dependent pathway. This work demonstrates a programmable "dual-signal logic-structural assembly-functional output" cascade at the suborganelle level, which would establish a new paradigm for DNA-based nanotherapeutics.