Chemical Editing of DNA-Mediated Nanoparticle Superlattices through a CRISPR-inspired Strategy

Biological systems employ molecular machinery to organize matter into functional structures and dynamically modify their organization in response to external signals. Translating such capabilities into synthetic nanomaterials requires strategies to selectively modify the interactions that define their structure. DNAbased assembly exploits sequence-specific molecular recognition to organize nanoscale components into prescribed architectures, yet post-assembly modification of structural DNA bonds remains challenging. Here, we demonstrate that enzymatic reactions, such as DNA-backbone covalent scission using CRISPRmediated editing of DNA linkers, provide targeted chemical modification of assembled 3D nanomaterials. Guide RNAs (gRNAs) direct Cas9 and Cas12a nucleases to selectively cleave DNA duplexes linking nanoparticles within ordered superlattices. Fluorescence measurements, optical microscopy, and timeresolved small-angle X-ray scattering (SAXS) reveal how molecular bond cleavage propagates into domain erosion, fragmentation, and loss of long-range lattice order. We extend this strategy to superlattices assembled from DNA-origami frames, demonstrating programmable disassembly through chemical cleavage of interframe DNA linkages. Importantly, sequence-selective disassembly can be realized within mixed populations of DNA-origami lattices, where Cas9 selectively disrupts lattices containing the recognized linker sequence, while non-targeted lattices retain their structure within the same reaction environment. These results establish sequence-specific chemical modification of DNA bonds as a strategy for selectively transforming DNA-based nanomaterials. This approach extends DNA programmability beyond encoding the initial assembly to directing post-assembly transformations, providing a pathway toward nanomaterials whose organization can be selectively modified through guided enzymatic processes,