A DNA origami framework cryptosystem with nanoconfinement control of fluorescence logic permutations

The confinement-controlled molecular interactions in living systems are fundamental for governing information conversion and transmission in metabolic processes. Artificial systems that mimic this confinement effect at the nanoscale provide valuable insights into programmable molecular information processing. Here, we introduce DNA origami framework cryptosystem (DOFC), a strategy that leverages DNA origami for nanoscale information exchange and logical operations to enhance cryptographic capabilities. Spatial confinement enforces localized FRET interactions, adding a direct mode of nanoscale information transmission beyond encoding. By harnessing the vast fluorescence permutations enabled by DNA origami frameworks (~100 nanometers in size), we achieve an extensive cryptographic key size of 1040 bits. Furthermore, by integrating the diverse folding possibilities of a 7249-nucleotide-long DNA scaffold, the total key size can be expanded to 1742 bits. In addition, addressable Förster resonance energy transfer (FRET) enhances security through logical verification. This strategy advances the field of cryptography by merging the confinement effect with nano-addressable DNA frameworks, expanding the potential for secure nanoscale information transmission.