High-speed 3D DNA PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography

DNA origami information storage is a promising alternative to silicon-based data storage, offering a molecular cryptography technique concealing information within DNA origami. Routing, sliding, and interlacing staple strands lead to a large 700-bit key size. Practical DNA data storage requires high information density, robust security, and accurate and rapid information retrieval. Consequently, advanced readout techniques and large encryption key sizes are essential. Here, we report an enhanced DNA origami cryptography protocol in 2D and 3D DNA origami, increasing the encryption key size. We employ all-DNA-based steganography with fast readout through high-speed DNA-PAINT super-resolution imaging. By combining DNA-PAINT data with unsupervised clustering, we achieve an accuracy of up to 89%, despite the flexibility in the 3D DNA origami shown by oxDNA simulation. Furthermore, we propose criteria that ensure complete information retrieval for the DNA origami cryptography. Our findings show that DNA-based cryptography is a secure and versatile solution for storing information.