Two-dimensional data storage using a DNA molecular register

Existing molecular data-storage systems still mainly encode information along one-dimensional chemical sequences or linear molecular coordinates, leaving the spatial addressability of molecular architectures insufficiently explored. Here we report a physical two-dimensional DNA molecular register, termed a spatially addressable molecular breadboard (SAMB), in which digital bits are assigned to predefined molecular coordinates rather than to positions along a one-dimensional sequence. SAMB is built by hierarchical assembly of DNA origami single modules into a globally registered two-dimensional address space. In this register, each data or parity bit is encoded by the presence or absence of streptavidin at a defined coordinate site and read out from local topographic height differences, whereas the fiducial marker (FM) site defines register orientation and coordinate alignment. As a proof of concept, we encode a Petersen graph payload in a 49-coordinate SAMB register and demonstrate in situ atomic force microscopy (AFM) readout, coordinate-based bit calling, and graph reconstruction. We further incorporate three block-wise even-parity positions as proof-of-concept design elements. In a randomly selected test subset of 56 readable SAMB structures, the 45 graph-bit positions yielded a raw graph-bit accuracy of 86.79%, with false-positive and false-negative rates of 7.32% and 25.00%, respectively; the three parity-bit positions, evaluated separately, yielded a raw site-readout accuracy of 82.14%. These results show that DNA nanostructures can serve as physical two-dimensional molecular registers for coordinate-addressed data storage and provide a basis for topography-readable molecular information systems.