Structure-based DNA memory with Boolean random access

Abstract

Structure-based DNA memory represents a paradigm shift from nucleotide-encoded storage, circumventing the costly repetitive synthesis and sequencing dependencies while harnessing the programmable architecture of DNA nanostructures. However, the absence of random-access capability has constrained practical implementation. Here, we implement a Boolean search-enabled random-access scheme for structural DNA memory, wherein data is encoded on DNA origami tiles with orthogonally dimensioned index strands (1D/2D/3D addressing). Boolean operations are executed by hybridizing biotinylated probes to target index combinations, enabling the magnetic extraction of specific files. Atomic force microscopy validation confirms the precise retrieval of data across single-, dual-, and triple-indexed libraries. This approach establishes a robust framework for enabling random access in complex structural DNA databases.