Spatially Convergent Encoding of Linked Data Through Assembled DNA Nanostructures

DNA-based storage is a promising candidate for next-generation data media, providing a powerful strategy for preserving digital information in molecular formats. As information complexity increases, multiple DNA molecules are often used to encode related data elements, but their independent distribution can compromise information linkage during amplification-based readout. Although microdroplet PCR reduces amplification bias through spatial compartmentalization, stochastic partitioning of individual DNA molecules may hinder the recovery of associated information. Here, we present a Y-shaped DNA nanostructure system that integrates multiple related DNA sequences into a single molecular scaffold, enabling physical co-localization of linked information before compartmentalization. The Y-shaped architecture serves as a unified input unit for microdroplet PCR, allowing coordinated amplification and accurate recovery of associated data within individual droplets. By maintaining molecular linkage during processing, this strategy improves the uniformity of DNA-encoded linked information recovery. Overall, this system provides a programmable framework for DNA data organization and droplet-based retrieval of linked information.