Archival data storage using DNA proximity graphs

Abstract

DNA offers a promising medium for long-term archival data storage, but data-specific DNA synthesis remains costly. Here we introduce SPAN (Synthesis-free Proximity-graph Archiving in Nucleic acids), a synthesis-independent storage architecture in which information is written as a physical pattern and encoded in the spatial relationships of randomly barcoded DNA molecules. Barcodes are deposited onto an optically patterned surface, and an enzymatic reaction records neighboring barcode pairs. Sequencing these pairs produces a proximity graph from which the information is decoded. We demonstrate this principle by writing a 136-bit pattern using photolithography and recovering 90% of the bits. Our cost analysis estimates lower writing costs than any existing DNA storage method. Using established commercial optical writing technologies, we project a further five-order-of-magnitude cost reduction to below flash memory costs. Although readout is more expensive, this trade-off is attractive for deep archival storage, where information is written once and rarely, if ever, retrieved.