ProbeFS: Hierarchical DNA File Systems via Biochemical Content Addressability and Parallelism

DNA storage offers exceptional density, durability, and energy efficiency, yet existing DNA file systems provide only flat storage abstractions with no hierarchical directory structure. Directly applying conventional hierarchy to DNA storage is impractical: hierarchy creates cross-file dependencies whose resolution demands multi-round DNA sequencing, either through sequential directory traversal at read time or cascading propagation at write time. We observe that two inherent biochemical properties of DNA—content-addressability via Watson-Crick base pairing and massive parallelism via concurrent molecular hybridization—can effectively address this overhead. We present ProbeFS, a hierarchical DNA file system co-designed with these properties. ProbeFS introduces path identifiers, a DNA encoding in which files sharing a common ancestor share subsequences, enabling (1) probe-based path resolution that locates files without directory traversal, (2) one-shot file retrieval that fetches entire directory subtrees in a single hybridization without knowing file identities in advance, and (3) chained delta updates that efficiently modify immutable DNA strands. Wet-lab experiments, thermodynamic simulations at scales up to 100K files, and in silico evaluation show that ProbeFS reduces read amplification by up to 5,124× and serialized sequencing rounds by up to 54×, achieving end-to-end retrieval latency of 1.3-2.7 hours—comparable to Amazon S3 Glacier Flexible Retrieval.