SDC2021: Scalable and Dynamic File Operations for DNA-based Data Storage

DNA-based data storage systems have the potential to offer unprecedented increases in density and longevity over conventional storage mediums. Starting from the assumption that advances in synthesis and sequencing technology will soon make DNA-based storage cost competitive with conventional media, we will need ways of organizing, accessing, and manipulating the data stored in DNA to harness its full potential. There are a range of possible storage system designs. This talk will cover three systems that the speaker co-developed and prototyped at NC State / DNAli Data Technologies. First, we'll show how we expanded the set of uniquely addressable files by nesting primers, the chemical labels that identify each file, to ensure that system capacity can reach the high densities afforded by DNA. Second, in our File Preview system, we exploit the thermodynamics of primer bindings to create a new file access operation that allows either full or partial access of a file's data, thereby saving sequencing bandwidth when a partial file read is sufficient. While the first two systems rely on double-stranded DNA, the third system, DORIS, is comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA). The overhang serves as a physical address for accessing specific DNA strands as well as enabling a range of in-storage file operations like renaming and deletion. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it.

Learning Objectives
Describe a typical architecture for DNA-based Storage System and its key components.
Explain how strand design, data encoding, and a few key molecular biology techniques enable scalable file access and new access modes.
Describe a new architecture that uses a single-strand overhang and T7 promoter to provide in-storage file operations and repeatable information access by transcribing information from DNA without destroying it.

Presented by
James Tuck
NC State University / DNAli Data Technologies
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