Abstract
Synthetic DNA-based data storage systems (1–12) have received significant attention due to the promise of ultrahigh storage density. However, all proposed systems suffer from high cost, read-write latency and error-rates that render them impractical. One means to avoid synthesizing DNA is to use readily available native DNA. As native DNA content is fixed, one may adopt an alternative recording strategy that modifies the DNA topology to encode desired information. Here, we report the first macromolecular storage paradigm in which data is written in the form of “nicks (punches)” at predetermined positions on the sugar-phosphate backbone of native dsDNA. The platform accommodates parallel nicking on multiple “orthogonal” genomic DNA fragments, paired nicking and disassociation for creating “toehold” regions that enable single-bit random access and strand displacement. As a proof of concept, we used the multiple-turnover programmable restriction enzyme Pyrococcus furiosus Argonaute (13) to punch files into the PCR products of Escherichia coli genomic DNA. The encoded data is reliably reconstructed through simple read alignment.
One sentence summary We propose a novel cost-efficient and low-latency method for DNA-based data storage that uses native DNA and a programmable nickase to record data in the form of nicks and also enables strand displacement computing and bitwise random access.
