PT  - JOURNAL ARTICLE
AU  - S Kasra Tabatabaei
AU  - Boya Wang
AU  - Nagendra Bala Murali Athreya
AU  - Behnam Enghiad
AU  - Alvaro Gonzalo Hernandez
AU  - Christopher J. Fields
AU  - Jean-Pierre Leburton
AU  - David Soloveichik
AU  - Huimin Zhao
AU  - Olgica Milenkovic
TI  - DNA Punch Cards: Storing Data on Native DNA Sequences via Nicking
AID  - 10.1101/672394
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 672394
4099  - http://biorxiv.org/content/early/2020/01/07/672394.short
4100  - http://biorxiv.org/content/early/2020/01/07/672394.full
AB  - Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all platforms proposed so far suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern optical and magnetic storage devices. One means to avoid synthesizing DNA and to reduce the system error-rates is to use readily available native DNA. As the symbol/nucleotide content of native DNA 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 and paired nicking and disassociation for creating “toehold” regions that enable single-bit random access and strand displacement in-memory computations. As a proof of concept, we used the programmable restriction enzyme Pyrococcus furiosus Argonaute to punch two files into the PCR products of Escherichia coli genomic DNA. The encoded data is accurately reconstructed through high-throughput sequencing and read alignment.