RT Journal Article
SR Electronic
T1 DNA Punch Cards: Encoding Data on Native DNA Sequences via Nicking
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 672394
DO 10.1101/672394
A1 S Kasra Tabatabaei
A1 Boya Wang
A1 Nagendra Bala Murali Athreya
A1 Behnam Enghiad
A1 Alvaro Gonzalo Hernandez
A1 Jean-Pierre Leburton
A1 David Soloveichik
A1 Huimin Zhao
A1 Olgica Milenkovic
YR 2019
UL http://biorxiv.org/content/early/2019/08/04/672394.abstract
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 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 computations. As a proof of concept, we used the programmable restriction enzyme Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA. The encoded data is reliably reconstructed through simple read alignment.