DNA punch cards for storing data on native DNA sequences via enzymatic nicking

S. Kasra Tabatabaei, Boya Wang, Nagendra Bala Murali Athreya, Behnam Enghiad, Alvaro Gonzalo Hernandez, Christopher J. Fields, Jean-Pierre Leburton, David Soloveichik, Huimin Zhao () and Olgica Milenkovic ()
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S. Kasra Tabatabaei: University of Illinois at Urbana-Champaign
Boya Wang: University of Texas at Austin
Nagendra Bala Murali Athreya: University of Illinois at Urbana-Champaign
Behnam Enghiad: University of Illinois at Urbana-Champaign
Alvaro Gonzalo Hernandez: University of Illinois at Urbana-Champaign
Christopher J. Fields: University of Illinois at Urbana-Champaign
Jean-Pierre Leburton: University of Illinois at Urbana-Champaign
David Soloveichik: University of Texas at Austin
Huimin Zhao: University of Illinois at Urbana-Champaign
Olgica Milenkovic: University of Illinois at Urbana-Champaign

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA. As the sequence content of native DNA is fixed, one can modify the topology instead to encode information. Here, we introduce DNA punch cards, a macromolecular storage mechanism in which data is written in the form of nicks at predetermined positions on the backbone of native double-stranded DNA. The platform accommodates parallel nicking on orthogonal DNA fragments and enzymatic toehold creation that enables single-bit random-access and in-memory computations. We use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA and accurately reconstruct the encoded data through high-throughput sequencing and read alignment.

Date: 2020
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15588-z

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DOI: 10.1038/s41467-020-15588-z

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