DNA Punch Cards: Encoding Data on Native DNA Sequences via Nicking
DNA Punch Cards: Encoding Data on Native DNA Sequences via Nicking
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 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.
Tabatabaei S Kasra、Wang Boya、Zhao Huimin、Milenkovic Olgica、Leburton Jean-Pierre、Athreya Nagendra Bala Murali、Enghiad Behnam、Hernandez Alvaro Gonzalo、Soloveichik David
Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignDepartment of Electrical and Computer Engineering, University of Texas at AustinCenter for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign||Department of Chemical and Biomolecular engineering, University of Illinois at Urbana-Champaign||Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-ChampaignDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-ChampaignDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-ChampaignDepartment of Chemical and Biomolecular engineering, University of Illinois at Urbana-ChampaignRoy J. Carver Biotechnology Center, University of Illinois at Urbana-ChampaignDepartment of Electrical and Computer Engineering, University of Texas at Austin
分子生物学生物工程学
Tabatabaei S Kasra,Wang Boya,Zhao Huimin,Milenkovic Olgica,Leburton Jean-Pierre,Athreya Nagendra Bala Murali,Enghiad Behnam,Hernandez Alvaro Gonzalo,Soloveichik David.DNA Punch Cards: Encoding Data on Native DNA Sequences via Nicking[EB/OL].(2025-03-28)[2025-04-27].https://www.biorxiv.org/content/10.1101/672394.点此复制
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