Technical Program

Paper Detail

Paper Title DNA Punch-Cards: Implementations and Coding-Theoretic Approaches
Paper IdentifierTU3.R1.3
Authors Olgica Milenkovic, University of Illinois at Urbana-Champaign, United States
Session Applications to Scientific Discovery
Location Le Théatre (Parterre), Level -1
Session Time Tuesday, 09 July, 14:30 - 16:10
Presentation Time Tuesday, 09 July, 15:10 - 15:30
Abstract Recent implementations of synthetic DNA-based data storage systems have demonstrated several promising applications of macromolecular recorders. However, the proposed systems suffer from high cost, read-write latency and error-rates that render them non-competitive with traditional silicon-based devices. One means to avoid synthesizing DNA is to use readily available, naturally occurring DNA. As the nucleotide sequences of native DNA are fixed, they cannot be edited to accommodate arbitrary user-defined content. Hence, instead of changing the sequence content, one may adopt an alternative recording strategy -- akin to card punching -- that modifies the topology of native DNA to encode desired information. We describe the first macromolecular storage paradigm in which data is written in the form of “nicks” at predetermined positions on the sugar-phosphate backbone of double– stranded native DNA. The platform accommodates parallel nicking on one and multiple genomic DNA fragments, and paired nicking and disassociation for creating “toehold” regions that enable single-bit random access and strand displacement. It also provides a large mass of inexpensive DNA that may be used for multiple, error-free readout cycles via current sequencing technologies. As a proof of concept, we used the multiple-turnover programmable artificial restriction enzymes to punch both text and image files into the PCR products of Escherichia coli genomic DNA fragments in vitro. The encoded data was reliably reconstructed through sequence alignment and read coverage analysis. The described storage implementation is accompanied by a number of new coding and information theory questions. This is a joint work with S Kasra Tabatabaei, Boya Wang, Nagendra Bala Murali Athreya, Behnam Enghiad, Alvaro Gonzalo Hernandez, Jean-Pierre Leburton, David Soloveichik, Huimin Zhao.