DNA Punch Cards: Storing Data on Native DNA Sequences via Nicking

Abstract

Synthetic DNA-based data storage systems (1-11) have received significant attention due to the promise of ultrahigh storage density. 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. As a proof of concept, we used the multiple-turnover programmable restriction enzyme Pyrococcus furiosus Argonaute (12) to punch files into the PCR

Secure data storage on DNA hard drives

“…Here in the example, only oligonucleotide complementary to green overhang is added, so the green site is read as '1' while the red '0'. 10 Based on this platform, we now demonstrate that we can write, erase and rewrite data on the DNA-HDs. In order to facilitate the proof of concept, the DNA-HD is designed with five sites with ssDNA overhangs between two REF sites (see sequences in Table S2), which we name D1-D5 ( Fig.2A).…”

“…However, fundamental challenges, including the Therefore, alternatives are desperately needed which are not only for improving the encoding and writing strategy for the simple static data storage in DNA sequence but also for dynamic data operation such as rewritable capability and computing towards a realistic DNA computer. Employing existing native DNA strands rather than always synthesizing new strand are new routes, for instance, the DNA punch card method and the catalog DNA method (10,11). 5 Data storage in 3D structures of DNA (12)(13)(14) or protein is another option as this may offer easier routes for data writing only by mixing components to build molecules.…”

“…The information encoded in 3D structures of these molecules can be conveniently read by single-molecule methods such as nanopore sensing (15)(16)(17)(18)(19). We proposed a method for storing data on DNA 10 nanostructures along double-stranded DNA (dsDNA) by mixing and incubating oligonucleotides and scaffolds (20). This method has intrinsic advantages in writing cost as we only need 2n oligonucleotide components for building libraries containing 2 n (~5.2×10 33 for n=112) different molecules.…”

“…ERASE: A designed ssDNA strand erases D3 by removing the bound biotin-streptavidin using a strand displacement reaction. REWRITE: After erasing, new data can be encoded by adding new biotinylated ssDNA strand, completing the writing-erasing-rewriting 10 cycle. (C) Characterisation of the performance of the system.…”

“…Figures S5 and S6. 10 In this study, we demonstrate the original innovation only by showing encoding words, but our platform has the full capability to be scaled up using droplet microfluidics which can be automated in parallel to store a large amount of data. Our approach indeed has an inherently lower density compared to data storage in the DNA sequence which is ~10 6 of that in hard drives 15 (2).…”