Mobile and Self‐Sustained Data Storage in an Extremophile Genomic DNA

Abstract

DNA has been pursued as a novel biomaterial for digital data storage. While large-scale data storage and random access have been achieved in DNA oligonucleotide pools, repeated data accessing requires constant data replenishment, and these implementations are confined in professional facilities. Here, a mobile data storage system in the genome of the extremophile Halomonas bluephagenesis, which enables dual-mode storage, dynamic data maintenance, rapid readout, and robust recovery. The system relies on two key components: A versatile genetic toolbox for the integration of 10-100 kb scale synthetic DNA into H. bluephagenesis genome and an efficient error correction coding scheme targeting noisy nanopore sequencing reads. The storage and repeated retrieval of 5 KB data under non-laboratory conditions are demonstrated. The work highlights the potential of DNA data storage in domestic and field scenarios, and expands its application domain from archival data to frequently accessed data.

FECDO-Flexible and Efficient Coding for DNA Odyssey

“…The exponentially growth of the global datasphere has been stimulating the demand of exploring novel storage media since the beginning of twenty-first century [1][2][3][4]. Inspired by the storage of biological information, DNA has been employed as functional carrier for digital data in recent years, which surpasses traditional storage media in density and durability [5][6][7][8][9][10][11][12][13][14]. However, the cost of storing large-scale data in DNA remains unaffordable despite the constant decrease in expenses of DNA synthesis and DNA sequencing, which hinders the popularization of DNA data storage [3,15].…”

“…The first one is data transcoding, namely, transforming data (normally in the form of binary stream) into nucleotide sequence. Various encoding methods have been explored during the past decade [5][6][7][8][9][10][11][12][13][14][15]. However, the natural bound of 2 bit per nucleotide confined the utility of this approach [16][17].…”

“…These features include homopolymer runs (e.g., TTTTT), inappropriate secondary structure, heavily repeated subsequences, etc. Some studies attempted to avoid these sequences by designing special sequence screening algorithms [8,14]. However, these algorithms resulted in a decrease of the storage density, since the sequence space available for encoding is reduced.…”

Highly Robust DNA Data Storage Based on Controllable GC Content and homopolymer of 64-Element Coded Tables

“…Thanks to its rapidity and accuracy, the latest third-generation DNA molecular sequencing technology makes it easier to read and write the information content stored in DNA molecules [5]. In conjunction with third-generation DNA molecular sequencing technologies, several random read strategies have been proposed to achieve selective access to stored information [6][7][8], further enhancing the utility and scalability of DNA data storage.…”

Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing

“…DNA data storage has emerged as an innovative digital data storage medium owing to its durability and storage density. − As DNA molecules, which have a length per base of 0.34 nm, consist of four different bases (A, T, G, and C), the theoretical information density of DNA molecules greatly surpasses that of conventional electrical media . However, an ideal encoding rate of 2 bits per nucleotide cannot be achieved in practice owing to several limitations, particularly those originating from errors in current DNA writing and reading technologies. , Numerous errors can arise from both the DNA synthesis and sequencing process, which lead to erroneous insertions, deletions, and substitutions of bases in the data-encoded molecules or decoded data .…”