Random access in large-scale DNA data storage

Organick, Lee; Ang, Siena Dumas; Chen, Yuan Jyue; Lopez, Randolph; Yekhanin, Sergey; Makarychev, Konstantin; Rácz, Miklós Z.; Kamath, Govinda M.; Gopalan, Parikshit; Nguyen, Bichlien H.; Takahashi, Christopher N.; Newman, Sharon; Parker, Hsing Yeh; Rashtchian, Cyrus; Stewart, Kendall; Gupta, Gagan; Carlson, Robert H.; Mulligan, John; Carmean, Douglas M.; Seelig, Georg; Ceze, Luís; Strauß, Karin

doi:10.1038/nbt.4079

Cited by 543 publications

(845 citation statements)

References 15 publications

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“…Error correction coding is performed to correct errors within each oligonucleotide and to deal with missing oligonucleotides. Two of the state-of-the-art works [1] and [4] use very distinct schemes for the error correction and decoding and are discussed below.…”

Section: Previous Workmentioning

confidence: 99%

“…The work in [4] uses large block length RS codes to correct both erasures and errors. However the RS codes operate on symbol-level errors (16-bit symbols in their work) and hence are not optimal for single base errors (i.e.…”

Section: Previous Workmentioning

confidence: 99%

“…The longevity of DNA-based storage makes it ideal as an archival medium to store the knowledge gained by humanity over the millennia. Along with high density data storage, DNA-based storage systems allow efficient duplication of data and random access using PCR-based techniques [3] [4].…”

Section: Introductionmentioning

confidence: 99%

“…Since both the DNA synthesis and sequencing processes are inherently error-prone, error correction coding based on the characteristics of this noise is critical for reliable decoding of data. There has been a series of recent works on DNA-based storage such as [1], [4], [5], [6], [7] and [8] which focus on error correction and random-access retrieval, among other aspects. Figure 1 shows a schematic of a typical DNA-based storage system.…”

Section: Introductionmentioning

confidence: 99%

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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Chandak

Tatwawadi

Lau

et al. 2019

Preprint

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With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based storage systems can offer significantly higher storage densities (petabytes/gram) and durability (thousands of years) than current technologies. Specifically, DNA has been found to be stable over extended periods of time which has been demonstrated in the analysis of organisms long since extinct. Recent advances in DNA sequencing and synthesis pipelines have made DNA-based storage a promising candidate for the storage technology of the future.Recently, there have been multiple efforts in this direction, focusing on aspects such as error correction for synthesis/sequencing errors and erasure correction for handling missing sequences. The typical approach is to use separate codes for handling errors and erasures, but there is limited understanding of the efficiency of this framework. Furthermore, the existing techniques use short block-length codes and heavily rely on read consensus, both of which are known to be suboptimal in coding theory.In this work, we study the tradeoff between the writing and reading costs involved in DNA-based storage and propose a practical scheme to achieve an improved tradeoff between these quantities. Our scheme breaks with the traditional separation framework and instead uses a single large block-length LDPC code for both erasure and error correction. We also introduce novel techniques to handle insertion and deletion errors introduced by the synthesis process. For a range of writing costs, the proposed scheme achieves 30-40% lower reading costs than state-of-the-art techniques on experimental data obtained using array synthesis and Illumina sequencing.

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Section: Previous Workmentioning

confidence: 99%

Section: Previous Workmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Chandak

Tatwawadi

Lau

et al. 2019

Preprint

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“…The ability to chemically assemble oligodeoxynucleotide (ODN) on a solid support efficiently has made a broad impact in the last few decades on many research areas including molecular biology, chemical biology, synthetic biology, data storage, nanotechnology, and medicine . However, the success of ODN synthesis is mainly limited to unmodified ODNs.…”

Section: Introductionmentioning

confidence: 99%

Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid‐Phase Synthesis

et al. 2018

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Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2‐methoxyethyl, 4‐methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc (i. e. dimethyl‐1,3‐dithian‐2‐ylmethoxycarbonyl) phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non‐nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6‐chloropurine using the same strategy are described.

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Synthetic Polymers with Finely Regulated Monomer Sequences: Properties and Emerging Applications

Laurent

Szweda

Lutz

2022

Macromolecular Engineering

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The design of synthetic polymers with controlled monomer sequences is an important emerging trend in polymer science. This new field of research is bio‐inspired by sequence‐defined biopolymers such as proteins and nucleic acids. The chemical synthesis of nonnatural sequence‐controlled polymers (SCPs) has been described in several reviews. However, there is currently little information about the properties and applications of these polymers. In this context, the aim of this article is to give a comprehensive view on these aspects. After a general introduction and a short section about the synthesis of SCPs, the physicochemical properties of these synthetic macromolecules are described in detail. For instance, emphasis is put on the bulk and solution self‐assembly of SCPs. In the last part of this article, potential applications are reviewed and discussed. Overall, SCPs, which are more time‐consuming to synthesize than regular commodity polymers, are not meant to be used in high‐scale applications but more in specialty technologies with high‐added value. For instance, application areas such as data storage, anti‐counterfeiting technologies, catalysis, and photovoltaics are described in this article.

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Random access in large-scale DNA data storage

Cited by 543 publications

References 15 publications

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid‐Phase Synthesis

Synthetic Polymers with Finely Regulated Monomer Sequences: Properties and Emerging Applications

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