A DNA-Based Archival Storage System

Bornholt, James; Lopez, Randolph; Carmean, Douglas M.; Ceze, Luís; Seelig, Georg; Strauß, Karin

doi:10.1145/2980024.2872397

Cited by 89 publications

(133 citation statements)

References 26 publications

(37 reference statements)

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“…While there are approaches that generate significantly longer strands of DNA, those are based on writing short strands of DNA and stitching them together 9 , which is currently not a scalable approach. As a consequence, all recently proposed systems 3–8,10 stored information on DNA molecules of one-two hundred nucleotides. The second technological constraint is that the DNA molecules are stored in a pool and cannot be spatially ordered.…”

Section: Introductionmentioning

confidence: 99%

A Characterization of the DNA Data Storage Channel

Heckel

Mikutis

Grass

2019

Sci Rep

193

181

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Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by sampling from this DNA pool. Moreover, imperfections in writing (synthesis), reading (sequencing), storage, and handling of the DNA, in particular amplification via PCR, lead to a loss of DNA molecules and induce errors within the molecules. In order to design DNA storage systems, a qualitative and quantitative understanding of the errors and the loss of molecules is crucial. In this paper, we characterize those error probabilities by analyzing data from our own experiments as well as from experiments of two different groups. We find that errors within molecules are mainly due to synthesis and sequencing, while imperfections in handling and storage lead to a significant loss of sequences. The aim of our study is to help guide the design of future DNA data storage systems by providing a quantitative and qualitative understanding of the DNA data storage channel.

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Section: Introductionmentioning

confidence: 99%

A Characterization of the DNA Data Storage Channel

Heckel

Mikutis

Grass

2019

Sci Rep

193

181

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“…DNA, carrier of genetic information and arguably nature’s largest biopolymer, has already been used as a macromolecular carrier of information, able to archive 2 – 4 , manage (DNA hard disk) 5 and encrypt data 6 – 8 easily retrieved by well-established read-out tools 9 . Moreover, immense storage densities can be achieved, i.e.…”

Section: Introductionmentioning

confidence: 99%

Multifunctional sequence-defined macromolecules for chemical data storage

et al. 2018

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Sequence-defined macromolecules consist of a defined chain length (single mass), end-groups, composition and topology and prove promising in application fields such as anti-counterfeiting, biological mimicking and data storage. Here we show the potential use of multifunctional sequence-defined macromolecules as a storage medium. As a proof-of-principle, we describe how short text fragments (human-readable data) and QR codes (machine-readable data) are encoded as a collection of oligomers and how the original data can be reconstructed. The amide-urethane containing oligomers are generated using an automated protecting-group free, two-step iterative protocol based on thiolactone chemistry. Tandem mass spectrometry techniques have been explored to provide detailed analysis of the oligomer sequences. We have developed the generic software tools Chemcoder for encoding/decoding binary data as a collection of multifunctional macromolecules and Chemreader for reconstructing oligomer sequences from mass spectra to automate the process of chemical writing and reading.

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“…In previous work, we demonstrated the ability to write over 200 megabytes of information in about 2 billion nucleotides while recovering all data using random access without any bit errors using Illumina SBS technology 7 . Our group and others have demonstrated random access by selective PCR amplification of a given file without having to read all the data stored in a particular DNA pool 3,5,8,9 . Despite its low error rate and high throughput, SBS technology has several shortcomings in the context of DNA storage.…”

Section: Introductionmentioning

confidence: 99%

DNA assembly for nanopore data storage readout

et al. 2019

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Synthetic DNA is becoming an attractive substrate for digital data storage due to its density, durability, and relevance in biological research. A major challenge in making DNA data storage a reality is that reading DNA back into data using sequencing by synthesis remains a laborious, slow and expensive process. Here, we demonstrate successful decoding of 1.67 megabytes of information stored in short fragments of synthetic DNA using a portable nanopore sequencing platform. We design and validate an assembly strategy for DNA storage that drastically increases the throughput of nanopore sequencing. Importantly, this assembly strategy is generalizable to any application that requires nanopore sequencing of small DNA amplicons.

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A DNA-Based Archival Storage System

Cited by 89 publications

References 26 publications

A Characterization of the DNA Data Storage Channel

A Characterization of the DNA Data Storage Channel

Multifunctional sequence-defined macromolecules for chemical data storage

DNA assembly for nanopore data storage readout

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