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Cited by 137DNA and Biological ComputingAdvanced Data Storage TechnologiesAlgorithms and Data Compression

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Demonstration of End-to-End Automation of DNA Data Storage.

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Takahashi, Christopher N., Nguyen, Bichlien H., Strauss, Karin, Ceze, Luis·2019·Scientific Reports
DOI 10.1038/s41598-019-41228-8PMC PMC6428863

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Abstract

Synthetic DNA has emerged as a novel substrate to encode computer data with the potential to be orders of magnitude denser than contemporary cutting edge techniques. However, even with the help of automated synthesis and sequencing devices, many intermediate steps still require expert laboratory technicians to execute. We have developed an automated end-to-end DNA data storage device to explore the challenges of automation within the constraints of this unique application. Our device encodes data into a DNA sequence, which is then written to a DNA oligonucleotide using a custom DNA synthesizer, pooled for liquid storage, and read using a nanopore sequencer and a novel, minimal preparation protocol. We demonstrate an automated 5-byte write, store, and read cycle with a modular design enabling expansion as new technology becomes available.

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Crossref · 10.1038/s41598-019-41228-8

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Figure 1 An overview of the write-store-read process. Data is encoded, with error correction, into DNA bases, which are synthesized into physical DNA molecules and stored. When a user wishes to read the data, the stored DNA is read by a DNA sequencer into bases and the decoding software corrects any errors retrieving the original data. (a) The logical flow from bits to bases to DNA and back. (b) A block diagram representation of the system hardware’s three modules: synthesis, storage, and sequencing. (c) A photograph showing the completed system. Highlighted are the storage vessel and the nanopore loading fixture. The majority of the remaining hardware is responsible for synthesis. (d) Overview of enzymatic preparation for DNA sequencing. An arbitrary 1 kilobase “extension segment” of DNA is PCR-amplified with TAQ polymerase, and a Bsa-I restriction site is added by the primer, leaving an A-tail and a TCGC sticky end after digestion. The extension segment is then T/A ligated to the standard Oxford Nanopore Technology (ONT) LSK-108 kit sequencing adapter, creating the “extended adapter,” which ensures that sufficient bases are read for successful base calling. For sequencing, the payload hairpin and extended adapter are ligated, forming a sequence-ready construct that does not require purification.
Figure 1 An overview of the write-store-read process. Data is encoded, with error correction, into DNA bases, which are synthesized into physical DNA molecules and stored. When a user wishes to read the data, the stored DNA is read by a DNA sequencer into bases and the decoding software corrects any errors retrieving the original data. (a) The logical flow from bits to bases to DNA and back. (b) A block diagram representation of the system hardware’s three modules: synthesis, storage, and sequencing. (c) A photograph showing the completed system. Highlighted are the storage vessel and the nanopore loading fixture. The majority of the remaining hardware is responsible for synthesis. (d) Overview of enzymatic preparation for DNA sequencing. An arbitrary 1 kilobase “extension segment” of DNA is PCR-amplified with TAQ polymerase, and a Bsa-I restriction site is added by the primer, leaving an A-tail and a TCGC sticky end after digestion. The extension segment is then T/A ligated to the standard Oxford Nanopore Technology (ONT) LSK-108 kit sequencing adapter, creating the “extended adapter,” which ensures that sufficient bases are read for successful base calling. For sequencing, the payload hairpin and extended adapter are ligated, forming a sequence-ready construct that does not require purification.CC BY · PubMed Central
Figure 2 Synthesis and sequencing process quality. (a) Insertion, deletion, and substitution frequency by locus for a synthesized and PCR-amplified 100-mer. Below: An overview of errors. Above: An expanded view of the central 60 bases. The terminal 20 bases come from primers used in amplification and therefore are not representative of synthesis quality. (b) Combined write-to-read quality of synthesis, ligation, and sequencing. Bases −60 to −4 (below, grey) are adapter bases. Bases −3 to 0 (below, red) are the ligation scar. Bases 0 to 39 (below, blue) are the synthesized payload region with 8 bases of padding on the 3′ end. (c) Distribution of nanopore read lengths with unligated, 1D and 2D read lengths identified.
Figure 2 Synthesis and sequencing process quality. (a) Insertion, deletion, and substitution frequency by locus for a synthesized and PCR-amplified 100-mer. Below: An overview of errors. Above: An expanded view of the central 60 bases. The terminal 20 bases come from primers used in amplification and therefore are not representative of synthesis quality. (b) Combined write-to-read quality of synthesis, ligation, and sequencing. Bases −60 to −4 (below, grey) are adapter bases. Bases −3 to 0 (below, red) are the ligation scar. Bases 0 to 39 (below, blue) are the synthesized payload region with 8 bases of padding on the 3′ end. (c) Distribution of nanopore read lengths with unligated, 1D and 2D read lengths identified.CC BY · PubMed Central

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Metadata

Authors
Takahashi, C. N., Nguyen, B. H., Strauss, K., & Ceze, L.
Affiliations
  • University of Washington (US)
  • Microsoft (United States) (US)
Corresponding author
Takahashi, Christopher N.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2019-03-21
Volume
9
Issue
1
Pages
4998-4998
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-019-41228-8
PMC
PMC6428863
OpenAlex
W2897609915
Cited by
137
References
17
Citations by year
2026: 6 · 2025: 16 · 2024: 21 · 2023: 27 · 2022: 22 · 2021: 19 · 2020: 16 · 2019: 10
FWCI
5.54
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Microsoft Research
  • United States Department of Defense | Defense Advanced Research Projects Agency (W911-NF-18-2-0034)
  • Defense Sciences Office, DARPA (W911-NF-18-2-0034)
Topics
  • Physical Sciences › Mathematics › Theoretical Computer Science › DNA and Biological Computing
  • Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
  • Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Keywords
DNA data storage, synthetic DNA, end-to-end automation, nanopore sequencing, data encoding
MeSH terms
Automation, DNA, Humans, Information Storage and Retrieval, Sequence Analysis, DNA, Computational Biology

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