DNA assembly for nanopore data storage readout
Open accessAbstract
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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The error rate of second-generation synthesis and sequencing technology is less than 5%, while that of third-generation is about 10-15%.
“The error rate of the second-generation synthesis and sequencing technology is less than 5%, while that of the third-generation is about 10–15% [31, 32].”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [31]
A DNA assembly strategy was established to overcome the problem in reading short DNA strands by Nanopore sequencer.
“Lopez et al. (2019) established a DNA assembly strategy to overcome the problem in reading short DNA strands by Nanopore sequencer.”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Lopez et al., 2019
Nanopore sequencing commercialized by Oxford Nanopore Technologies has been used because of its ease of implementation, automation, and portability.
“sequencing using protein nanopores, commercialized by Oxford Nanopore Technologies, has been used because of its ease of implementation, automation, and portability”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [86]
Sufficient pore utilization for high sequencing throughput can only be realized for long fragments (>1 kb).
“sufficient pore utilization for high sequencing throughput can only be realized for long fragments (>1 kb).”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [86]
The process of combining oligo libraries via Gibson assembly or overlap extension PCR reintroduces difficult-to-automatize steps into the sequencing workflow, calling into question nanopore sequencing's claims of improved portability and ease of automation over SBS.
“This process, usually performed via Gibson assembly or overlap extension PCR,70,81,86 reintroduces several difficult-to-automatize steps into the sequencing workflow, which calls the approach’s claims of improved portability and ease of automation over SBS into question.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [86]
The high error rate of nanopore sequencing necessitates clustering of sequence information, higher sequencing coverage, and additional postprocessing of sequencing data.
“necessitates the clustering of sequence information, and thus, higher sequencing coverage and additional postprocessing of sequencing data.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [86]
The largest data size retrieved using nanopore sequencing is currently about 1.67 MB, compared with around 200 MB for SBS.
“the largest data size retrieved using the technology is currently about 1.67 MB, compared with around 200 MB for SBS.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [86]
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Development of Synthetic DNA Circuit and Networks for Molecular Information Processing
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DNA Coil Dynamics and Hydrodynamic Gating of Pressure‐Biased Nanopores
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Advancing DNA and RNA Modification Detection via Nanopore Sequencing
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- Authors
- Lopez, R., Chen, Y.-J., Dumas Ang, S., Yekhanin, S., Makarychev, K., Racz, M. Z., Seelig, G., Strauss, K., & Ceze, L.
- Affiliations
- University of Washington (US)
- Microsoft (United States) (US)
- Venue
- Nature Communications
- Published
- 2019-07-03
- Volume
- 10
- Issue
- 1
- Pages
- 2933-2933
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6610119
- OpenAlex
- W2955617048
- Cited by
- 142
- References
- 32
- Citations by year
- 2026: 13 · 2025: 27 · 2024: 17 · 2023: 28 · 2022: 17 · 2021: 25 · 2020: 14 · 2019: 1
- FWCI
- 4.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- United States Department of Defense | Defense Advanced Research Projects Agency (Molecular Informatics)
- Microsoft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DNA data storage, nanopore sequencing, synthetic DNA, data readout, sequencing throughput
- MeSH terms
- DNA, Information Storage and Retrieval, Sequence Analysis, DNA, Databases, Genetic, Nanotechnology, Nanopores
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