Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction
Open accessAbstract
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. The current hamstring of DNA data storage systems—both in cost and speed—is synthesis. The key idea for breaking this bottleneck pursued in this work is to move beyond the low-error and expensive synthesis employed almost exclusively in today’s systems, towards cheaper, potentially faster, but high-error synthesis technologies. Here, we demonstrate a DNA storage system that relies on massively parallel light-directed synthesis, which is considerably cheaper than conventional solid-phase synthesis. However, this technology has a high sequence error rate when optimized for speed. We demonstrate that even in this high-error regime, reliable storage of information is possible, by developing a pipeline of algorithms for encoding and reconstruction of the information. In our experiments, we store a file containing sheet music of Mozart, and show perfect data recovery from low synthesis fidelity DNA.
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Antkowiak et al.'s method has a logical density of 0.8 bits/nt.
“Moreover, its logical density (1.75 bits/nt) is double that of Antkowiak et al.’s method (0.8 bits/nt) [20] with only about 2.5% reduction in error correction capability.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [20]
Yazdi et al.'s method has a logical density of 1.75 bits/nt.
“Moreover, its logical density (1.75 bits/nt) is double that of Antkowiak et al.’s method (0.8 bits/nt) [20] with only about 2.5% reduction in error correction capability.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [20]
Yazdi et al.'s method has only about 2.5% reduction in error correction capability compared to Antkowiak et al.'s method.
“Moreover, its logical density (1.75 bits/nt) is double that of Antkowiak et al.’s method (0.8 bits/nt) [20] with only about 2.5% reduction in error correction capability.”
From Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage (2023) · cites this paper as [20]
Following the original introduction of the inner-outer encoding scheme, the vast majority of subsequent works used such a scheme for DNA data storage.
“Following the original introduction of the inner-outer encoding scheme, the vast majority of subsequent works used such a scheme for DNA data storage.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
For both low and large error rates dominated by deletion errors, one also uses physical redundancy to recover the original information.
“However, both for low and large error rates, dominated by deletion errors, one also uses physical redundancy to recover the original information.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
In Antkowiak et al., noisy sequences were first clustered by similarity, then information on multiple erroneous copies was combined to construct a sequence with fewer errors via alignment and majority voting.
“For example, in Antkowiak et al.,42 the noisy sequences were first clustered by similarity, then the information on multiple erroneous copies was combined to construct a sequence with fewer errors. This was achieved by an alignment step within the clusters and subsequent majority voting.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
Antkowiak et al. proved that the combination of synthesis processes that produce lower quality DNA oligos (photolithographic synthesis) and appropriate error-correction codes allows a major cost decrease in DNA data archives.
“Thus, Antkowiak et al. proved that the combination of synthesis processes that produce lower quality DNA oligos (i.e., photolithographic synthesis) and appropriate error-correction codes allows a major cost decrease in DNA data archives.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
Antkowiak et al. estimated that with photolithography to synthesize 10,000 copies of each oligo, a nucleotide reagent cost of 100 USD/g, and a logical density equal to 1 bit/nucleotide, the cost of 1 TB of data stored in DNA would be ∼10-2 USD, with a chemical yield of 100%.
“With the use of photolithography to synthesize 10 000 copies of each oligo, with a nucleotide reagent cost of 100 USD/g and a logical density equal to 1 bit/nucleotide, the cost of 1 TB of data stored in DNA would be ∼10–2 USD, with a chemical yield of 100%.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
In 2020, Antkowiak et al. proposed that synthesis costs will drop to around 10^6 USD/TB (2-3 orders of magnitude reduction) as a result of improved synthesis strategies, including large parallelization, optimization of reagents, and combination of nonvolatile DNA-based memories with logical operations.
“In 2020, Antkowiak et al. proposed that synthesis costs will drop to around 106 USD/TB (i.e., 2–3 orders of magnitude reduction) as a result of improved synthesis strategies, including large parallelization, optimization of reagents, and combination of nonvolatile DNA-based memories with logical operations”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
Even if a chemical yield of 100% is impossible to achieve in industrial conditions, DNA data storage will be competitive against tape storage (20 USD/TB cost) even at 0.1% chemical yield.
“Even if this chemical yield is impossible to achieve in industrial conditions, DNA data storage will be competitive against tape storage (20 USD/TB cost) even at 0.1% chemical yield.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
In the 0.1% chemical yield case, the cost of photolithographic DNA storage would be ∼10 USD/TB, and synthesis conditions would be similar to surface chemistry (1000× reagent excess), demonstrating that optimization of chemical DNA synthesis processes is compatible with DNA data storage applications.
“In the latter case, the cost of photolithographic DNA storage would be ∼10 USD/TB, and synthesis conditions would be similar to the one used in surface chemistry (1000× reagent excess), which demonstrates that an optimization of chemical DNA synthesis processes is compatible with DNA data storage applications.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [42]
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Data Readout Techniques for DNA‐Based Information Storage
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An image cryptography method by highly error-prone DNA storage channel
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Self-citationGel-based electrochemical DNA synthesis for quasi-solid-state data storage
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GradHC: highly reliable gradual hash-based clustering for DNA storage systems
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Molecular Circuit-Controlled Nanoparticle Folders for Programmable DNA Information Access
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RFS-codec: A Novel Encoding Approach to Store Image Data in DNA
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The DNA Storage Channel: Capacity and Error ProbabilityPreprint
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Accelerated, high-quality photolithographic synthesis of RNA microarrays in situ
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Self-citationNanopore decoding with speed and versatility for data storage
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Achieving the Capacity of a DNA Storage Channel with Linear Coding Schemes
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Self-citationRobust Indexing for the Sliced Channel: Almost Optimal Codes for Substitutions and Deletions
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Polymerase Elongation onto Patterned DNA for Random Accessed DNA Data Storage
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DNA synthesis and assembly: From oligonucleotides to complete genomes
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Self-citationCyber and Information Security in the Bioeconomy
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DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage
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One-round-per-day CRISPR genome editing of E. coli for engineering green-chemical overproducer
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Self-citationLinked data storage using DNA origami nanostructures
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Studying the Cycle Complexity of DNA Synthesis
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Dna-storalator: a computational simulator for DNA data storage
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Design of DNA Storage Coding Scheme With LDPC Codes and Interleaving
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The Capacity of the Weighted Read Channel
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Survey of Sequence Reconstruction Problems and Their Applications in DNA-Based Storage
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Comparison of state-of-the-art error-correction coding for sequence-based DNA data storage
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Complex DNA Synthesis Sequences
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Towards long double-stranded chains and robust DNA-based data storage using the random code system
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- Authors
- Antkowiak, P. L., Lietard, J., Darestani, M. Z., Somoza, M. M., Stark, W. J., Heckel, R., & Grass, R. N.
- Affiliations
- ETH Zurich (CH)
- University of Vienna (AT)
- Rice University (US)
- Technical University of Munich (DE)
- Corresponding author
- Heckel, Reinhard
- Grass, Robert N.
- ORCID
- Venue
- Nature Communications
- Published
- 2020-10-22
- Volume
- 11
- Issue
- 1
- Pages
- 5345-5345
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7582880
- OpenAlex
- W3093968171
- Cited by
- 173
- References
- 30
- Citations by year
- 2026: 27 · 2025: 44 · 2024: 41 · 2023: 25 · 2022: 18 · 2021: 16 · 2020: 2
- FWCI
- 4.95
- 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)
- mediaTUM (Technical University of Munich) (submittedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- Rice University
- Austrian Science Fund (P27275, FWF P27275, P 30596, P27275 and P30596)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Keywords
- DNA data storage, information reconstruction, error correction, encoding algorithms, archival storage, solid-phase synthesis
- MeSH terms
- Algorithms, Base Sequence, DNA, Light, Monte Carlo Method, Gene Library, Information Storage and Retrieval, Sequence Analysis, DNA, Oligonucleotide Array Sequence Analysis, Photochemical Processes, Chemistry Techniques, Synthetic
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