DNA punch cards for storing data on native DNA sequences via enzymatic nicking
Open accessAbstract
Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA. As the sequence content of native DNA is fixed, one can modify the topology instead to encode information. Here, we introduce DNA punch cards, a macromolecular storage mechanism in which data is written in the form of nicks at predetermined positions on the backbone of native double-stranded DNA. The platform accommodates parallel nicking on orthogonal DNA fragments and enzymatic toehold creation that enables single-bit random-access and in-memory computations. We use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA and accurately reconstruct the encoded data through high-throughput sequencing and read alignment.
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A strategy toward decreasing the costs of stored DNA data may be the enzymatic synthesis of DNA strands.
“A strategy toward decreasing the costs of stored DNA data may be the enzymatic synthesis of DNA strands.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [72]
In DNA punch cards, a pattern of nicking positions is realized on the backbone of native dsDNA, and information is encoded by absence (0) or presence (1) of nicks.
“Indeed, a pattern of nicking positions was precisely realized on the backbone of native dsDNA, and here, information was encoded by means of absence (i.e., 0) or presence (i.e., 1) of nicks.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [72]
On the basis of enzymatic modification of DNA, nicks enable adding functionalities to the DNA punch card storage system, such as single-bit random access, pooling, and in-memory computation.
“On the basis of enzymatic modification of DNA, nicks enable adding several functionalities to the storage system, for example, single-bit random access, pooling, and in-memory computation.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [72]
The DNA punch cards system was able to store only up to 14 kB of digital information.
“However, the DNA punch cards system was able to store only up to 14 kB of digital information.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [72]
Tabatabaei et al.'s DNA punch cards encode information in the sequence of bases of DNA strands by using their sugar-phosphate backbone topologically.
“The use of double-stranded DNA as a storage medium was also exploited in recent work by Tabatabaei et al.72 on DNA punch cards. This macromolecular storage technology was used to encode the information in the sequence of bases of the DNA strands by using their sugar–phosphate backbone, i.e., topologically.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [72]
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“2 KB; 392 KB 450 Own bit mapping Not needed Enzymatic nicking (Pf Ago) [25]”
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10 Years of Natural Data Storage
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- Authors
- Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J.-P., Soloveichik, D., Zhao, H., & Milenkovic, O.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- The University of Texas at Austin (US)
- Corresponding author
- Zhao, Huimin
- ORCID
- Venue
- Nature Communications
- Published
- 2020-04-08
- Volume
- 11
- Issue
- 1
- Pages
- 1742-1742
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7142088
- OpenAlex
- W3015846461
- Cited by
- 120
- References
- 41
- Citations by year
- 2026: 13 · 2025: 15 · 2024: 12 · 2023: 25 · 2022: 15 · 2021: 25 · 2020: 14 · 2019: 1
- FWCI
- 6.41
- 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)
- Funders
- United States Department of Defense | Defense Advanced Research Projects Agency (W911NF-18-2-0032)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- DNA data storage, DNA nicking, Argonaute proteins, Pyrococcus furiosus, in-memory computing, DNA topology
- MeSH terms
- Base Sequence, DNA, Sequence Analysis, DNA, Pyrococcus furiosus, Argonaute Proteins
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