A DNA-Based Archival Storage System
Open accessAbstract
Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm3 (109 GB/mm3), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Sequencing coverage of oligonucleotides in DNA data storage systems is very uneven, requiring modern error correction codes capable of handling sequence dropout.
“However, the sequencing coverage (number of read counts of a unique sequence) of an oligonucleotide (henceforth referred to simply as “oligo”) was found to be very uneven, requiring modern error correction codes capable of handling sequence dropout7–12.”
From Quantifying Molecular Bias in DNA Data Storage (2019) · cites this paper as [11]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
A Method for the Construction of Minimum-Redundancy Codes
Huffman, D. A. (1952) · Proceedings of the IRE · doi:10.1109/jrproc.1952.273898 · Cited by 6,363 · see citing works
Molecular Computation of Solutions to Combinatorial Problems
Adleman, L. M. (1994) · Science · doi:10.1126/science.7973651 · Cited by 4,474 · see citing works
Polynomial Codes Over Certain Finite Fields
Reed, I. S., & Solomon, G. (1960) · Journal of the Society for Industrial and Applied Mathematics · doi:10.1137/0108018 · Cited by 3,693 · see citing works
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., et al. (2010) · Science · doi:10.1126/science.1190719 · Cited by 2,638 · see citing works
Next-Generation Digital Information Storage in DNA
Church, G. M., Gao, Y., & Kosuri, S. (2012) · Science · doi:10.1126/science.1226355 · Cited by 1,441 · see citing works
Towards Practical, High-Capacity, Low-Maintenance Information Storage in Synthesized DNA
Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E. M., Sipos, B., & Birney, E. (2013) · Nature · doi:10.1038/nature11875 · Cited by 1,220 · see citing works
Neural network computation with DNA strand displacement cascades
Qian, L., Winfree, E., & Bruck, J. (2011) · Nature · doi:10.1038/nature10262 · Cited by 1,079 · see citing works
Synthesis of deoxyoligonucleotides on a polymer support
Matteucci, M. D., & CARUTHERS, M. H. (1981) · Journal of the American Chemical Society · doi:10.1021/ja00401a041 · Cited by 893 · see citing works
Large-scale de novo DNA synthesis: technologies and applications
Kosuri, S., & Church, G. M. (2014) · Nature Methods · doi:10.1038/nmeth.2918 · Cited by 869 · see citing works
Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes
Grass, R. N., Heckel, R., Puddu, M., Paunescu, D., & Stark, W. J. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201411378 · Cited by 754 · see citing works
Hiding messages in DNA microdots
Clelland, C. T., Risca, V. I., & Bancroft, C. (1999) · Nature · doi:10.1038/21092 · Cited by 638 · see citing works
The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils
Allentoft, M. E., Collins, M., Harker, D., Haile, J., Oskam, C. L., Hale, M. L., Campos, P. F., Samaniego, J. A., Gilbert, M. T. P., Willerslev, E., et al. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.1745 · Cited by 633 · see citing works
Programmable chemical controllers made from DNA
Chen, Y.-J., Dalchau, N., Srinivas, N., Phillips, A., Cardelli, L., Soloveichik, D., & Seelig, G. (2013) · Nature Nanotechnology · doi:10.1038/nnano.2013.189 · Cited by 486 · see citing works
Self-citationA Rewritable, Random-Access DNA-Based Storage System
Tabatabaei Yazdi, S. M. H., Yuan, Y., Ma, J., Zhao, H., & Milenkovic, O. (2015) · Scientific Reports · doi:10.1038/srep14138 · Cited by 401 · see citing works
Landscape of Next-Generation Sequencing Technologies
Niedringhaus, T. P., Milanova, D., Kerby, M. B., Snyder, M. P., & Barron, A. E. (2011) · Analytical Chemistry · doi:10.1021/ac2010857 · Cited by 380 · see citing works
Cryptography with DNA binary strands
Leier, A., Richter, C., Banzhaf, W., & Rauhe, H. (2000) · Biosystems · doi:10.1016/s0303-2647(00)00083-6 · Cited by 288 · see citing works
Approximate storage in solid-state memories
Sampson, A., Nelson, J., Strauß, K., & Ceze, L. (2013) · IEEE/ACM International Symposium on Microarchitecture (MICRO) · doi:10.1145/2540708.2540712 · Cited by 218 · see citing works
Self-citationLong-Term Storage of Information in DNA
Bancroft, C., Bowler, T. G., Bloom, B., & Clelland, C. T. (2001) · Science · doi:10.1126/science.293.5536.1763c · Cited by 192 · see citing works
Nucleic acid sequence design via efficient ensemble defect optimization
Zadeh, J. N., Wolfe, B. R., & Pierce, N. A. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21633 · Cited by 190 · see citing works
Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules
Schwartz, J. J., Lee, C., & Shendure, J. (2012) · Nature Methods · doi:10.1038/nmeth.2137 · Cited by 94 · see citing works
High-Density Image Storage Using Approximate Memory Cells
Guo, Q. J., Strauß, K., Ceze, L., & Malvar, H. S. (2016) · International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS) · doi:10.1145/2872362.2872413 · Cited by 52 · see citing works
Self-citationDNA-based molecular architecture with spatially localized components
Muscat, R. A., Strauß, K., Ceze, L., et al. (2013) · Proceedings - International Symposium on Computer Architecture/Proceedings · doi:10.1145/2485922.2485938 · Cited by 37 · see citing works
Self-citationChain Reaction Systems Based on Loop Dissociation of DNA
Takahashi, K., Yaegashi, S., Kameda, A., et al. (2006) · Lecture notes in computer science · doi:10.1007/11753681_27 · Cited by 28 · see citing works
A Crossbar Interconnection Network in DNA
Talawar, B. (2015) · doi:10.1109/ipdpsw.2015.103 · Cited by 4 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [25]25. Sony. Sony develops magnetic tape technology with the world's highest recording density. http://www.sony. net/SonyInfo/News/Press/201404/14-044E/, 2014.
Cited by
Sorted by citations
DNA Fountain enables a robust and efficient storage architecture
Erlich, Y., & Zielinski, D. (2017) · Science · doi:10.1126/science.aaj2038 · Cited by 898 · see citing works
Random access in large-scale DNA data storage
Organick, L., Ang, S. D., Chen, Y.-J., Lopez, R., Yekhanin, S., Makarychev, K., Racz, M. Z., Kamath, G., Gopalan, P., Nguyen, B., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4079 · Cited by 775 · see citing works
Self-citationEncoding information into polymers
Rutten, M. G. T. A., Vaandrager, F. W., Elemans, J. A. A. W., & Nolte, R. J. M. (2018) · Nature Reviews Chemistry · doi:10.1038/s41570-018-0051-5 · Cited by 216 · see citing works
Choi, Y., Ryu, T., Lee, A. C., Choi, H., Lee, H., Park, J., Song, S.-H., Kim, S., Kim, H., Park, W., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-43105-w · Cited by 128 · see citing works
Quantifying Molecular Bias in DNA Data Storage
Chen, Y.-J., Takahashi, C. N., Organick, L., Stewart, K., Ang, S. D., Weiss, P., Peck, B., Seelig, G., Ceze, L., & Strauss, K. (2019) · doi:10.1101/566554 · Cited by 109 · see citing works
Self-citationHao, Y., Li, Q., Fan, C., & Wang, F. (2021) · Small Structures · doi:10.1002/sstr.202000046 · Cited by 90 · see citing works
Addressable configurations of DNA nanostructures for rewritable memory
Chandrasekaran, A. R., Levchenko, O., Patel, D. S., MacIsaac, M., & Halvorsen, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx777 · Cited by 79 · see citing works
- Authors
- Bornholt, J., Lopez, R., Carmean, D. M., Ceze, L., Seelig, G., & Strauss, K.
- Affiliations
- University of Washington (US)
- Microsoft (United States) (US)
- University of Washington, Seattle, WA, USA
- Venue
- ACM SIGOPS Operating Systems Review
- Published
- 2016-03-25
- Volume
- 50
- Issue
- 2
- Pages
- 637-649
- ISSN
- 0163-5980 (ISSN-L)
- OpenAlex
- W4234461109
- Cited by
- 77
- References
- 24
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 6 · 2023: 8 · 2022: 5 · 2021: 11 · 2020: 11 · 2019: 15 · 2018: 11 · 2017: 4 · 2016: 1
- FWCI
- 5.34
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- ACM SIGOPS Operating Systems Review (publishedVersion)
- Funders
- National Science Foundation (1409831)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- DNA data storage, archival storage, key-value stores, random access, redundancy, storage density, storage reliability, DNA synthesis, storage architecture
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
