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CRISPR-Cas Encoding of a Digital Movie into the Genomes of a Population of Living Bacteria
Open accessAbstract
DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome. Here we use the CRISPR-Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of the CRISPR-Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.
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“In 2017, Shipman et al. encoded five frames of a galloping mare from Eadweard Muybridge’s “The Human and Animal Locomotion Photographs” [19]. In their experiment, CRISPR-Cas was used to integrate an encoded short movie into the genomes of a population of living bacteria.”
From DNA Data Storage. (2023) · cites this paper as [19]
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Metadata
- Authors
- Shipman, S. L., Nivala, J., Macklis, J. D., & Church, G. M.
- Affiliations
- Harvard University (US)
- Corresponding author
- Church, George M.
- Venue
- Nature
- Published
- 2017-07
- Volume
- 547
- Issue
- 7663
- Pages
- 345-349
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5842791
- OpenAlex
- W2735589681
- Cited by
- 361
- References
- 30
- Citations by year
- 2026: 24 · 2025: 24 · 2024: 35 · 2023: 37 · 2022: 40 · 2021: 39 · 2020: 38 · 2019: 49 · 2018: 62 · 2017: 12
- FWCI
- 17.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institute on Aging (T32AG000222)
- National Institute of Mental Health (R01MH103910)
- National Human Genome Research Institute (P50HG005550, RM1HG008525)
- National Institute of Neurological Disorders and Stroke (R01NS045523)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Physical Sciences › Mathematics › Theoretical Computer Science › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- CRISPR-Cas, DNA data storage, living cells, Escherichia coli, adaptive immunity, spacer acquisition, genome editing, bacterial adaptation
- MeSH terms
- Gene Editing, Base Sequence, Biotechnology, Escherichia coli, Motion Pictures, Oligonucleotides, Genome, Bacterial, Integrases, Microbial Viability, CRISPR-Cas Systems
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 ›
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