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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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Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
Molecular Computation of Solutions to Combinatorial Problems
Adleman, L. M. (1994) · Science · doi:10.1126/science.7973651 · Cited by 4,474
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
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
Self-citationTowards 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
Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus
Deveau, H., Barrangou, R., Garneau, J. E., Labonté, J., Fremaux, C., Boyaval, P., Romero, D. A., Horvath, P., & Moineau, S. (2007) · Journal of Bacteriology · doi:10.1128/jb.01412-07 · Cited by 1,196
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Semenova, E., Jore, M. M., Datsenko, K. A., Semenova, A., Westra, E. R., Wanner, B., van der Oost, J., Brouns, S. J. J., & Severinov, K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104144108 · Cited by 726
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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
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