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.
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?
Shipman et al. (2017) encoded five frames of a galloping mare from Eadweard Muybridge's "The Human and Animal Locomotion Photographs" using CRISPR-Cas to integrate an encoded short movie into genomes of living bacteria.
“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]
The paper’s Abstract says the authors encoded five frames of Eadweard Muybridge’s Horse in Motion as a short movie in a population of bacteria. It also explains that the CRISPR-Cas system acquired the encoded sequences into genomic arrays. Our copy does not identify the frames as coming from “The Human and Animal Locomotion Photographs”; it calls the work Horse in Motion. (LLM, conf=0.87)
Experimental — accuracy not yet measured
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
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
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 6,304 · 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
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
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 · see citing works
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 · see citing works
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
Whole-organism lineage tracing by combinatorial and cumulative genome editing
McKenna, A., Findlay, G. M., Gagnon, J. A., Horwitz, M. S., Schier, A. F., & Shendure, J. (2016) · Science · doi:10.1126/science.aaf7907 · Cited by 766 · see citing works
Semenova, E., Jore, M. M., Datsenko, K. A., Semenova, A., Westra, E. R., Wanner, B. L., John van der, O. O. S. T., Brouns, S. J. J., & Severinov, K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104144108 · Cited by 726 · see citing works
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
Yosef, I., Goren, M. G., & Qimron, U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks216 · Cited by 680 · 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
CRISPR-based adaptive and heritable immunity in prokaryotes
John van der, O. O. S. T., Jore, M. M., Westra, E. R., Lundgren, M., & Brouns, S. J. J. (2009) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2009.05.002 · Cited by 524 · see citing works
Westra, E. R., van Erp, P. B. G., Künne, T., Wong, S. P., Staals, R. H. J., Seegers, C. L. C., Bollen, S., Jore, M. M., Semenova, E., Severinov, K., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.03.018 · Cited by 511 · see citing works
pLogo: a probabilistic approach to visualizing sequence motifs
O'Shea, J. P., Chou, M. F., Quader, S., Ryan, J. K., Church, G. M., & Schwartz, D. (2013) · Nature Methods · doi:10.1038/nmeth.2646 · Cited by 491 · see citing works
Self-citationSynthetic recording and in situ readout of lineage information in single cells
Frieda, K. L., Linton, J. M., Hormoz, S., Choi, J., Chow, K.-H. K., Singer, Z. S., Budde, M. W., Elowitz, M. B., & Cai, L. (2017) · Nature · doi:10.1038/nature20777 · Cited by 440 · see citing works
CRISPR–Cas adaptation: insights into the mechanism of action
Amitai, G., & Sorek, R. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2015.14 · Cited by 411 · see citing works
Zhirnov, V., Zadegan, R. M., Sandhu, G. S., Church, G. M., & Hughes, W. L. (2016) · Nature Materials · doi:10.1038/nmat4594 · Cited by 307 · see citing works
Self-citationAdaptation in CRISPR-Cas Systems
Sternberg, S. H., Richter, H., Charpentier, E., & Qimron, U. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.030 · Cited by 251 · see citing works
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems
Wang, J., Li, J., Zhao, H., Sheng, G., Wang, M., Yin, M., & Wang, Y. (2015) · Cell · doi:10.1016/j.cell.2015.10.008 · Cited by 248 · see citing works
Molecular recordings by directed CRISPR spacer acquisition
Shipman, S. L., Nivala, J., Macklis, J. D., & Church, G. M. (2016) · Science · doi:10.1126/science.aaf1175 · Cited by 243 · see citing works
Self-citationWestra, E. R., Semenova, E., Datsenko, K. A., Jackson, R. N., Wiedenheft, B., Severinov, K., & Brouns, S. J. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003742 · Cited by 216 · see citing works
Diversity of CRISPR loci in Escherichia coli
Díez‐Villaseñor, C., Almendros, C., García‐Martínez, J., & Mojica, F. J. M. (2010) · Microbiology · doi:10.1099/mic.0.036046-0 · Cited by 194 · see citing works
Foreign DNA capture during CRISPR–Cas adaptive immunity
Nuñez, J. K., Harrington, L. B., Kranzusch, P. J., Engelman, A., & Doudna, J. A. (2015) · Nature · doi:10.1038/nature15760 · Cited by 193 · see citing works
Strong bias in the bacterial CRISPR elements that confer immunity to phage
Páez-Espino, D., Morovic, W., Sun, C. L., Thomas, B. C., Ueda, K.-I., Stahl, B., Barrangou, R., & Banfield, J. F. (2013) · Nature Communications · doi:10.1038/ncomms2440 · Cited by 175 · see citing works
Persisting Viral Sequences Shape Microbial CRISPR-based Immunity
Weinberger, A. D., Sun, C. L., Pluciński, M. M., Denef, V. J., Thomas, B. C., Horvath, P., Barrangou, R., Gilmore, M. S., Getz, W. M., & Banfield, J. F. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002475 · Cited by 143 · see citing works
Davis, J. R. (1996) · Art Journal · doi:10.1080/00043249.1996.10791743 · Cited by 126 · see citing works
CRISPR Associated Diversity within a Population of Sulfolobus islandicus
Held, N. L., Herrera, A., Cadillo‐Quiroz, H., & Whitaker, R. J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012988 · Cited by 116 · see citing works
A population‐based temporal logic gate for timing and recording chemical events
Hsiao, V., Hori, Y., Rothemund, P. W. K., & Murray, R. M. (2016) · Molecular Systems Biology · doi:10.15252/msb.20156663 · Cited by 94 · see citing works
Pervasive generation of oppositely oriented spacers during CRISPR adaptation
Shmakov, S., Savitskaya, E. E., Semenova, E., Logacheva, M. D., Datsenko, K. A., & Severinov, K. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku226 · Cited by 65 · see citing works
DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array
Yosef, I., Shitrit, D., Goren, M. G., Burstein, D. E., Pupko, T., & Qimron, U. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300108110 · Cited by 59 · see citing works
Davis, J. (1996) · Art Journal · doi:10.2307/777811 · Cited by 16 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The next generation of CRISPR–Cas technologies and applications
Pickar-Oliver, A., & Gersbach, C. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0131-5 · Cited by 1,459 · see citing works
Principles and Applications of Nucleic Acid Strand Displacement Reactions
Simmel, F. C., Yurke, B., & Singh, H. R. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00580 · Cited by 792 · see citing works
Molecular Digital Data Storage Using DNA
Ceze, L., Nivala, J., & Strauss, K. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0125-3 · Cited by 551 · see citing works
Self-citationThe CRISPR-Cas toolbox and gene editing technologies
Liu, G., Lin, Q., Jin, S., & Gao, C. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.12.002 · Cited by 410 · see citing works
Developmental barcoding of whole mouse via homing CRISPR
Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M. (2018) · Science · doi:10.1126/science.aat9804 · Cited by 363 · see citing works
Self-citationCRISPR Ethics: Moral Considerations for Applications of a Powerful Tool
Brokowski, C., & Adli, M. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.05.044 · Cited by 320 · see citing works
Peng, S., Bie, B., Sun, Y., Liu, M., Cong, H., Zhou, W., Xia, Y., Tang, H. Y., Deng, H., & Zhou, X. (2018) · Nature Communications · doi:10.1038/s41467-018-03650-w · Cited by 266 · see citing works
Molecular mechanisms of CRISPR–Cas spacer acquisition
McGinn, J., & Marraffini, L. A. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0071-7 · Cited by 257 · see citing works
DNA storage: research landscape and future prospects
Dong, Y., Sun, F., Ping, Z., Ouyang, Q., & Qian, L. (2020) · National Science Review · doi:10.1093/nsr/nwaa007 · Cited by 224 · see citing works
Microfluidics for Biomedical Analysis
Yang, Y. S., Chen, Y., Tang, H., Zong, N., & Jiang, X. (2019) · Small Methods · doi:10.1002/smtd.201900451 · Cited by 218 · see citing works
Encoding 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
A time-resolved, multi-symbol molecular recorder via sequential genome editing
Choi, J., Chen, W., Minkina, A., Chardon, F. M., Suiter, C. C., Regalado, S. G., Domcke, S., Hamazaki, N., Lee, C., Martin, B., et al. (2022) · Nature · doi:10.1038/s41586-022-04922-8 · Cited by 202 · see citing works
Multiplex recording of cellular events over time on CRISPR biological tape
Sheth, R. U., Yim, S. S., Wu, F. L., & Wang, H. H. (2017) · Science · doi:10.1126/science.aao0958 · Cited by 195 · see citing works
Kuşcu, M., Dinc, E., Bilgin, B. A., Ramezani, H., & Akan, Ö. B. (2019) · Proceedings of the IEEE · doi:10.1109/jproc.2019.2916081 · Cited by 186 · see citing works
Development of CRISPR-Cas systems for genome editing and beyond
Zhang, F. (2019) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583519000052 · Cited by 185 · see citing works
DNA-based memory devices for recording cellular events
Sheth, R. U., & Wang, H. H. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0052-8 · Cited by 173 · see citing works
Bacteria as genetically programmable producers of bioactive natural products
Hug, J. J., Krug, D., & Müller, R. (2020) · Nature Reviews Chemistry · doi:10.1038/s41570-020-0176-1 · Cited by 150 · see citing works
Type II-C CRISPR-Cas9 Biology, Mechanism, and Application
Mir, A., Edraki, A., Lee, J., & Sontheimer, E. J. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00855 · Cited by 148 · see citing works
Transcriptional recording by CRISPR spacer acquisition from RNA
Schmidt, F., Cherepkova, M. Y., & Platt, R. J. (2018) · Nature · doi:10.1038/s41586-018-0569-1 · Cited by 147 · see citing works
Engineering PGPMOs through Gene Editing and Systems Biology: A Solution for Phytoremediation?
Basu, S., Rabara, R. C., Negi, S., & Shukla, P. (2018) · Trends in Biotechnology · doi:10.1016/j.tibtech.2018.01.011 · Cited by 138 · see citing works
An Artificial Chromosome for Data Storage
Chen, W., Han, M., Zhou, J., Ge, Q., Wang, P., Zhang, X., Zhu, S., Song, L., & Yuan, Y. (2021) · National Science Review · doi:10.1093/nsr/nwab028 · Cited by 136 · see citing works
Synthetic genetic circuits for programmable biological functionalities
Xia, P., Ling, H., Foo, J. L., & Chang, M. W. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.04.015 · Cited by 129 · see citing works
Synthetic DNA applications in information technology
Meiser, L. C., Nguyen, B. H., Chen, Y.-J., Nivala, J., Strauß, K., Ceze, L., & Grass, R. N. (2022) · Nature Communications · doi:10.1038/s41467-021-27846-9 · Cited by 129 · see citing works
Self-citationHow type II CRISPR–Cas establish immunity through Cas1–Cas2-mediated spacer integration
Xiao, Y., Ng, S., Nam, K. H., & Ke, A. (2017) · Nature · doi:10.1038/nature24020 · Cited by 121 · see citing works
DNA punch cards for storing data on native DNA sequences via enzymatic nicking
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. (2020) · Nature Communications · doi:10.1038/s41467-020-15588-z · Cited by 120 · see citing works
Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research
Ke, Y., Castro, C. E., & Choi, J. H. (2018) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-062117-120904 · Cited by 120 · see citing works
Emerging applications for DNA writers and molecular recorders
Farzadfard, F., & Lu, T. K. (2018) · Science · doi:10.1126/science.aat9249 · Cited by 102 · see citing works
Rational engineering of synthetic microbial systems: from single cells to consortia
Bittihn, P., Din, M. O., Tsimring, L. S., & Hasty, J. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.02.009 · Cited by 93 · see citing works
Parallel molecular data storage by printing epigenetic bits on DNA
Zhang, C., Wu, R., Sun, F., Lin, Y., Liang, Y., Liang, Y., Chen, Y., Teng, J., Song, Z., Liu, N., et al. (2024) · Nature · doi:10.1038/s41586-024-08040-5 · Cited by 93 · see citing works
Hao, Y., Li, Q., Fan, C., & Wang, F. (2021) · Small Structures · doi:10.1002/sstr.202000046 · Cited by 90 · see citing works
High-throughput DNA synthesis for data storage
Yu, M., Tang, X., Li, Z., Wang, W., Wang, S., Li, M., Yu, Q., Xie, S., Zuo, X., & Chen, C. Q. (2024) · Chemical Society Reviews · doi:10.1039/d3cs00469d · Cited by 90 · see citing works
Wang, S., Mao, X., Wang, F., Zuo, X., & Fan, C. (2023) · Advanced Materials · doi:10.1002/adma.202307499 · Cited by 85 · see citing works
Robust direct digital-to-biological data storage in living cells.
Yim, S. S., McBee, R. M., Song, A. M., Huang, Y., Sheth, R. U., & Wang, H. H. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00711-4 · Cited by 83 · see citing works
Pataranutaporn, P., Vujic, A., Kong, D. S., Maes, P., & Sra, M. (2020) · Augmented Humans International Conference (AHs) · doi:10.1145/3384657.3384783 · Cited by 81 · see citing works
Lineage tracing and analog recording in mammalian cells by single-site DNA writing
Loveless, T. B., Grotts, J. H., Schechter, M. W., Forouzmand, E., Carlson, C. K., Agahi, B. S., Liang, G., Ficht, M., Liu, B., Xie, X. S., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00769-8 · Cited by 78 · see citing works
Recording gene expression order in DNA by CRISPR addition of retron barcodes
Bhattarai-Kline, S., Lear, S. K., Fishman, C. B., Lopez, S. C., Lockshin, E. R., Schubert, M. G., Nivala, J., Church, G. M., & Shipman, S. L. (2022) · Nature · doi:10.1038/s41586-022-04994-6 · Cited by 78 · see citing works
Self-citationScaling up genetic circuit design for cellular computing: advances and prospects
Xiang, Y., Dalchau, N., & Wang, B. (2018) · Natural Computing · doi:10.1007/s11047-018-9715-9 · Cited by 78 · see citing works
Yang, B., Zhang, X., Li, J., Tian, J., Wu, Y.-P., Yu, F., Wang, R., Wang, H., Zhang, D., Liu, Y., et al. (2019) · CCS Chemistry · doi:10.31635/ccschem.019.20180011 · Cited by 75 · see citing works
Nucleic Acid Databases and Molecular-Scale Computing
Song, X., & Reif, J. (2019) · ACS Nano · doi:10.1021/acsnano.9b02562 · Cited by 73 · see citing works
The First Minds: Caterpillars, Karyotes, and Consciousness
Reber, A. S. (2018) · doi:10.1093/oso/9780190854157.001.0001 · Cited by 65 · see citing works
Uncertainties in synthetic DNA-based data storage
Xu, C., Zhao, C., Ma, B., & Liu, H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab230 · Cited by 65 · see citing works
Enabling technology and core theory of synthetic biology
Zhang, X., Liu, C., Dai, J., Yuan, Y., Gao, C., Feng, Y. F., Wu, B., Wei, P., You, C., Wang, X., et al. (2023) · Science China Life Sciences · doi:10.1007/s11427-022-2214-2 · Cited by 65 · see citing works
Symbolic recording of signalling and cis-regulatory element activity to DNA
Chen, W., Choi, J., Li, X., Nathans, J. F., Martin, B., Yang, W., Hamazaki, N., Qiu, C., Lalanne, J., Regalado, S. G., et al. (2024) · Nature · doi:10.1038/s41586-024-07706-4 · Cited by 65 · see citing works
DNA-based construction at the nanoscale: emerging trends and applications
Xavier, P. L., & Chandrasekaran, A. R. (2017) · Nanotechnology · doi:10.1088/1361-6528/aaa120 · Cited by 65 · see citing works
DNA as a digital information storage device: hope or hype?
Panda, D., Molla, K. A., Baig, M. J., Swain, A., Behera, D., & Dash, M. (2018) · 3 Biotech · doi:10.1007/s13205-018-1246-7 · Cited by 64 · see citing works
Kong, L., Huang, L., Lin, L., Zheng, Z., Li, Y., Wang, Q., & Liu, G. (2023) · IEEE Internet of Things Journal · doi:10.1109/jiot.2023.3255412 · Cited by 59 · see citing works
Prokaryotic reverse transcriptases: from retroelements to specialized defense systems
González-Delgado, A., Mestre, M. R., Martínez‐Abarca, F., & Toro, N. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab025 · Cited by 58 · see citing works
CRISPR-based gene expression control for synthetic gene circuits
Santos‐Moreno, J., & Schaerli, Y. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200020 · Cited by 57 · see citing works
Open-ended molecular recording of sequential cellular events into DNA
Loveless, T. B., Carlson, C. K., Helmy, C. A. D., Hu, V. J., Ross, S. K., Demelo, M. C., Murtaza, A., Liang, G., Ficht, M., Singhai, A., et al. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01764-5 · Cited by 57 · see citing works
Klompe, S. E., & Sternberg, S. H. (2018) · The CRISPR Journal · doi:10.1089/crispr.2018.0012 · Cited by 57 · see citing works
Carbon-based archiving: current progress and future prospects of DNA-based data storage.
Ping, Z., Ma, D., Huang, X., Chen, S., Liu, L., Guo, F., Zhu, S. J., & Shen, Y. (2019) · GigaScience · doi:10.1093/gigascience/giz075 · Cited by 55 · see citing works
Methods and applications of CRISPR/Cas system for genome editing in stem cells
Yang, G., & Huang, X. (2019) · Cell Regeneration · doi:10.1016/j.cr.2019.08.001 · Cited by 55 · see citing works
Selective loading and processing of prespacers for precise CRISPR adaptation
Kim, S., Loeff, L., Colombo, S., Jergic, S., Brouns, S. J. J., & Joo, C. (2020) · Nature · doi:10.1038/s41586-020-2018-1 · Cited by 54 · see citing works
Engineered living materials (ELMs) design: From function allocation to dynamic behavior modulation
Wang, Y., Liu, Y., Li, J., Chen, Y., Liu, S., & Zhong, C. (2022) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2022.102188 · Cited by 51 · see citing works
CRISPR–Cas9 in genome editing: Its function and medical applications
Khadempar, S., Familghadakchi, S., Motlagh, R. A., Farahani, N., Dashtiahangar, M., Rezaei, H., & Hayat, S. M. G. (2018) · Journal of Cellular Physiology · doi:10.1002/jcp.27476 · Cited by 51 · see citing works
Encoding Carbon Nanotubes with Tubular Nucleic Acids for Information Storage
Zhang, Y., Li, F., Li, M., Mao, X., Jing, X., Liu, X., Li, Q., Li, J., Wang, L., Fan, C., et al. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b09116 · Cited by 49 · see citing works
Fei, Z., Gupta, N., Li, M., Xiao, P., & Hu, X. (2023) · Science Advances · doi:10.1126/sciadv.adg9933 · Cited by 47 · see citing works
Song, Y., Kim, S., Heller, M. J., & Huang, X. C. (2018) · Nature Communications · doi:10.1038/s41467-017-02705-8 · Cited by 47 · see citing works
Liu, Y., Ren, Y., Li, J., Wang, F., Wang, F., Ma, C., Chen, D., Jiang, X., Fan, C., Zhang, H., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo7415 · Cited by 46 · see citing works
A temporally resolved DNA framework state machine in living cells
Zhao, Y., Cao, S., Wang, Y., Li, F., Lin, L., Guo, L., Wang, F., Chao, J., Zuo, X., Zhu, Y. J., et al. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00707-4 · Cited by 44 · see citing works
Novel Modalities in DNA Data Storage
Lim, C. K., Nirantar, S., Yew, W. S., & Poh, C. L. (2021) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.12.008 · Cited by 44 · see citing works
A Mixed Culture of Bacterial Cells Enables an Economic DNA Storage on a Large Scale
Hao, M., Qiao, H., Gao, Y., Wang, Z., Qiao, X., Chen, X., & Qi, H. (2020) · Communications Biology · doi:10.1038/s42003-020-01141-7 · Cited by 41 · see citing works
Methods for lineage tracing on the organism-wide level
Spanjaard, B., & Junker, J. P. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2017.11.004 · Cited by 41 · see citing works
Constraining DNA Sequences With a Triplet-Bases Unpaired
Li, X., Wang, B., Lv, H., Yin, Q., Zhang, Q., & Wei, X. (2020) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2020.2971644 · Cited by 41 · see citing works
Replicate after reading: on the extraction and evocation of cultural information
Boudry, M. (2018) · Biology & Philosophy · doi:10.1007/s10539-018-9637-z · Cited by 40 · see citing works
An outlook on the current challenges and opportunities in DNA data storage
Raza, M. H., Desai, S. S., Aravamudhan, S., & Zadegan, R. M. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108155 · Cited by 40 · see citing works
Szweda, R., Tschopp, M., Félix, O., Decher, G., & Lutz, J. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201810559 · Cited by 40 · see citing works
Pseudomonas putida in the quest of programmable chemistry
Martínez‐García, E., & de Lorenzo, V. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.03.012 · Cited by 40 · see citing works
CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system
Lee, J., Lim, H., Jang, H. S., Hwang, B., Lee, J. H., Cho, J., Lee, J. H., & Bang, D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky820 · Cited by 39 · see citing works
Diwo, C., & Budiša, N. (2018) · Genes · doi:10.3390/genes10010017 · Cited by 39 · see citing works
Huang, C., Guo, L., Wang, J., Wang, N., & Huo, Y. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10819-1 · Cited by 39 · see citing works
Efficient retroelement-mediated DNA writing in bacteria
Farzadfard, F., Gharaei, N., Citorik, R. J., & Lu, T. K. (2021) · Cell Systems · doi:10.1016/j.cels.2021.07.001 · Cited by 39 · see citing works
Ledbetter, M. P., Craig, J. M., Karadeema, R. J., Noakes, M. T., Kim, H. C., Abell, S. J., Huang, J. R., Anderson, B. A., Krishnamurthy, R., Gundlach, J. H., et al. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.9b09808 · Cited by 38 · see citing works
Saunders, A. B., Huang, K. W., Vondrak, C., Hughes, C., Smolyar, K., Sen, H., Philson, A. C., Nemesh, J. C., Wysoker, A., Kashin, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34334-1 · Cited by 36 · see citing works
CRISPR‐Enabled Tools for Engineering Microbial Genomes and Phenotypes
Tarasava, K., Oh, E. J., Eckert, C. A., & Gill, R. T. (2018) · Biotechnology Journal · doi:10.1002/biot.201700586 · Cited by 37 · see citing works
Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering
Tellechea‐Luzardo, J., Winterhalter, C., Widera, P., Kozyra, J., de Lorenzo, V., & Krasnogor, N. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00400 · Cited by 36 · see citing works
DNA-Templated Synthesis of Fluorescent Silver Nanoclusters
Chandler, M. R., Shevchenko, O., Vivero-Escoto, J. L., Striplin, C. D., & Afonin, K. A. (2020) · Journal of Chemical Education · doi:10.1021/acs.jchemed.0c00158 · Cited by 36 · see citing works
Digital data storage on DNA tape using CRISPR base editors
Sadremomtaz, A., Glass, R. F., Guerrero, J. E., LaJeunesse, D., Josephs, E. A., & Zadegan, R. M. (2023) · Nature Communications · doi:10.1038/s41467-023-42223-4 · Cited by 35 · see citing works
Trace Reconstruction Problems in Computational Biology
Bhardwaj, V., Pevzner, P. A., Rashtchian, C., & Safonova, Y. (2020) · IEEE Transactions on Information Theory · doi:10.1109/tit.2020.3030569 · Cited by 35 · see citing works
Kohman, R. E., Kunjapur, A. M., Hysolli, E., Wang, Y., & Church, G. M. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201707976 · Cited by 33 · see citing works
Self-citationMobile and Self‐Sustained Data Storage in an Extremophile Genomic DNA
Sun, F., Dong, Y., Ni, M., Ping, Z., Sun, Y., Ouyang, Q., & Qian, L. (2023) · Advanced Science · doi:10.1002/advs.202206201 · Cited by 33 · see citing works
CRISPR adaptation from a structural perspective
Sasnauskas, G., & Šikšnys, V. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.05.015 · Cited by 33 · see citing works
Genome expansion by a CRISPR trimmer-integrase
Wang, J. Y., Tuck, O. T., Skopintsev, P., Soczek, K. M., Li, G., Al-Shayeb, B., Zhou, J., & Doudna, J. A. (2023) · Nature · doi:10.1038/s41586-023-06178-2 · Cited by 33 · see citing works
Efficient data reconstruction: The bottleneck of large-scale application of DNA storage
Cao, B., Zheng, Y., Shao, Q., Liu, Z., Xie, L., Zhao, Y., Wang, B., Zhang, Q., & Wei, X. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113699 · Cited by 31 · see citing works
Reconstruction Codes for DNA Sequences With Uniform Tandem-Duplication Errors
Yehezkeally, Y., & Schwartz, M. (2019) · IEEE Transactions on Information Theory · doi:10.1109/tit.2019.2940256 · Cited by 31 · see citing works
Design considerations for advancing data storage with synthetic DNA for long-term archiving
Ezekannagha, C., Becker, A., Heider, D., & Hattab, G. (2022) · Materials Today Bio · doi:10.1016/j.mtbio.2022.100306 · Cited by 31 · see citing works
“Cell Disk” DNA Storage System Capable of Random Reading and Rewriting
Hou, Z., Qiang, W., Wang, X., Chen, X., Hu, X., Han, X., Shen, W., Zhang, B., Peng, X., Shi, W., et al. (2024) · Advanced Science · doi:10.1002/advs.202305921 · Cited by 30 · see citing works
Multiplex genomic recording of enhancer and signal transduction activity in mammalian cellsPreprint
Chen, W., Choi, J., Nathans, J. F., Agarwal, V., Martin, B., Nichols, E. K., Leith, A., Lee, C., & Shendure, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.05.467434 · Cited by 30 · see citing works
A brief review on DNA storage, compression, and digitalization
Cevallos, Y., Nakano, T., Tello-Oquendo, L., Rushdi, A. A., Inca, D., Santillán, I., Shirazi, A. Z., & Samaniego, N. (2021) · Nano Communication Networks · doi:10.1016/j.nancom.2021.100391 · Cited by 29 · see citing works
Recording transcriptional histories using Record-seq
Tanna, T., Schmidt, F., Cherepkova, M. Y., Okoniewski, M. J., & Platt, R. J. (2020) · Nature Protocols · doi:10.1038/s41596-019-0253-4 · Cited by 29 · see citing works
Preservation and Encryption in DNA Digital Data Storage
Zhang, Y., Ren, Y., Liu, Y., Wang, F., Zhang, H., & Liu, K. (2022) · ChemPlusChem · doi:10.1002/cplu.202200183 · Cited by 28 · see citing works
DNA-Based Data Storage Systems: A Review of Implementations and Code Constructions
Milenković, O., & Pan, C. (2024) · IEEE Transactions on Communications · doi:10.1109/tcomm.2024.3367748 · Cited by 27 · see citing works
Real-time observation of CRISPR spacer acquisition by Cas1–Cas2 integrase
Budhathoki, J. B., Xiao, Y., Schuler, G. A., Hu, C., Cheng, A., Ding, F., & Ke, A. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0415-7 · Cited by 26 · see citing works
Terabit-scale high-fidelity diamond data storage
Zhou, J., Su, J. Q., Guan, J., Yang, Y., Ji, W., Wang, M.-Q., Shi, F., Xia, K., Wang, Y., & Du, J. (2024) · Nature Photonics · doi:10.1038/s41566-024-01573-1 · Cited by 25 · see citing works
Empowering DNA-Based Information Processing: Computation and Data Storage
Li, K., Chen, H., Li, D., Yang, C. J., Zhang, H., & Zhu, Z. (2024) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.4c13948 · Cited by 25 · see citing works
Coding for Optimized Writing Rate in DNA Storage
Jain, S., Farnoud, F., Schwartz, M., & Bruck, J. (2020) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit44484.2020.9174253 · Cited by 25 · see citing works
DNA Origami‐Based Single‐Molecule CRISPR Machines for Spatially Resolved Searching
Hao, Y., Li, M., Zhang, Q., Shi, J., Li, J., Li, Q., Fan, C., & Wang, F. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202205460 · Cited by 25 · see citing works
Molecular recording: transcriptional data collection into the genome
Lear, S. K., & Shipman, S. L. (2022) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102855 · Cited by 25 · see citing works
Self-citationEngineered bacterial swarm patterns as spatial records of environmental inputs
Doshi, A., Shaw, M., Tonea, R., Moon, S., Minyety, R., Doshi, A., Laine, A. F., Guo, J., & Danino, T. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01325-2 · Cited by 25 · see citing works
Opportunities in biotechnology
Gartland, K. M. A., & Gartland, J. S. (2018) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2018.06.303 · Cited by 25 · see citing works
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › 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 ›
Are you an author, or do you see a problem with this page? Request a review
