Enzymatic DNA synthesis for digital information storage.
Open accessAbstract
DNA is an emerging storage medium for digital data but its adoption is hampered by limitations of phosphoramidite chemistry, which was developed for single-base accuracy required for biological functionality. Here, we establish a de novo enzymatic DNA synthesis strategy designed from the bottom-up for information storage. We harness a template-independent DNA polymerase for controlled synthesis of sequences with user-defined information content. We demonstrate retrieval of 144-bits, including addressing, from perfectly synthesized DNA strands using batch-processed Illumina and real-time Oxford Nanopore sequencing. We then develop a codec for data retrieval from populations of diverse but imperfectly synthesized DNA strands, each with a ~30% error tolerance. With this codec, we experimentally validate a kilobyte-scale design which stores 1 bit per nucleotide. Simulations of the codec support reliable and robust storage of information for large-scale systems. This work paves the way for alternative synthesis and sequencing strategies to advance information storage in DNA.
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?
Terminator-free TdT-based DNA synthesis was proved to be a superior combination with Nanopore sequencer, which is optimal for sequencing long DNA strands with high error rate.
“It is worth mentioning that, in the study by Lee et al. (2019), the terminator free TdT-based DNA synthesis was proved to be a superior combination with Nanopore sequencer which is optimal for sequencing of long DNA strands with high error rate.”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Lee et al., 2019
TdT-based enzymatic DNA synthesis has already been applied to data storage applications.
“Indeed, two groups of Jensen et al. (2018) and Lee et al. (2018) have already applied TdT-based enzymatic DNA synthesis method to data storage applications.”
From Large-Scale de Novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities (2021) · cites this paper as Lee et al., 2018
Recent progress in nucleic acid synthesis and sequencing continues to reduce the cost of writing and reading DNA, foreshadowing future commercially competitive DNA-based information storage.
“Recent progress in nucleic acid synthesis and sequencing technologies continue to reduce the cost of writing and reading DNA, foreshadowing future commercially competitive DNA-based information storage1,3–5.”
From Random access DNA memory using Boolean search in an archival file storage system (2021) · cites this paper as [5]
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
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works
The Elements of Statistical Learning
Hastie, T., Friedman, J., & Tibshirani, R. (2001) · Springer Series in Statistics · doi:10.1007/978-0-387-21606-5 · Cited by 24,162 · see citing works
The Proceedings of the National Academy of Sciences
Richards, J. W. (1915) · Science · doi:10.1126/science.42.1074.161 · Cited by 13,941 · see citing works
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288 · see citing works
Binary Codes capable of currecting deletions, insertions, and reversals
Levenshtein, V. I. (1965) · Soviet physics. Doklady · Cited by 10,387 · see citing works
Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis
Beaucage, S. L., & Caruthers, M. H. (1981) · Tetrahedron Letters · doi:10.1016/s0040-4039(01)90461-7 · Cited by 2,013 · see citing works
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892 · see citing works
A Sequencing Method Based on Real-Time Pyrophosphate
Ronaghi, M., Uhlén, M., & Nyrén, P. (1998) · Science · doi:10.1126/science.281.5375.363 · Cited by 1,630 · 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
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
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
Slowing DNA Translocation in a Solid-State Nanopore
Fologea, D., Uplinger, J., Thomas, B. R., McNabb, D. S., & Li, J. (2005) · Nano Letters · doi:10.1021/nl051063o · Cited by 567 · see citing works
Thermal Conversion of Nonpriming Deoxyribonucleic Acid to Primer
Bollum, F. J. (1959) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)69770-4 · Cited by 541 · see citing works
A 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
Real-time selective sequencing using nanopore technology
Loose, M., Malla, S., & Stout, M. (2016) · Nature Methods · doi:10.1038/nmeth.3930 · Cited by 399 · see citing works
Portable and Error-Free DNA-Based Data Storage
Yazdi, S. M. H. T., Gabrys, R., & Milenkovic, O. (2017) · Scientific Reports · doi:10.1038/s41598-017-05188-1 · Cited by 361 · see citing works
Forward Error Correction for DNA Data Storage
Blawat, M., Gaedke, K., Hütter, I., Chen, X.-M., Turczyk, B., Inverso, S., Pruitt, B. W., & Church, G. M. (2016) · Procedia Computer Science · doi:10.1016/j.procs.2016.05.398 · Cited by 333 · see citing works
Self-citationReliable communication over channels with insertions, deletions, and substitutions
Davey, M. C., & Mackay, D. (2001) · IEEE Transactions on Information Theory · doi:10.1109/18.910582 · Cited by 332 · see citing works
LeProust, E. M., Peck, B. J., Spirin, K., McCuen, H. B., Moore, B., Namsaraev, E., & Caruthers, M. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq163 · Cited by 326 · see citing works
Deoxynucleotide-polymerizing Enzymes of Calf Thymus Gland
Kato, K., Gonalves, J. M., Houts, G. E., & Bollum, F. J. (1967) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)99635-3 · Cited by 324 · see citing works
De novo DNA synthesis using polymerase-nucleotide conjugates.
Palluk, S., Arlow, D. H., de Rond, T., Barthel, S., Kang, J. S., Bector, R., Baghdassarian, H. M., Truong, A. N., Kim, P. W., Singh, A. K., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4173 · Cited by 316 · see citing works
Enzymatic end-to-end joining of DNA molecules
Lobban, P. E., & Kaiser, A. D. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90468-3 · Cited by 314 · 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-citationMcNally, B., Singer, A., Yu, Z., Sun, Y., Weng, Z., & Meller, A. (2010) · Nano Letters · doi:10.1021/nl1012147 · Cited by 270 · 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-citationA survey of results for deletion channels and related synchronization channels
Mitzenmacher, M. (2009) · Probability Surveys · doi:10.1214/08-ps141 · Cited by 235 · see citing works
Terminal Deoxynucleotidyl Transferase: The Story of a Misguided DNA Polymerase
Motea, E., & Berdis, A. (2009) · Biochimica et Biophysica Acta · doi:10.1016/j.bbapap.2009.06.030 · Cited by 222 · see citing works
Long-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
Deng, G., & Wu, R. J. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.16.4173 · Cited by 181 · see citing works
Oligodeoxyribonucleotide-primed Reactions Catalyzed by Calf Thymus Polymerase
Bollum, F. J. (1962) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)73964-7 · Cited by 122 · see citing works
Jensen, M. A., & Davis, R. W. (2018) · Biochemistry · doi:10.1021/acs.biochem.7b00937 · Cited by 106 · see citing works
Lashkari, D. A., Hunicke‐Smith, S., Norgren, R. M., Davis, R. W., & Brennan, T. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.17.7912 · Cited by 79 · see citing works
A brief review of DNA and RNA chemical synthesis
Caruthers, M. H. (2011) · Biochemical Society Transactions · doi:10.1042/bst0390575 · Cited by 79 · see citing works
Molecular Biology of Terminal Transferas
Chang, L. M. S., Bollum, F. J., & Gallo, R. C. (1986) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238609113608 · Cited by 76 · see citing works
Biochemical properties of purified human terminal deoxynucleotidyltransferase.
Deibel, M. R., & Colemán, M. S. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)85653-3 · Cited by 67 · see citing works
Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing
Torre, R. D., Larkin, J., Singer, A., & Meller, A. (2012) · Nanotechnology · doi:10.1088/0957-4484/23/38/385308 · Cited by 66 · see citing works
Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing
Zamft, B. M., Marblestone, A. H., Kording, K. P., Schmidt, D., Martin-Alarcon, D. A., Tyo, K. E. J., Boyden, E. S., & Church, G. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043876 · Cited by 58 · see citing works
Self-citationGenotyping by apyrase-mediated allele-specific extension
Ahmadian, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.24.e121 · Cited by 54 · see citing works
Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis.
Mathews, A. S., Yang, H., & Montemagno, C. (2016) · Organic & Biomolecular Chemistry · doi:10.1039/c6ob01371f · Cited by 50 · see citing works
A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation
Kwok, C. K., Ding, Y., Sherlock, M. E., Assmann, S. M., & Bevilacqua, P. C. (2013) · Analytical Biochemistry · doi:10.1016/j.ab.2013.01.008 · Cited by 43 · see citing works
Competitive enzymatic reaction to control allele-specific extensions
Hultin, E. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni048 · Cited by 34 · see citing works
Chemical Synthesis of Oligonucleotides Using Acetone as a Washing Solvent
Gaytán, P. (2009) · BioTechniques · doi:10.2144/000113206 · Cited by 15 · see citing works
Free-running enzymatic oligonucleotide synthesis for data storage applications.
Jensen, M. A., Griffin, P. B., & Davis, R. W. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/355719 · Cited by 5 · see citing works
Vega, M. A., Granell, P., Lasorsa, C. A., Lerner, B., & Pérez, M. (2016) · Journal of Physics Conference Series · doi:10.1088/1742-6596/687/1/012029 · Cited by 2 · see citing works
Flagged first, then by citations
5 of the 51 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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
Recent progress in non-native nucleic acid modifications
McKenzie, L. K., El-Khoury, R., Thorpe, J. D., Damha, M. J., & Hollenstein, M. (2021) · Chemical Society Reviews · doi:10.1039/d0cs01430c · Cited by 300 · see citing works
Organoid intelligence (OI): the new frontier in biocomputing and intelligence-in-a-dish
Smirnova, L., Caffo, B. S., Gracias, D. H., Huang, Q., Pantoja, I. E. M., Tang, B., Zack, D. J., Berlinicke, C. A., Boyd, J. L., Harris, T. D., et al. (2023) · Frontiers in Science · doi:10.3389/fsci.2023.1017235 · Cited by 290 · see citing works
DNA synthesis technologies to close the gene writing gap
Hoose, A., Vellacott, R., Storch, M., Freemont, P. S., & Ryadnov, M. G. (2023) · Nature Reviews Chemistry · doi:10.1038/s41570-022-00456-9 · Cited by 271 · see citing works
Emerging Approaches to DNA Data Storage: Challenges and Prospects
Doricchi, A., Platnich, C. M., Gimpel, A., Horn, F., Earle, M., Lanzavecchia, G., Cortajarena, A. L., Liz-Marzán, L. M., Liu, N., Heckel, R., et al. (2022) · ACS Nano · doi:10.1021/acsnano.2c06748 · Cited by 235 · see citing works
Data storage in DNA with fewer synthesis cycles using composite DNA letters.
Anavy, L., Vaknin, I., Atar, O., Amit, R., & Yakhini, Z. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0240-x · Cited by 229 · 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
Expanding chemistry through in vitro and in vivo biocatalysis
Kissman, E. N., Sosa, M. B., Millar, D. C., Koleski, E. J., Thevasundaram, K., & Chang, M. C. Y. (2024) · Nature · doi:10.1038/s41586-024-07506-w · Cited by 178 · see citing works
Antkowiak, P. L., Lietard, J., Darestani, M. Z., Somoza, M. M., Stark, W. J., Heckel, R., & Grass, R. N. (2020) · Nature Communications · doi:10.1038/s41467-020-19148-3 · Cited by 173 · 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
Reading and Writing Digital Data in DNA
Meiser, L. C., Antkowiak, P. L., Koch, J., Chen, W. D., Kohll, A. X., Stark, W. J., Heckel, R., & Grass, R. N. (2020) · Nature Protocols · doi:10.1038/s41596-019-0244-5 · Cited by 164 · see citing works
Towards practical and robust DNA-based data archiving using the yin–yang codec system
Ping, Z., Chen, S., Zhou, G., Huang, X., Zhu, S. J., Zhang, H., Lee, H. H., Lan, Z., Cui, J., Chen, T., et al. (2022) · Nature Computational Science · doi:10.1038/s43588-022-00231-2 · Cited by 148 · see citing works
Self-citationRandom access DNA memory using Boolean search in an archival file storage system
Banal, J. L., Shepherd, T. R., Berleant, J., Huang, H., Reyes, M., Ackerman, C. M., Blainey, P. C., & Bathe, M. (2021) · Nature Materials · doi:10.1038/s41563-021-01021-3 · Cited by 143 · 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
Dynamic and scalable DNA-based information storage
Lin, K. N., Volkel, K., Tuck, J. M., & Keung, A. J. (2020) · Nature Communications · doi:10.1038/s41467-020-16797-2 · Cited by 117 · see citing works
Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage
Lee, H., Wiegand, D. J., Griswold, K., Punthambaker, S., Chun, H., Kohman, R. E., & Church, G. M. (2020) · Nature Communications · doi:10.1038/s41467-020-18681-5 · Cited by 116 · see citing works
Self-citationModern approaches to therapeutic oligonucleotide manufacturing
Obexer, R., Nassir, M., Moody, E. R., Baran, P. S., & Lovelock, S. L. (2024) · Science · doi:10.1126/science.adl4015 · Cited by 115 · see citing works
Robust data storage in DNA by de Bruijn graph-based de novo strand assembly
Song, L., Geng, F., Gong, Z.-Y., Chen, X., Tang, J., Gong, C., Zhou, L., Xia, R., Han, M., Xu, J.-Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33046-w · Cited by 98 · see citing works
Aerolysin nanopores decode digital information stored in tailored macromolecular analytes
Cao, C., Krapp, L. F., Al Ouahabi, A., König, N. F., Cirauqui, N., Radenovic, A., Lutz, J.-F., & Peraro, M. D. (2020) · Science Advances · doi:10.1126/sciadv.abc2661 · Cited by 97 · see citing works
Enzymatic DNA Synthesis by Engineering Terminal Deoxynucleotidyl Transferase
Lu, X., Li, J., Li, C., Lou, Q., Peng, K., Cai, B., Liu, Y., Yao, Y., Lu, L., Tian, Z., et al. (2022) · ACS Catalysis · doi:10.1021/acscatal.1c04879 · Cited by 97 · 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
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
Engineering polymerases for applications in synthetic biology
Nikoomanzar, A., Chim, N., Yik, E. J., & Chaput, J. C. (2020) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583520000050 · Cited by 84 · 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
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
Wang, S., Mao, X., Wang, F., Zuo, X., & Fan, C. (2023) · Advanced Materials · doi:10.1002/adma.202307499 · Cited by 85 · see citing works
An alternative approach to nucleic acid memory
Dickinson, G. D., Mortuza, G. M., Clay, W., Piantanida, L., Green, C. M., Watson, C., Hayden, E. J., Andersen, T., Kuang, W., Graugnard, E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22277-y · Cited by 82 · 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
Xu, C., Ma, B., Gao, Z., Dong, X., Zhao, C., & Liu, H. (2021) · Science Advances · doi:10.1126/sciadv.abk0100 · Cited by 79 · see citing works
Choi, Y., Bae, H. J., Lee, A. C., Choi, H., Lee, D., Ryu, T., Hyun, J., Kim, S., Kim, H., Song, S., et al. (2020) · Advanced Materials · doi:10.1002/adma.202001249 · Cited by 77 · see citing works
Technological challenges and milestones for writing genomes
Ostrov, N., Beal, J., Ellis, T., Gordon, D. B., Karas, B. J., Lee, H. H., Lenaghan, S. C., Schloss, J. A., Stracquadanio, G., Trefzer, A. C., et al. (2019) · Science · doi:10.1126/science.aay0339 · Cited by 76 · see citing works
Self-citationSong, L.-F., Deng, Z.-H., Gong, Z.-Y., Li, L.-L., & Li, B.-Z. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.689797 · Cited by 74 · see citing works
Multicomponent molecular memory
Arcadia, C. E., Kennedy, E., Geiser, J. D., Dombroski, A., Oakley, K., Chen, S., Sprague, L. W., Ozmen, M., Sello, J. K., Weber, P. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14455-1 · Cited by 74 · see citing works
Designing Uncorrelated Address Constrain for DNA Storage by DMVO Algorithm
Cao, B., Ii, X., Zhang, X., Wang, B., Zhang, Q., & Wei, X. (2020) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2020.3011582 · Cited by 69 · 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
DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access
Bögels, B. W. A., Nguyen, B. H., Ward, D., Gascoigne, L., Schrijver, D. P., Pistikou, A. M., Joesaar, A., Yang, S., Voets, I. K., Mulder, W. J. M., et al. (2023) · Nature Nanotechnology · doi:10.1038/s41565-023-01377-4 · Cited by 67 · see citing works
Semiautomated synthesis of sequence-defined polymers for information storage
Lee, J. M., Kwon, J.-H., Lee, S. J., Jang, H., Kim, D., Song, J., & Kim, K. T. (2022) · Science Advances · doi:10.1126/sciadv.abl8614 · Cited by 62 · see citing works
Reconfigurable A-motif, i-motif and triplex nucleic acids for smart pH-responsive DNA hydrogels
Hu, Y., & Ying, J. Y. (2022) · Materials Today · doi:10.1016/j.mattod.2022.12.003 · Cited by 63 · see citing works
Information-Theoretic Foundations of DNA Data Storage
Shomorony, I., & Heckel, R. (2022) · Foundations and Trends® in Communications and Information Theory · doi:10.1561/0100000117 · Cited by 62 · 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
Barthel, S., Palluk, S., Hillson, N. J., Keasling, J. D., & Arlow, D. H. (2020) · Genes · doi:10.3390/genes11010102 · Cited by 56 · see citing works
Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies
Bush, J., Singh, S., Vargas, M., Oktay, E., Hu, C.-H., & Veneziano, R. (2020) · Molecules · doi:10.3390/molecules25153386 · Cited by 58 · see citing works
Current and Emerging Methods for the Synthesis of Single-Stranded DNA
Hao, M., Qiao, J., & Qi, H. (2020) · Genes · doi:10.3390/genes11020116 · Cited by 55 · see citing works
Multiplex enzymatic synthesis of DNA with single-base resolution
Verardo, D., Adelizzi, B., Rodriguez-Pinzon, D. A., Moghaddam, N., Thomée, E., Loman, T., Godron, X., & Horgan, A. M. (2023) · Science Advances · doi:10.1126/sciadv.adi0263 · Cited by 53 · see citing works
Chandak, S., Neu, J., Tatwawadi, K., Mardia, J., Lau, B. T., Kubit, M. A., Hulett, R., Griffin, P. B., Wootters, M. K., Weissman, T., et al. (2020) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp40776.2020.9053441 · Cited by 51 · see citing works
Controlled enzymatic synthesis of oligonucleotides
Pichon, M. M., & Hollenstein, M. (2024) · Communications Chemistry · doi:10.1038/s42004-024-01216-0 · Cited by 50 · see citing works
Advances in biocatalytic and chemoenzymatic synthesis of nucleoside analogues
Cosgrove, S. C., & Miller, G. J. (2022) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2022.2039620 · Cited by 49 · see citing works
Information stored in nanoscale: Encoding data in a single DNA strand with Base64
Zhang, Y., Kong, L., Wang, F., Li, B., Ma, C., Chen, D., Liu, K., Fan, C., & Zhang, H. (2020) · Nano Today · doi:10.1016/j.nantod.2020.100871 · Cited by 48 · see citing works
Adaptive coding for DNA storage with high storage density and low coverage
Cao, B., Zhang, X., Cui, S., & Zhang, Q. (2022) · npj Systems Biology and Applications · doi:10.1038/s41540-022-00233-w · Cited by 49 · see citing works
Minimum Free Energy Coding for DNA Storage
Cao, B., Zhang, X., Wu, J., Wang, B., Zhang, Q., & Wei, X. (2021) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2021.3056351 · Cited by 48 · see citing works
CMOS electrochemical pH localizer-imager
Jung, H. S., Jung, W., Wang, J., Abbott, J., Horgan, A. M., Fournier, M., Hinton, H., Hwang, Y., Godron, X., Nicol, R., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm6815 · Cited by 47 · see citing works
Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Tang, N. C., Su, J. C., Shmidov, Y., Kelly, G., Deshpande, S., Sirohi, P., Peterson, N., & Chilkoti, A. (2024) · Nature Communications · doi:10.1038/s41467-024-47519-7 · 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
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
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
Flamme, M., Hanlon, S. P., Marzuoli, I., Püntener, K., Sladojevich, F., & Hollenstein, M. (2022) · Communications Chemistry · doi:10.1038/s42004-022-00685-5 · Cited by 41 · see citing works
Evolving a Thermostable Terminal Deoxynucleotidyl Transferase
Chua, J. P. S., Go, M. K., Osothprarop, T., Mcdonald, S., Karabadzhak, A. G., Yew, W. S., Peisajovich, S. G., & Nirantar, S. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00078 · Cited by 40 · see citing works
Future trends in synthetic biology in Asia
Mao, N., Aggarwal, N., Poh, C. L., Cho, B., Kondo, A., Liu, C., Yew, W. S., & Chang, M. W. (2021) · Advanced Genetics · doi:10.1002/ggn2.10038 · Cited by 38 · see citing works
Reconstruction algorithms for DNA-storage systems
Sabary, O., Yucovich, A., Shapira, G., & Yaakobi, E. (2024) · Scientific Reports · doi:10.1038/s41598-024-51730-3 · Cited by 50 · see citing works
Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA
Kawabe, H., Thomas, C. A., Hoshika, S., Kim, M., Kim, M., Miessner, L., Kaplan, N. A., Craig, J. M., Gundlach, J. H., Laszlo, A. H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42406-z · Cited by 38 · see citing works
Li, K., Lu, X., Liao, J., Chen, H., Wei, L., Zhao, Y., Tang, D., Li, C., Tian, Z., Zhu, Z., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2410164121 · Cited by 36 · see citing works
A primordial DNA store and compute engine
Lin, K. N., Volkel, K., Cao, C., Hook, P. W., Polak, R. E., Clark, A. S., San‐Miguel, A., Timp, W., Tuck, J. M., Velev, O. D., et al. (2024) · Nature Nanotechnology · doi:10.1038/s41565-024-01771-6 · Cited by 38 · see citing works
Schaudy, E., Lietard, J., & Somoza, M. M. (2021) · ACS Synthetic Biology · doi:10.1021/acssynbio.1c00142 · Cited by 35 · see citing works
Towards the controlled enzymatic synthesis of LNA containing oligonucleotides
Sabat, N., Katkevica, D., Pajuste, K., Flamme, M., Stämpfli, A., Katkevičs, M., Hanlon, S. P., Bisagni, S., Püntener, K., Sladojevich, F., et al. (2023) · Frontiers in Chemistry · doi:10.3389/fchem.2023.1161462 · Cited by 35 · see citing works
Field‐Effect Transistor‐Based Biosensor for pH Sensing and Mapping
Ren, H., Liang, K., Li, D., Chen, Y., Tang, Y., Wang, Y., Li, F., Liu, G., & Zhu, B. (2023) · Advanced Sensor Research · doi:10.1002/adsr.202200098 · Cited by 32 · see citing works
Survey for a Decade of Coding for DNA Storage
Sabary, O., Kiah, H. M., Siegel, P. H., & Yaakobi, E. (2024) · IEEE Transactions on Molecular Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2024.3403488 · Cited by 33 · see citing works
A Survey on DNA-Based Cryptography and Steganography
Mahjabin, T., Olteanu, A., Xiao, Y., Han, W., Li, T., & Sun, W. (2023) · IEEE Access · doi:10.1109/access.2023.3324875 · Cited by 31 · see citing works
Enzymatic Synthesis of Designer DNA Using Cyclic Reversible Termination and a Universal Template
Hoff, K., Halpain, M., Garbagnati, G. F., Edwards, J. S., & Zhou, W. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00315 · Cited by 30 · see citing works
Improving error-correcting capability in DNA digital storage via soft-decision decoding
Ding, L., Wu, S., Hou, Z., Li, A., Xu, Y., Feng, H., Pan, W., & Ruan, J. (2023) · National Science Review · doi:10.1093/nsr/nwad229 · Cited by 27 · see citing works
Towards the enzymatic synthesis of phosphorothioate containing LNA oligonucleotides
Flamme, M., Hanlon, S. P., Iding, H., Puentener, K., Sladojevich, F., & Hollenstein, M. (2021) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2021.128242 · Cited by 30 · see citing works
Principles of Information Storage in Small-Molecule Mixtures
Rosenstein, J. K., Rose, C., Reda, S., Weber, P. M., Kim, E., Sello, J. K., Geiser, J. D., Kennedy, E., Arcadia, C. E., Dombroski, A., et al. (2020) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2020.2977304 · Cited by 31 · see citing works
Metastable hybridization-based DNA information storage to allow rapid and permanent erasure
Kim, J., Bae, J. H., Baym, M., & Zhang, D. Y. (2020) · Nature Communications · doi:10.1038/s41467-020-18842-6 · Cited by 29 · see citing works
Scaling logical density of DNA storage with enzymatically-ligated composite motifs
Yan, Y., Pinnamaneni, N., Chalapati, S., Crosbie, C., & Appuswamy, R. (2023) · Scientific Reports · doi:10.1038/s41598-023-43172-0 · 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
Terminal deoxynucleotidyl transferase-mediated formation of protein binding polynucleotides
Ashley, J. A., Schaap‐Johansen, A., Mohammadniaei, M., Naseri, M., Marcatili, P., Prado, M., & Sun, Y. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1263 · Cited by 28 · see citing works
On Coding for an Abstracted Nanopore Channel for DNA Storage
Hulett, R., Chandak, S., & Wootters, M. K. (2021) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit45174.2021.9518236 · Cited by 28 · 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
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
Decoding DNA data storage for investment
Stanley, P. M., Strittmatter, L. M., Vickers, A., & Lee, K. C. K. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107639 · Cited by 24 · see citing works
Zhang, X., Xu, J., Xing, X., Li, Y., Shang, H., & Chen, W. (2021) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2021.113564 · Cited by 25 · see citing works
Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis
Bhan, N., Callisto, A., Strutz, J., Glaser, J. I., Kalhor, R., Boyden, E. S., Church, G. M., Kording, K. P., & Tyo, K. E. J. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c07331 · Cited by 24 · see citing works
Self-citationAbdollahzadeh, H., Peeples, T. L., & Shahcheraghi, M. (2025) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2025.115673 · Cited by 24 · see citing works
Zeng, Z.-F., Cai, J.-H., Li, F., Weng, Y., Huang, Q., Yang, H., Huang, Q., & Wei, Y. (2021) · RSC Advances · doi:10.1039/d1ra05798g · Cited by 23 · see citing works
DNA-based data storage via combinatorial assemblyPreprint
Roquet, N., Bhatia, S. P., Flickinger, S. A., Mihm, S., Norsworthy, M. W., Leake, D., & Park, H. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.20.440194 · Cited by 24 · see citing works
Recent Progress in High-Throughput Enzymatic DNA Synthesis for Data Storage
Baek, D. J., Joe, S.-Y., Shin, H., Park, C., Jo, S., & Chun, H. (2024) · BioChip Journal · doi:10.1007/s13206-024-00146-2 · Cited by 24 · see citing works
Behyar, M. B., Nilghaz, A., Hasanzadeh, M., & Shadjou, N. (2024) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2024.117846 · Cited by 22 · see citing works
Zhao, X., Li, J., Fan, Q., Dai, J., Long, Y., Liu, R., Zhai, J., Pan, Q., & Li, Y. (2024) · Nature Communications · doi:10.1038/s41467-024-53455-3 · Cited by 22 · see citing works
Wang, G., He, C., Zou, J., Liu, J., Du, Y., & Chen, T. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00456 · Cited by 22 · see citing works
Lau, B. T., Chandak, S., Roy, S., Tatwawadi, K., Wootters, M. K., Weissman, T., & Ji, H. P. (2023) · Scientific Reports · doi:10.1038/s41598-023-29575-z · Cited by 22 · see citing works
A biological camera that captures and stores images directly into DNA
Lim, C. K., Yeoh, J. W., Kunartama, A. A., Yew, W. S., & Poh, C. L. (2023) · Nature Communications · doi:10.1038/s41467-023-38876-w · Cited by 24 · see citing works
How to make DNA data storage more applicable
Akash, A., Bencúrová, E., & Dandekar, T. (2023) · Trends in biotechnology · doi:10.1016/j.tibtech.2023.07.006 · Cited by 23 · see citing works
Non-Binary Codes for Correcting a Burst of at Most t Deletions
Wang, S., Tang, Y., Sima, J., Gabrys, R., & Farnoud, F. (2023) · IEEE Transactions on Information Theory · doi:10.1109/tit.2023.3340246 · Cited by 22 · see citing works
Buko, T., Tuczko, N., & Ishikawa, T. (2023) · BioTech · doi:10.3390/biotech12020044 · Cited by 21 · see citing works
“96 B ~50 ASCII codec Enzymatic DNA synthesis [24]”
Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate
Smith, J. A., Nguyen, B. H., Carlson, R., Bertram, J. G., Palluk, S., Arlow, D. H., & Strauß, K. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00044 · Cited by 21 · see citing works
Optimizing the Decoding Probability and Coverage Ratio of Composite DNA
Cohen, T., & Yaakobi, E. (2024) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit57864.2024.10619348 · Cited by 21 · see citing works
Long oligos: direct chemical synthesis of genes with up to 1728 nucleotides
Yin, Y., Arneson, R., Yuan, Y., & Fang, S. (2024) · Chemical Science · doi:10.1039/d4sc06958g · Cited by 21 · see citing works
Recent advances in generative biology for biotherapeutic discovery
Mock, M. L., LANGMEAD, C. J., Grandsard, P. J., Edavettal, S. C., & Russell, A. J. (2024) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2024.01.003 · Cited by 20 · see citing works
Cost‐Effective DNA Storage System with DNA Movable Type
Wang, C., Wei, D., Wei, Z., Yang, D., Xing, J., Wang, Y., Wang, X., Wang, P., Ma, G., Zhang, X., et al. (2024) · Advanced Science · doi:10.1002/advs.202411354 · Cited by 20 · see citing works
Synthetic genomes with altered genetic codes
Ostrov, N., Nyerges, Á., Chiappino-Pepe, A., Rudolph, A., Baas-Thomas, M. S., & Church, G. M. (2020) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2020.09.007 · Cited by 20 · see citing works
Self-citation
- Authors
- Lee, H. H., Kalhor, R., Goela, N., Bolot, J., & Church, G. M.
- Affiliations
- Harvard University (US)
- Corresponding author
- Lee, Henry H.
- Church, George M.
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2018-06-16
- Volume
- 10
- Issue
- 1
- Pages
- 2383-2383
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC6546792
- OpenAlex
- W2947129118
- Cited by
- 265
- References
- 51
- Citations by year
- 2026: 30 · 2025: 39 · 2024: 48 · 2023: 38 · 2022: 29 · 2021: 35 · 2020: 31 · 2019: 13 · 2018: 2
- FWCI
- 8.93
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DE‐FG02‐, DEFG0202ER63445, FG02-02ER63445, Grant DE-FG02-02ER63445)
- U.S. Department of Health and Human Services (R01-MH103910-02)
- National Institutes of Health (DE-FG02-02ER63445)
- National Institute of Mental Health (R01MH103910)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- DNA data storage, enzymatic DNA synthesis, terminal deoxynucleotidyl transferase, apyrase, nanopore sequencing
- MeSH terms
- Apyrase, DNA, DNA Nucleotidylexotransferase, Information Storage and Retrieval, Sequence Analysis, DNA, Nanopores
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
