Reading and Writing Digital Data in DNA
Abstract
Because of its longevity and enormous information density, DNA is considered a promising data storage medium. In this work, we provide instructions for archiving digital information in the form of DNA and for subsequently retrieving it from the DNA. In principle, information can be represented in DNA by simply mapping the digital information to DNA and synthesizing it. However, imperfections in synthesis, sequencing, storage and handling of the DNA induce errors within the molecules, making error-free information storage challenging. The procedure discussed here enables error-free storage by protecting the information using error-correcting codes. Specifically, in this protocol, we provide the technical details and precise instructions for translating digital information to DNA sequences, physically handling the biomolecules, storing them and subsequently re-obtaining the information by sequencing the DNA. Along with the protocol, we provide computer code that automatically encodes digital information to DNA sequences and decodes the information back from DNA to a digital file. The required software is provided on a Github repository. The protocol relies on commercial DNA synthesis and DNA sequencing via Illumina dye sequencing, and requires 1-2 h of preparation time, 1/2 d for sequencing preparation and 2-4 h for data analysis. This protocol focuses on storage scales of ~100 kB to 15 MB, offering an ideal starting point for small experiments. It can be augmented to enable higher data volumes and random access to the data and also allows for future sequencing and synthesis technologies, by changing the parameters of the encoder/decoder to account for the corresponding error rates.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Meiser et al. (2020) used a Reed-Solomon code for storing a full album of music in DNA.
“Meiser et al. (2020) have used a Reed–Solomon code for storing a full album of music in DNA [33].”
From DNA Data Storage. (2023) · cites this paper as [33]
The costs of column-based DNA synthesis range between 0.05 to 0.15 USD per nucleotide.
“The costs of this procedure range between 0.05 to 0.15 USD per nucleotide.11”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [11]
DNA synthesis is not the bottleneck in DNA random number generation; a standard synthesis can generate true randomness at a rate of 225 GB/s at a cost of 0.000014 USD/GB.
“Consequently, in contrast to DNA data storage38, DNA synthesis is not the bottleneck in DNA random number generation as such a standard synthesis can generate true randomness at a rate of 225 GB/s at a cost of 0.000014 USD/GB.”
From DNA synthesis for true random number generation (2020) · cites this paper as [38]
Cites
A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486 · see citing works
Error Detecting and Error Correcting Codes
Hamming, R. W. (1950) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1950.tb00463.x · Cited by 5,377 · 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
ERROR DETECTING AND ERROR CORRECTING CODES
Chauhan, N., Yadav, P., & Kumari, P. (2014) · Cited by 3,270 · 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
Oxford Nanopore MinION Sequencing and Genome Assembly
Lu, H., Giordano, F., & Ning, Z. (2016) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2016.05.004 · Cited by 936 · see citing works
Mackay, D. (2005) · IEE Proceedings - Communications · doi:10.1049/ip-com:20050237 · Cited by 900 · 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
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
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
Roads towards fault-tolerant universal quantum computation
Campbell, E. T., Terhal, B. M., & Vuillot, C. (2017) · Nature · doi:10.1038/nature23460 · Cited by 596 · see citing works
Singleton, R. C. (1964) · IEEE Transactions on Information Theory · doi:10.1109/tit.1964.1053661 · Cited by 546 · see citing works
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
Keller, A., Graefen, A., Ball, M., Matzas, M., Boisguerin, V., Maixner, F., Leidinger, P., Backes, C., Khairat, R., Forster, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms1701 · Cited by 437 · see citing works
Channel coding: The road to channel capacity
Costello, D. J., & Forney, G. D. (2007) · Proceedings of the IEEE · doi:10.1109/jproc.2007.895188 · Cited by 404 · 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
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
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
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
DNA-Based Storage: Trends and Methods
Yazdi, S. M. H. T., Kiah, H. M., Garcia-Ruiz, E., Ma, J., Zhao, H., & Milenkovic, O. (2015) · IEEE Transactions on Molecular, Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2016.2537305 · Cited by 278 · see citing works
Enzymatic DNA synthesis for digital information storage.
Lee, H. H., Kalhor, R., Goela, N., Bolot, J., & Church, G. M. (2018) · doi:10.1101/348987 · Cited by 265 · 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
Chain and conformation stability of solid-state DNA: implications for room temperature storage
Bonnet, J., Colotte, M., Coudy, D., Couallier, V., Portier, J., Morin, B., & Tuffet, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1060 · Cited by 182 · see citing works
Michelson, A. M., & Todd, A. R. (1955) · Journal of the Chemical Society (Resumed) · doi:10.1039/jr9550002632 · Cited by 174 · see citing works
2017 IEEE International Symposium on Information Theory (ISIT)
(2017) · doi:10.1109/isit37237.2017 · Cited by 155 · see citing works
Paunescu, D., Puddu, M., Soellner, J. O. B., Stoessel, P. R., & Grass, R. N. (2013) · Nature Protocols · doi:10.1038/nprot.2013.154 · Cited by 151 · see citing works
Multiplexed gene synthesis in emulsions for exploring protein functional landscapes
Plesa, C., Sidore, A. M., Lubock, N. B., Zhang, D., & Kosuri, S. (2018) · Science · doi:10.1126/science.aao5167 · Cited by 124 · see citing works
Fundamental limits of DNA storage systems
Heckel, R., Shomorony, I., Ramchandran, K., & Tse, D. N. C. (2017) · 2017 IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit.2017.8007106 · Cited by 123 · see citing works
Self-citationRadiocarbon AMS Dates for Paleolithic Cave Paintings
Valladas, H., Tisnérat-Laborde, N., Cachier, H., Arnold, M., de Quirós, F. B., Cabrera-Valdés, V, Clottes, J., Courtin, J., Fortea-Pérez, J. J., Gonzáles-Sainz, C., et al. (2001) · Radiocarbon · doi:10.1017/s0033822200041643 · Cited by 89 · see citing works
Maurer, K., Cooper, J., Caraballo, M., Crye, J., Suciu, D., Ghindilis, A., Leonetti, J. A., Wang, W., Rossi, F. M., Stöver, A. G., et al. (2006) · PLoS ONE · doi:10.1371/journal.pone.0000034 · Cited by 80 · see citing works
Capacity Results for the Noisy Shuffling Channel
Shomorony, I., & Heckel, R. (2019) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit.2019.8849789 · Cited by 54 · see citing works
Kutschera, W., & Rom, W. (2000) · Nuclear Instruments and Methods in Physics Research Section B Beam Interactions with Materials and Atoms · doi:10.1016/s0168-583x(99)01196-9 · Cited by 27 · see citing works
Gottesman, D. (2016) · Nature · doi:10.1038/nature20479 · Cited by 10 · see citing works
A Characterization of the DNA Data Storage Channel
Heckel, R., Mikutis, G., & Grass, R. N. (2019) · Scientific Reports · doi:10.1038/s41598-019-45832-6 · Cited by 9 · see citing works
Costello, J. D., & Forney, G. D. (2007) · Proceedings of the IEEE · Cited by 8 · see citing works
Heckel, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4093 · Cited by 8 · see citing works
A coupon collector's problem with bonuses
Nakata, T., & Kubo, I. (2006) · Discrete Mathematics & Theoretical Computer Science · doi:10.46298/dmtcs.3515 · Cited by 6 · see citing works
Improving communication for interdisciplinary teams working on storage of digital information in DNA
Hesketh, E. E., Sayir, J., & Goldman, N. (2018) · F1000Research · doi:10.12688/f1000research.13482.1 · Cited by 5 · see citing works
A brief history of the development of error correcting codes
Reed, I. S. (2000) · Computers & Mathematics with Applications · doi:10.1016/s0898-1221(00)00112-7 · Cited by 4 · see citing works
Губернаторов, О. И. (1974) · Radiotekhnika · Cited by 2 · see citing works
Flagged first, then by citations
1 of the 42 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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
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 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
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
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
Wang, S., Mao, X., Wang, F., Zuo, X., & Fan, C. (2023) · Advanced Materials · doi:10.1002/adma.202307499 · Cited by 85 · see citing works
Bioinspired Cell Silicification: From Extracellular to Intracellular
Lei, Q., Guo, J., Kong, F., Cao, J., Wang, L., Zhu, W., & Brinker, C. J. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c00814 · Cited by 83 · 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
DNA-Based Storage: Models and Fundamental Limits
Shomorony, I., & Heckel, R. (2021) · IEEE Transactions on Information Theory · doi:10.1109/tit.2021.3058966 · Cited by 68 · 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
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‐Based Concatenated Encoding System for High‐Reliability and High‐Density Data Storage
Ren, Y., Zhang, Y., Liu, Y., Wu, Q., Su, J., Wang, F., Chen, D., Fan, C., Liu, K., & Zhang, H. (2022) · Small Methods · doi:10.1002/smtd.202101335 · Cited by 55 · see citing works
Information Theory in Computational Biology: Where We Stand Today
Chanda, P., Costa, E., Hu, J. K., Sukumar, S., Hemert, J. V., & Walia, R. R. (2020) · Entropy · doi:10.3390/e22060627 · Cited by 55 · 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
Cooperative sequence clustering and decoding for DNA storage system with fountain codes
Jeong, J., Park, S., Kim, J.-W., No, J., Jeon, H. H., Lee, J. W., No, A., Kim, S., & Park, H. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab246 · Cited by 49 · see citing works
Zheng, L. L., Li, J. Z., Wen, M., Xi, D., Zhu, Y., Wei, Q. L., Zhang, X., Ke, G., Xia, F., & Gao, Z. F. (2023) · Science Advances · doi:10.1126/sciadv.adf5868 · Cited by 50 · see citing works
Houghton, M. C., Kashanian, S. V., Derrien, T. L., Masuda, K., & Vollmer, F. (2024) · ACS Photonics · doi:10.1021/acsphotonics.3c01570 · Cited by 50 · 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
Fei, Z., Gupta, N., Li, M., Xiao, P., & Hu, X. (2023) · Science Advances · doi:10.1126/sciadv.adg9933 · Cited by 47 · see citing works
DNA synthesis for true random number generation
Meiser, L. C., Koch, J., Antkowiak, P. L., Stark, W. J., Heckel, R., & Grass, R. N. (2020) · Nature Communications · doi:10.1038/s41467-020-19757-y · Cited by 45 · 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
Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries
Lietard, J., Léger, A., Erlich, Y., Sadowski, N., Timp, W., & Somoza, M. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab505 · Cited by 44 · see citing works
Phage display technology and its impact in the discovery of novel protein-based drugs
Hutchings, C. J., & Sato, A. K. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2367023 · Cited by 42 · 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
A digital twin for DNA data storage based on comprehensive quantification of errors and biases
Gimpel, A. L., Stark, W. J., Heckel, R., & Grass, R. N. (2023) · Nature Communications · doi:10.1038/s41467-023-41729-1 · Cited by 38 · see citing works
Design of Constraint Coding Sets for Archive DNA Storage
Yin, Q., Zheng, Y., Wang, B., & Zhang, Q. (2021) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2021.3127271 · 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
DNA-Based Molecular Computing, Storage, and Communications
Liu, Q., Yang, K., Xie, J., & Sun, Y. (2021) · IEEE Internet of Things Journal · doi:10.1109/jiot.2021.3083663 · Cited by 36 · see citing works
Xie, R., Zan, X., Chu, L., Su, Y., Xu, P., & Liu, W. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05237-9 · Cited by 32 · 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
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
A robust and efficient DNA storage architecture based on modulation encoding and decoding
Zan, X., Xie, R., Yao, X., Xu, P., & Liu, W. (2022) · doi:10.1101/2022.05.25.490755 · Cited by 27 · 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
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
A Hierarchical Error Correction Strategy for Text DNA Storage
Zan, X., Yao, X., Xu, P., Chen, Z., Xie, L., Li, S., & Liu, W. (2021) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-021-00476-x · Cited by 22 · see citing works
Buko, T., Tuczko, N., & Ishikawa, T. (2023) · BioTech · doi:10.3390/biotech12020044 · Cited by 21 · see citing works
“Meiser et al. (2020) have used a Reed–Solomon code for storing a full album of music in DNA [33].”
MethodAn Effective DNA‐Based File Storage System for Practical Archiving and Retrieval of Medical MRI Data
Rasool, A., Hong, J., Hong, Z., Li, Y., Zou, C., Chen, H., Qu, Q., Wang, Y., Jiang, Q., Huang, X., et al. (2024) · Small Methods · doi:10.1002/smtd.202301585 · Cited by 19 · see citing works
CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage
Zheng, Y., Wu, J., & Wang, B. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.644945 · Cited by 21 · see citing works
A Tutorial on Coding Methods for DNA-Based Molecular Communications and Storage
Xiang, L., Liu, Q., Chen, S., Yan, K., Wu, W., & Yang, K. (2023) · IEEE Internet of Things Journal · doi:10.1109/jiot.2023.3332903 · Cited by 19 · see citing works
Liu, Q., Liu, Q., Zhang, J., Zhang, C., Qian, L., Qi, H., Li, Y., & Song, D. (2025) · Science Advances · doi:10.1126/sciadv.adw2613 · Cited by 18 · see citing works
Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing
Xu, C., Ma, B., Dong, X., Lei, L., Hao, Q., Zhao, C., & Liu, H. (2023) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.3c01860 · Cited by 18 · see citing works
DNA-QLC: an efficient and reliable image encoding scheme for DNA storage
Zheng, Y., Cao, B., Zhang, X., Cui, S., Wang, B., & Zhang, Q. (2024) · BMC Genomics · doi:10.1186/s12864-024-10178-5 · Cited by 17 · see citing works
Batch Optimization for DNA Synthesis
Makarychev, K., Rácz, M. Z., Rashtchian, C., & Yekhanin, S. (2022) · IEEE Transactions on Information Theory · doi:10.1109/tit.2022.3184903 · Cited by 16 · see citing works
Nanopore Deciphering Single Digital Polymers Towards High‐Density Data Storage
Hu, Z., Liu, Y., Xin, K., Yu, R., Zhang, L., & Ying, Y. (2023) · Chemistry - A European Journal · doi:10.1002/chem.202203919 · Cited by 16 · see citing works
Error Probability Bounds for Coded-Index DNA Storage Systems
Weinberger, N. (2022) · IEEE Transactions on Information Theory · doi:10.1109/tit.2022.3176917 · Cited by 15 · see citing works
Gimpel, A. L., Stark, W. J., Heckel, R., & Grass, R. N. (2024) · Digital Discovery · doi:10.1039/d4dd00220b · Cited by 15 · see citing works
Information decay and enzymatic information recovery for DNA data storage
Meiser, L. C., Gimpel, A. L., Deshpande, T., Libort, G., Chen, W. D., Heckel, R., Nguyen, B. H., Strauß, K., Stark, W. J., & Grass, R. N. (2022) · Communications Biology · doi:10.1038/s42003-022-04062-9 · Cited by 12 · see citing works
Engineering DNA Materials for Sustainable Data Storage Using a DNA Movable-Type System
Gong, Z.-Y., Song, L., Pei, G., Dong, Y.-F., Li, B., & Yuan, Y. (2023) · Engineering · doi:10.1016/j.eng.2022.05.023 · Cited by 13 · see citing works
Towards next-generation DNA encryption via an expanded genetic system
Huang, X., Hou, Z., Qiang, W., Wang, H., Wang, X., Chen, X., Hu, X., Dai, J., Li, L., & Zhao, G. (2024) · National Science Review · doi:10.1093/nsr/nwae469 · Cited by 14 · see citing works
Storing Images in DNA via base128 Encoding
Wang, K., Cao, B., Ma, T., Zhao, Y., Zheng, Y., Wang, B., Zhou, S., & Zhang, Q. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01592 · Cited by 12 · see citing works
Robust multi-read reconstruction from noisy clusters using deep neural network for DNA storage
Qin, Y., Zhu, F., Xi, B., & Song, L. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.02.019 · Cited by 13 · see citing works
Encoding of non-biological information for its long-term storage in DNA
Гарафутдинов, Р. Р., Chemeris, D. A., Sakhabutdinova, A. R., Kiryanova, O. Y., Mikhaylenko, C. I., & Chemeris, A. V. (2022) · Biosystems · doi:10.1016/j.biosystems.2022.104664 · Cited by 12 · see citing works
Encoding Information into Polyethylene Glycol Using an Alcohol-Isocyanate “Click” Reaction
Nagy, L., Kuki, Á., Nagy, T., Vadkerti, B., Erdélyi, Z., Kárpáti, L., Zsuga, M., & Kéki, S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21041318 · Cited by 11 · see citing works
VSD: A Novel Method for Video Segmentation and Storage in DNA Using RS Code
Hong, J., Rasool, A., Wang, S., Ziou, D., & Jiang, Q. (2024) · Mathematics · doi:10.3390/math12081235 · Cited by 10 · see citing works
Research progress in high-throughput DNA synthesis and its applications
Liu, C. B., Zhuang, W., Liu, L., Chen, Y., Yang, C., Chen, H., Yao, Y., Sun, X., & Hu, W. W. (2025) · Journal of Materials Chemistry B · doi:10.1039/d5tb00869g · Cited by 10 · see citing works
An image cryptography method by highly error-prone DNA storage channel
Zan, X., Chu, L., Xie, R., Su, Y., Yao, X., Xu, P., & Liu, W. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1173763 · Cited by 10 · see citing works
Content-based filter queries on DNA data storage systems
El-Shaikh, A., & Seeger, B. (2023) · Scientific Reports · doi:10.1038/s41598-023-34160-5 · Cited by 10 · see citing works
DUHI: Dynamically updated hash index clustering method for DNA storage
Wang, P., Cao, B., Ma, T., Wang, B., Zhang, Q., & Zheng, P. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107244 · Cited by 10 · see citing works
Zhang, A., Kondhare, D., Leonard, P., & Seela, F. (2021) · Chemistry - A European Journal · doi:10.1002/chem.202005199 · Cited by 10 · see citing works
Kondhare, D., Leonard, P., & Seela, F. (2021) · The Journal of Organic Chemistry · doi:10.1021/acs.joc.1c01283 · Cited by 10 · see citing works
Zhong, W., Geng, C., Fu, Z., Mao, C., Zheng, Y., Wang, S., Liu, K., Yang, Y., Lü, C., & Jiang, X. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.4c04637 · Cited by 9 · see citing works
A generative adversarial network for multiple reads reconstruction in DNA storage
Zheng, X., Xie, R., Yao, X., Su, Y., Chu, L., Xu, P., & Liu, W. (2024) · Scientific Reports · doi:10.1038/s41598-024-83806-5 · Cited by 9 · see citing works
Stable DNA Storage Encoding Scheme Based on Repeating Substring Tree
Wu, J., Wang, P., Zheng, Y., Wang, B., Zhang, Q., & Zheng, P. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3586008 · Cited by 9 · see citing works
Liu, X., Zheng, Y., Li, X., Wang, B., Zhou, S., Cao, B., & Zheng, P. (2026) · Expert Systems with Applications · doi:10.1016/j.eswa.2026.131726 · Cited by 10 · see citing works
Current and emerging opportunities in biological medium‐based computing and digital data storage
Bennet, D., Vo‐Dinh, T., & Zenhausern, F. (2021) · Nano Select · doi:10.1002/nano.202100275 · Cited by 9 · see citing works
One-time-pad cipher algorithm based on confusion mapping and DNA storage technology
Peng, W., Cui, S., & Song, C. (2021) · PLoS ONE · doi:10.1371/journal.pone.0245506 · Cited by 9 · see citing works
Gel-based electrochemical DNA synthesis for quasi-solid-state data storage
Feng, D., Xu, C., Ma, B., Zhao, C., & Liu, H. (2024) · Chemical Engineering Journal · doi:10.1016/j.cej.2024.150485 · Cited by 9 · see citing works
Exploring DNA Computers: Advances in Storage, Cryptography and Logic Circuits
Xie, X., Wang, S., Chen, Z., Yu, Y., Hu, X., Ma, N., Ji, M., & Tian, Y. (2024) · ChemBioChem · doi:10.1002/cbic.202400670 · Cited by 9 · see citing works
Cao, B., Li, X., Wang, B., He, T., Zheng, Y., Zhang, X., & Zhang, Q. (2025) · Patterns · doi:10.1016/j.patter.2025.101288 · Cited by 9 · see citing works
Weindel, F., Gimpel, A. L., Grass, R. N., & Heckel, R. (2023) · Allerton Conference on Communication, Control, and Computing · doi:10.1109/allerton58177.2023.10313494 · Cited by 10 · see citing works
Zhang, X., & Zhou, F. (2024) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2024.3356522 · Cited by 8 · see citing works
Information Density Enhancement Using Lossy Compression in DNA Data Storage
Seo, S., Tandon, A., Lee, K. W., Lee, J., & Park, S. H. (2024) · Advanced Materials · doi:10.1002/adma.202403071 · Cited by 8 · see citing works
Xu, Y., Ding, L., Wu, S., & Ruan, J. (2024) · Advanced Science · doi:10.1002/advs.202402951 · Cited by 6 · see citing works
On the efficient digital code representation in DNA-based data storage
Cevallos, Y., Tello-Oquendo, L., Inca, D., Samaniego, N., Santillán, I., Shirazi, A. Z., & Gomez, G. A. (2020) · ACM International Conference on Nanoscale Computing and Communication (NANOCOM) · doi:10.1145/3411295.3411314 · Cited by 8 · see citing works
Polymerase Elongation onto Patterned DNA for Random Accessed DNA Data Storage
Kang, T., Lim, D., Lee, W. J., & Song, Y. (2025) · BioChip Journal · doi:10.1007/s13206-025-00214-1 · Cited by 7 · see citing works
Exploring the intersection of natural sciences and information technology via entropy and randomness
Luescher, A. M., Heckel, R., & Grass, R. N. (2025) · Nature Communications · doi:10.1038/s41467-025-62353-1 · Cited by 10 · see citing works
DNA synthesis and assembly: From oligonucleotides to complete genomes
Liu, C., Yang, Y., Zhuang, W., Zhang, L., Wang, G., Hu, J., Yao, Y., Ye, C., & Hu, W. (. (2025) · Chemical Engineering Journal · doi:10.1016/j.cej.2025.168771 · Cited by 6 · see citing works
Li, X., Zheng, Y., Shao, Q., Wang, J., Li, W., Bin, W. A. N. G., Zhou, S., Cao, B., & Zheng, P. (2026) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2026.01.028 · Cited by 7 · see citing works
Combinatorial constraint coding based on the EORS algorithm in DNA storage
Xiaoru, L., & Ling, G. (2021) · PLoS ONE · doi:10.1371/journal.pone.0255376 · Cited by 7 · see citing works
Rapid Information Retrieval from DNA Storage with Microfluidic Very Large‐Scale Integration Platform
Liu, D., & Cheow, L. F. (2023) · Small · doi:10.1002/smll.202309867 · Cited by 7 · see citing works
Robust DNA Image Storage Decoding with Residual CNN
Ruan, C., Yang, L. H., Han, R., Gao, S., Wu, H., & Ling, N. (2024) · IEEE International Symposium on Circuits and Systems proceedings · doi:10.1109/iscas58744.2024.10558127 · Cited by 6 · see citing works
Batch Optimization for DNA Synthesis
Makarychev, K., Rácz, M. Z., Rashtchian, C., & Yekhanin, S. (2021) · IEEE International Symposium on Information Theory (ISIT) · doi:10.1109/isit45174.2021.9517820 · Cited by 5 · see citing works
DBTRG: De Bruijn Trim rotation graph encoding for reliable DNA storage
Zhao, Y., Cao, B., Wang, P., Wang, K., & Wang, B. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.004 · Cited by 6 · see citing works
Liu, Q., Liu, Q., Zhang, J., Li, X., Qi, H., Li, Y., & Song, D. (2025) · Small · doi:10.1002/smll.202501720 · Cited by 5 · see citing works
Tandon, A., Lee, J., Nam, Y., Seo, S., & Park, S. H. (2025) · Chemistry of Materials · doi:10.1021/acs.chemmater.5c00330 · Cited by 5 · see citing works
Weindel, F., Gimpel, A. L., Grass, R. N., & Heckel, R. (2025) · IEEE Transactions on Molecular Biological and Multi-Scale Communications · doi:10.1109/tmbmc.2025.3610330 · Cited by 5 · see citing works
Linked data storage using DNA origami nanostructures
Zhang, C., Xie, M., Wang, L., Fan, C., & Chao, J. (2025) · Nature Communications · doi:10.1038/s41467-025-66274-x · Cited by 8 · see citing works
Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing
Yeom, H., Kim, N., Lee, A. C., Kim, J., Kim, H., Choi, H., Song, S. W., Kwon, S., & Choi, Y. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.3c00308 · Cited by 5 · see citing works
The “biomolecular humanities”? New challenges and perspectives
Oras, E., de Groot, J., & Björkstén, U. (2025) · iScience · doi:10.1016/j.isci.2024.111679 · Cited by 5 · see citing works
ReLume: Enhancing DNA storage data reconstruction with flow network and graph partitioning
Xie, L., Cao, B., Wen, X., Zheng, Y., Wang, B., Zhou, S., & Zheng, P. (2025) · Methods · doi:10.1016/j.ymeth.2025.03.022 · Cited by 5 · see citing works
Constrained Channel Capacity for DNA-Based Data Storage Systems
Fan, K., Wu, H., & Yan, Z. (2022) · IEEE Communications Letters · doi:10.1109/lcomm.2022.3212200 · Cited by 5 · see citing works
Potter, L. N., & Palmer, X. (2023) · Springer eBooks · doi:10.1007/978-3-031-26034-6_4 · Cited by 5 · see citing works
Toward Smart Information Processing with Synthetic DNA Molecules
Chu, J., Zhang, Y., Wang, F., & Liu, H. (2021) · Macromolecular Rapid Communications · doi:10.1002/marc.202100084 · Cited by 5 · see citing works
Exploring potential biosafety implications in DNA information storage
Li, S., Shi, Y. X., Yang, J., Liu, H., Jia, L., & Liu, D. (2025) · Biosafety and Health · doi:10.1016/j.bsheal.2025.03.006 · Cited by 4 · see citing works
A study on improving bounds for batch verification of DNA synthesis using concurrent ZKP
Singh, R., & Selvakumar, R. (2023) · International Journal of Information Technology · doi:10.1007/s41870-023-01169-y · Cited by 4 · see citing works
Correcting deletion errors in DNA data storage with enzymatic synthesis
Tang, Y., & Farnoud, F. (2021) · IEEE Information Theory Workshop (ITW) · doi:10.1109/itw48936.2021.9611403 · Cited by 4 · see citing works
Comparison of state-of-the-art error-correction coding for sequence-based DNA data storage
Gimpel, A. L., Remschak, A., Stark, W. J., Heckel, R., & Grass, R. N. (2026) · Nature Communications · doi:10.1038/s41467-026-70548-3 · Cited by 3 · see citing works
- Authors
- Meiser, L. C., Antkowiak, P. L., Koch, J., Chen, W. D., Kohll, A. X., Stark, W. J., Heckel, R., & Grass, R. N.
- Affiliations
- ETH Zurich (CH)
- Rice University (US)
- Corresponding author
- Heckel, Reinhard
- Grass, Robert N.
- Venue
- Nature Protocols
- Published
- 2019-11-29
- Volume
- 15
- Issue
- 1
- Pages
- 86-101
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2989744057
- Cited by
- 164
- References
- 42
- Citations by year
- 2026: 19 · 2025: 35 · 2024: 29 · 2023: 28 · 2022: 19 · 2021: 25 · 2020: 9
- FWCI
- 4.38
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Protocols (publishedVersion)
- PubMed (publishedVersion)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Physical Sciences › Computer Science › Computer Networks and Communications › Advanced Data Storage Technologies
- Keywords
- DNA data storage, error-correcting codes, DNA synthesis, DNA sequencing
- MeSH terms
- Base Sequence, DNA, Models, Molecular, Nucleic Acid Conformation, Sequence Analysis, DNA
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
