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Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Nature volume 494, pages 77–80 (2013)Cite this article

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Abstract

Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage1 because of its capacity for high-density information encoding, longevity under easily achieved conditions2,3,4 and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information5,6,7 or were not amenable to scaling-up8, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival9. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information10 of 5.2 × 106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.

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Figure 1: Digital information encoding in DNA.
Figure 2: Scaling properties and robustness of DNA-based storage.

Accession codes

Primary accessions

Sequence Read Archive

Data deposits

Data are available at http://www.ebi.ac.uk/goldman-srv/DNA-storage and in the Sequence Read Archive (SRA) with accession number ERP002040.

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Acknowledgements

At the University of Cambridge: D. MacKay and G. Mitchison for advice on codes for run-length-limited channels. At CERN: B. Jones for discussions on data archival. At EBI: A. Löytynoja for custom multiple sequence alignment software, H. Marsden for computing base calls and for detecting an error in the original parity-check encoding, T. Massingham for computing base calls and advice on code theory and K. Gori, D. Henk, R. Loos, S. Parks and R. Schwarz for assistance with revisions to the manuscript. In the Genomics Core Facility at EMBL Heidelberg: V. Benes for advice on Next-Generation Sequencing protocols, D. Pavlinić for sequencing and J. Blake for data handling. C.D. is supported by a fellowship from the Swiss National Science Foundation (grant 136461). B.S. is supported by an EMBL Interdisciplinary Postdoctoral Fellowship under Marie Curie Actions (COFUND).

Author information

Authors and Affiliations

  1. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK ,

    Nick Goldman, Paul Bertone, Christophe Dessimoz, Botond Sipos & Ewan Birney

  2. Agilent Technologies, Genomics–LSSU, 5301 Stevens Creek Boulevard, Santa Clara, California 95051, USA ,

    Siyuan Chen & Emily M. LeProust

Authors
  1. Nick Goldman
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  2. Paul Bertone
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  3. Siyuan Chen
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  4. Christophe Dessimoz
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  5. Emily M. LeProust
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  6. Botond Sipos
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Contributions

N.G. and E.B. conceived and planned the project and devised the information-encoding methods. P.B. advised on oligo design and Next-Generation Sequencing protocols, prepared the DNA library and managed the sequencing process. S.C. and E.M.L. provided custom oligonucleotides. N.G. wrote the software for encoding and decoding information into/from DNA and analysed the data. N.G., E.B., C.D. and B.S. modelled the scaling properties of DNA storage. N.G. wrote the paper with discussions and contributions from all other authors. N.G. and C.D. produced the figures.

Corresponding author

Correspondence to Nick Goldman.

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Competing interests

S.C. and E.M.L. are employees of Agilent Technologies, a commercial provider of OLS pools. N.G. and E.B. are named inventors on a patent application on technologies described in this work.

Supplementary information

Supplementary Information 1

This file contains Supplementary Tables 1-4, Supplementary Figures 1-9, Supplementary Methods and Data, a Supplementary Discussion and Supplementary references. This file was replaced on 14 February 2013 to correct the DNA sequence in Supplementary Figure 8, which was misaligned. (PDF 2027 kb)

Supplementary Information 2

This file contains the full formal specification of the digital information encoding scheme. (PDF 244 kb)

Supplementary Information 3

This file contains FastQC QC report on Illumina HiSeq 2000 sequencing run. (PDF 411 kb)

Supplementary Data 1

This zipped file contains the five original files encoded and decoded in this study, namely wssnt10.txt (ASCII text file containing text of all 154 Shakespeare sonnets), watsoncrick.pdf (PDF of Watson & Crick’s (1953) paper describing the structure of DNA), MLK_excerpt_VBR_45-85.mp3 (MP3 file containing a 26 s excerpt from Martin Luther King's 1963 "I Have A Dream" speech), EBI.jp2 (JPEG 2000 format medium resolution colour photograph of the European Bioinformatics Institute) and View_huff3.cd.new (ASCII text file defining the Huffman code used to convert bytes of encoded files to base 3). (ZIP 646 kb)

Supplementary Data 2

This file contains the GATK ErrorRatePerCycle report on Illumina HiSeq 2000 sequencing run. (TXT 6 kb)

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Goldman, N., Bertone, P., Chen, S. et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013). https://doi.org/10.1038/nature11875

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