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Random access DNA memory in a scalable, archival file storage system

View ORCID ProfileJames L. Banal, View ORCID ProfileTyson R. Shepherd, View ORCID ProfileJoseph Berleant, Hellen Huang, View ORCID ProfileMiguel Reyes, Cheri M. Ackerman, View ORCID ProfilePaul C. Blainey, View ORCID ProfileMark Bathe
doi: https://doi.org/10.1101/2020.02.05.936369
James L. Banal
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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Tyson R. Shepherd
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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Joseph Berleant
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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Hellen Huang
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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Miguel Reyes
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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Cheri M. Ackerman
2Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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Paul C. Blainey
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142 USA
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Mark Bathe
1Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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  • For correspondence: mark.bathe@mit.edu
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ABSTRACT

DNA is an ultra-high-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. To overcome the second barrier, here we encapsulate data-encoding DNA file sequences within impervious silica capsules that are surface-labeled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling efficient and direct selection of sets of files with Boolean logic. We demonstrate random access of image files from an image database using fluorescence sorting with selection sensitivity of 1 in 106 files, which thereby enables 1 in 106N per N optical channels. Our strategy thereby offers retrieval of random file subsets from exabyte and larger-scale long-term DNA file storage databases, offering a scalable solution for random-access of archival files in massive molecular datasets.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Funding section section was updated to include additional grants that supported the work.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 22, 2021.
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Random access DNA memory in a scalable, archival file storage system
James L. Banal, Tyson R. Shepherd, Joseph Berleant, Hellen Huang, Miguel Reyes, Cheri M. Ackerman, Paul C. Blainey, Mark Bathe
bioRxiv 2020.02.05.936369; doi: https://doi.org/10.1101/2020.02.05.936369
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Random access DNA memory in a scalable, archival file storage system
James L. Banal, Tyson R. Shepherd, Joseph Berleant, Hellen Huang, Miguel Reyes, Cheri M. Ackerman, Paul C. Blainey, Mark Bathe
bioRxiv 2020.02.05.936369; doi: https://doi.org/10.1101/2020.02.05.936369

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