DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets.
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Software for sequence encoding and decoding is publicly available on GitHub (https://github.com/lcbb/DNA-Memory-Blocks/).
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We gratefully acknowledge discussions with C. Leiserson and T. B. Schardl on the scalability and generalizability of our barcoding approach. We thank G. Paradis, M. Jennings and M. Griffin of the Flow Cytometry Core at the Koch Institute at the Massachusetts Institute of Technology (MIT) and P. Rogers of the Flow Cytometry Facility at the Broad Institute of Harvard and MIT for assistance and discussions in developing the flow cytometry workflow. We also thank D. Mankus of the Nanotechnology Materials Core Facility at the Koch Institute at MIT for assistance in the imaging of the particles using the scanning electron microscope and A. Leshinsky of the Biopolymer and Proteomics Core at the Koch Institute at MIT for assistance in mass spectrometry characterization. M.B., J.L.B., T.R.S. and J.B. gratefully acknowledge funding from the Office of Naval Research (N00014-17-1-2609, N00014-16-1-2506, N00014-12-1-0621 and N00014-18-1-2290) and the National Science Foundation (CCF-1564025, CCF-1956054, HDR OAC-1940231 and CBET-1729397). Research was sponsored by the US Army Research Office and accomplished under cooperative agreement W911NF-19-2-0026 for the Institute for Collaborative Biotechnologies. Additional funding to J.B. was provided through a National Science Foundation Graduate Research Fellowship (grant no. 1122374). P.C.B. was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. C.M.A. was supported by National Institutes of Health grant F32CA236425.
The Massachusetts Institute of Technology has filed patents covering the encapsulation-based file system (US application number 16/097594) and microfluidics-based storage, access and retrieval of biopolymers using the same file system (US application number 16/012583) on behalf of the inventors (J.L.B., T.R.S., J.B. and M.B.) M.B. is the founder of Cache DNA and is a member of its Scientific Advisory Board. P.C.B. is a member of the Scientific Advisory Board of Cache DNA. H.H., M.R. and C.M.A. declare no competing interests.
Peer review information Nature Materials thanks Reinhard Heckel, William L. Hughes and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Banal, J.L., Shepherd, T.R., Berleant, J. et al. Random access DNA memory using Boolean search in an archival file storage system. Nat. Mater. (2021). https://doi.org/10.1038/s41563-021-01021-3