R&D: Random Access DNA Memory Using Boolean Search in Archival File Storage

Nature Materials has published an article written by James L. Banal, Tyson R. Shepherd, Joseph Berleant, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Hellen Huang, Miguel Reyes, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, and Broad Institute of MIT and Harvard, Cambridge, MA, USA, Cheri M. Ackerman, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Paul C. Blainey, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, and Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA, Mark Bathe, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, and Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Abstract: “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.“