Random access DNA memory using Boolean search in an archival file storage system

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 10 6 files, which thereby enables 1 in 10 6N 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.

Electrically Controlled Nanofluidic DNA Sluice for Data Storage Applications

“…One of the most promising avenues in the quest of ultradense storage systems is macromolecular data storage, in which DNA molecules stand out as primary candidates for massive storage media because of well-developed accompanying DNA “writing” (DNA synthesis) − and “reading” technologies (high-throughput DNA sequencing). − Furthermore, DNA and its derivatives are the only known macromolecules that enable random access , to select parts of the information content and large-scale amplification via polymerase chain reactions (PCRs) . DNA has also shown to lend itself to portable storage architectures with controllable data access, rewriting, and management, all in the presence of a large number of insertion–deletion errors inherent to inexpensive nanopore sequencers. , Recently, most research works have been geared toward DNA-based storage systems ,,,,− with very little attention to addressing the most prominent challenges encountered in all practical implementations of DNA-based data storage systems, i.e., the excessively high cost and delay of DNA synthesis and the incompatibility of DNA media with the existing silicon computing architectures that support data access, retrieval, and computing.…”

Algebraic Rules for the Percentage Composition of Oligomers in Genomes

“…One should also note about perspectives of using of DNA as an ultrahighdensity storage medium that could meet exponentially growing worldwide demand for archival data storage [Banal et al, 2021;Chandak et al, 2019]. Our results about algebraic features of DNA informatics can help in solving some engineering problems in this technological challenge.…”

Design considerations for advancing data storage with synthetic DNA for long-term archiving

“…To retrieve the data, different approaches based on DNA extraction or selective PCR amplification of the required synthetic DNA sample using a specific primer are often used during the retrieval process [ 24 ]. Other random access approaches based on microarray [ 37 ], immobilization of DNA molecules [ 38 ], digital microfluidic droplets [ 39 ], and DNA barcoded silica beads [ 40 ] have been explored to improve and enable random access.…”