Mixed Culture of Bacterial Cell for Large Scale DNA Storage

Abstract

45DNA emerged as novel material for mass data storage, the serious problem human society is facing. 46 Taking advantage of current synthesis capacity, massive oligo pool demonstrated its high-potential in 47 data storage in test tube. Herein, mixed culture of bacterial cells carrying mass oligo pool that was 48 assembled in a high copy plasmid was presented as a stable material for large scale data storage. Living 49 cells data storage was fabricated by a multiple-steps process, assembly, transformation and mixed culture. 50 The underlying principle was explored by deep bioinformatic analysis. Although homology assembly 51 showed sequence context dependent bias but the massive digital information oligos in mixed culture 52 were constant over multiple successive passaging. In pushing the limitation, over ten thousand distinct 53 oligos, totally 2304 Kbps encoding 445 KB digital data including texts and images, were stored in 54 bacterial cell, the largest archival data storage in living cell reported so far. The mixed culture of living 55 cell data storage opens up a new approach to simply bridge the in vitro and in vivo storage system with 56 combined advantage of both storage capability and economical information propagation. 57 1. Introduction: 58 While being biological material carrying genomic information, DNA has been proven of great potential 59 in storing information in its nucleic acid sequence for long-term in high density. The increased capability 60 of high throughput chip synthesis based writing and next generation sequencing based reading 61 technologies greatly advanced the development of synthesis nucleic acid mediated archival storage. 62Simply put, information was synthesized into DNA oligo molecule and then read out by sequencing. Till 63 now, a number of systems have been developed storing massive archival data into synthetic oligo pool. [1, 64 2] Classical electrical communication and computing algorithms such as Fountain and Reed-Solomon 65 code have been adapted for conversation of digital binary information to four letters nucleic acids 66 sequence and error correction. [3, 4] Restricted by current high throughput oligo synthesis techniques, oligo 67 with from 100 to around 200 nts in length was the major materials for information storage in test tube. 68However, the oligo size well fits with the major commercial sequencing platform, such as Illumina, [5] by 69 which sequence from 50 to 200 nucleotides can be obtained at single read from one oligo terminal end. 70Furthermore, the cost of chip-based synthesis achieved the lowest DNA synthesis, at least one or two 71 orders of magnitude lower than traditional column-based oligo synthesis. Thus far, as medium materials 72 synthesis oligo pool based in vitro system has been largely expanded for up to 200 MB information 73 storage. [6] 74 Besides test tubes, microbe cells are able to carry the synthesis DNA material with many advanced 75 features for archival information storage. In comparing with the cell-free in vitro syste...

Current and emerging opportunities in biological medium‐based computing and digital data storage

“…[49] B-v, Illustration of the mixed culture of the bacterial cell for large-scale data storage. [50] First, binary code was translated into nucleotide using the basic algorithm and then synthesized as a short-oligo pool. The oligo pool was assembled into plasmids and then transform into cells for stable data storage.…”