Robust direct digital-to-biological data storage in living cells.
Ontology highlight
ABSTRACT:
SUBMITTER: Yim SS
PROVIDER: S-EPMC7904632 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundEncoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and reading the data (biases and systematic error arising from synthesis and sequencing), and overall scalability.ResultsTo this end, we have developed and implemented an encoding scheme that is suitable for detecting and correcting errors that may arise during storage, writing, and reading, such as those arising from nucleotide substitutions, insertions, and deletions. We propose a scheme for parallelized long term storage of encoded sequences that relies on overlaps rather than the address blocks found in previously published work. Using computer simulations, we illustrate the encoding, sequencing, decoding, and recovery of encoded information, ultimately demonstrating the possibility of a successful round-trip read/write. These demonstrations show that in theory a precise control over error tolerance is possible. Even after simulated degradation of DNA, recovery of original data is possible owing to the error correction capabilities built into the encoding strategy. A secondary advantage of our method is that the statistical characteristics (such as repetitiveness and GC-composition) of encoded sequences can also be tailored without sacrificing the overall ability to store large amounts of data. Finally, the combination of the overlap-based partitioning of data with the LZMA compression that is integral to encoding means that the entire sequence must be present for successful decoding. This feature enables inordinately strong encryptions. As a potential application, an encrypted pathogen genome could be distributed and carried by cells without danger of being expressed, and could not even be read out in the absence of the entire DNA consortium.ConclusionsWe have developed a method for DNA encoding, using a significantly different fundamental approach from existing work, which often performs better than alternatives and allows for a great deal of freedom and flexibility of application.
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Project description:While the archival digital memory industry approaches its physical limits, the demand is significantly increasing, therefore alternatives emerge. Recent efforts have demonstrated DNA's enormous potential as a digital storage medium with superior information durability, capacity, and energy consumption. However, the majority of the proposed systems require on-demand de-novo DNA synthesis techniques that produce a large amount of toxic waste and therefore are not industrially scalable and environmentally friendly. Inspired by the architecture of semiconductor memory devices and recent developments in gene editing, we created a molecular digital data storage system called "DNA Mutational Overwriting Storage" (DMOS) that stores information by leveraging combinatorial, addressable, orthogonal, and independent in vitro CRISPR base-editing reactions to write data on a blank pool of greenly synthesized DNA tapes. As a proof of concept, this work illustrates writing and accurately reading of both a bitmap representation of our school's logo and the title of this study on the DNA tapes.
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Project description:Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 550 K, the computed growth velocities are much higher than those obtained from time-resolved reflectivity measurements, due to large deviations in the diffusion coefficients. As a consequence of the high fragility of AIST, experimental diffusivities display a dramatic increase in activation energies and prefactors at temperatures below 550 K. This property is essential to ensure fast crystallization at high temperature and a stable amorphous state at low temperature. On the other hand, no such change in the temperature dependence of the diffusivity is observed in our simulations, down to 450 K. We also attribute this different behavior to the fragility of the system, in combination with the very fast quenching times employed in the simulations.
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