Next-Generation Digital Information Storage in DNA

Church, George M.; Gao, Yuan; Kosuri, Sriram

doi:10.1126/science.1226355

Cited by 992 publications

(900 citation statements)

References 25 publications

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“…Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro 1–6 . A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time.…”

mentioning

confidence: 99%

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

Shipman

Nivala

Macklis

et al. 2017

Nature

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276

219

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DNA is an excellent medium for data archival. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro1–6. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity7. Harnessed, this system has the potential to write arbitrary information into the genome8. Here, we use the CRISPR-Cas system to encode images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We additionally uncover underlying principles of the CRISPR-Cas adaptation system, including sequence determinants of spacer acquisition relevant for understanding both the basic biology of bacterial adaptation as well as its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.

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mentioning

confidence: 99%

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

Shipman

Nivala

Macklis

et al. 2017

Nature

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276

219

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“…In absence of a new word devised for the circumstance, one should just admit that information can be separated from the idea of intention. For example, information does exist, even in absence of conscious conceivers and translators, in the non-monotonic arrangement of nucleotides in DNA (Avery, 2003;Church et al, 2012), the famous macromolecule selected at least on earth as the vector of heredity (Avery et al, 1944).…”

Section: The Physical Meaning Of Informationmentioning

confidence: 99%

Life is a Self-Organizing Machine Driven by the Informational Cycle of Brillouin

Michel

2013

Orig Life Evol Biosph

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Acquiring information is indisputably energy-consuming and conversely, the availability of information permits greater efficiency. Strangely, the scientific community long remained reluctant to establish a physical equivalence between the abstract notion of information and sensible thermodynamics. However, certain physicists such as Szilard and Brillouin proposed: (i) to give to information the status of a genuine thermodynamic entity (k B T ln2 joules/bit) and (ii) to link the capacity of storing information inferred from correlated systems, to that of indefinitely increasing organization. This positive feedback coupled to the self-templating molecular potential could provide a universal basis for the spontaneous rise of highly organized structures, typified by the emergence of life from a prebiotic chemical soup. Once established, this mechanism ensures the longevity and robustness of life envisioned as a general system, by allowing it to accumulate and optimize microstate-reducing recipes, thereby giving rise to strong nonlinearity, decisional capacity and multistability. Mechanisms possibly involved in priming this cycle are proposed.

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“…With the recent development of archival DNA-based storage devices [4], [5] and rewritable, random-access storage media [6], a new family of reconstruction questions has emerged regarding how to design sequences which can be easily and accurately reconstructed based on their substrings, in the presence of read and write errors. The write process reduces to DNA synthesis, while the read process involves both DNA sequencing and assembly.…”

Section: Introductionmentioning

confidence: 99%

Codes for DNA Sequence Profiles

Kiah

Puleo

Milenković

2016

IEEE Trans. Inform. Theory

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We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings observed through a noisy channel. This problem of reconstructing sequences from traces was first investigated in the noiseless setting under the name of "Markov type" analysis. Here, we explain the connection between the reconstruction problem and the problem of DNA synthesis and sequencing, and introduce the notion of a DNA storage channel. We analyze the number of sequence equivalence classes under the channel mapping and propose new asymmetric coding techniques to combat the effects of synthesis and sequencing noise. In our analysis, we make use of restricted de Bruijn graphs and Ehrhart theory for rational polytopes.

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Next-Generation Digital Information Storage in DNA

Cited by 992 publications

References 25 publications

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

Life is a Self-Organizing Machine Driven by the Informational Cycle of Brillouin

Codes for DNA Sequence Profiles

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