Encoding Information in Synthetic Metabolomes

Kennedy, Eamonn; Arcadia, Christopher E.; Geiser, Joseph D.; Weber, Peter M.; Rose, Christopher; Rubenstein, Brenda M.; Rosenstein, Jacob K.

doi:10.1101/627745

Cited by 8 publications

(16 citation statements)

References 37 publications

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“…In its current form, the well-plate approach is not scalable and does not offer the desired storage densities. Nevertheless, there are several related efforts underway for designing scalable positional data storage systems using MALDI plates 19 or microfluidic devices 20 . These solutions are currently not able to handle large data volumes but are expected to improve significantly in the near future.…”

Section: Resultsmentioning

confidence: 99%

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

et al. 2020

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Synthetic DNA-based data storage systems have received significant attention due to the promise of ultrahigh storage density and long-term stability. However, all known platforms suffer from high cost, read-write latency and error-rates that render them noncompetitive with modern storage devices. One means to avoid the above problems is using readily available native DNA. As the sequence content of native DNA is fixed, one can modify the topology instead to encode information. Here, we introduce DNA punch cards, a macromolecular storage mechanism in which data is written in the form of nicks at predetermined positions on the backbone of native double-stranded DNA. The platform accommodates parallel nicking on orthogonal DNA fragments and enzymatic toehold creation that enables single-bit random-access and in-memory computations. We use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic DNA and accurately reconstruct the encoded data through high-throughput sequencing and read alignment.

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Section: Resultsmentioning

confidence: 99%

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

et al. 2020

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“…A simple summary of the preceding analysis is that a library of M unique molecules can produce a binary mixture representing as few as log 2 M bits and as many as M bits of information (Equation (7)). There are at least 10 5 known biological metabolites [28,52]), and far more synthetically feasible small molecules. Even among small organic molecules, there are potentially more than 10 60 unique compounds [5], and within this vast space, there may be many potential targets for megabyte-and gigabyte-scale small-molecule libraries.…”

Section: Diversified Small-molecule Memorymentioning

confidence: 99%

“…Although few chemistries are as mature as those available for DNA, we show that diversified small-molecule approaches have intrinsic capacities for gigabyte-scale data storage. In addition to new experimental [2,3,28] and theoretical tools for interrogating heterogeneous mixtures of molecules, this new perspective may also contribute to new ways of quantifying the information contained in the chemical states of living systems. Figure 1.…”

Section: Introductionmentioning

confidence: 99%

Principles of Information Storage in Small-Molecule Mixtures

Rosenstein

Rose

Reda

et al. 2020

IEEE Trans.on Nanobioscience

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Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of smaller non-polymeric molecules to preserve, process, and transmit information. In this paper, we present a general framework for quantifying chemical memory, which is not limited to polymers and extends to mixtures of molecules of all types. We show that the theoretical limit for molecular information is two orders of magnitude denser by mass than DNA, although this comes with different practical constraints on total capacity. We experimentally demonstrate kilobyte-scale information storage in mixtures of small synthetic molecules, and we consider some of the new perspectives that will be necessary to harness the information capacity available from the vast non-genomic chemical space.

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“…Multiple strategies were put forward for digital information storage using organic molecules, including oligopeptides 3 and metabolomes 4 . Recently, 'DNA memory' using DNA origami technology was proposed to be a novel strategy to store digital information.…”

Section: Introductionmentioning

confidence: 99%

Towards Practical and Robust DNA-Based Data Archiving Using ‘Yin-Yang Codec’ System

Ping

Chen

Huang

et al. 2019

Preprint

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Motivation: DNA has been reported as a promising medium of data storage for its remarkable durability and space-efficient storage capacity. Here, we propose a robust DNA-based data storage method based on a new codec algorithm, namely 'Yin-Yang'.Results: Using this strategy, we successfully stored different formats of files in one synthetic DNA oligonucleotide pool. Compared to most DNA-based data storage coding schemes presented to date, this codec system can efficiently achieve a variety of user goals (e.g. reduce homopolymer length to 3 or 4 at most, maintain balanced GC content between 40% and 60% and simple secondary structure with the Gibbs free energy above -30 kcal/mol). We tested this codec by an end-to-end experiment including encoding, DNA synthesis, sequencing and decoding. We demonstrate successful retrieval of 2.02 Megabits /3 files using this method. The original information was fully retrieved after sequencing and decoding. Compared to the previously reported methods, our strategy exhibits great potential at achieving high storing capacity per nucleotide (230 PB/gram) and high fidelity of data recovery.

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Encoding Information in Synthetic Metabolomes

Cited by 8 publications

References 37 publications

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Principles of Information Storage in Small-Molecule Mixtures

Towards Practical and Robust DNA-Based Data Archiving Using ‘Yin-Yang Codec’ System

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