Molecular digital data storage using DNA

Ceze, Luís; Nivala, Jeff; Strauß, Karin

doi:10.1038/s41576-019-0125-3

Cited by 411 publications

(415 citation statements)

References 61 publications

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“…In the era of Big Data, molecular DNA has become an increasingly attractive medium for the storage and archiving of digital data [1][2][3][4][5][6] . This is primarily attributed to its ultra-high storage density, which is currently estimated to be in the hundreds of petabytes per gram DNA 7 .…”

Section: Spontaneous Quenching Of Reactions By the Diffusion Of Excesmentioning

confidence: 99%

“…Many time-consuming steps of expensive and harsh reactions with the accumulation of toxic by-products greatly limit chemical synthesis as the demand for longer and larger quantities of DNA oligonucleotides increases 11 . 3 Recently, the use of terminal deoxynucleotidyl transferase (TdT), a template-independent polymerase, to synthesize DNA oligonucleotides was shown to be a promising alternative to chemical synthesis [12][13][14] . Because synthesis reactions are performed under aqueous conditions, many limiting aspects of the phosphoramidite chemistry can be circumvented or improved upon.…”

Section: Spontaneous Quenching Of Reactions By the Diffusion Of Excesmentioning

confidence: 99%

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Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

Lee

Wiegand

Griswold

et al. 2020

Preprint

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New storage technologies are needed to keep up with the global demands of data generation. DNA is an ideal storage medium due to its stability, information density and ease of readout with advanced sequencing techniques. However, progress in writing DNA is stifled by the continued reliance on chemical synthesis methods. The enzymatic synthesis of DNA is a promising alternative, but thus far has not been well demonstrated in a highly parallelized manner. Here, we report a novel multiplexed enzymatic DNA synthesis method using maskless photolithography. Rapid uncaging of Co 2+ ions by patterned UV light activates Terminal deoxynucleotidyl Transferase (TdT) for spatially-selective synthesis on an array surface. Spontaneous quenching of reactions by the diffusion of excess caging molecules confines synthesisto light patterns and controls the extension length. We show that our multiplexed synthesis method can be used to store digital data by encoding 12 unique DNA oligonucleotide sequences with music from the 1985 Nintendo video game Super Mario Brothers TM , which is equivalent to 84 trits or 110 bits of data.In the era of Big Data, molecular DNA has become an increasingly attractive medium for the storage and archiving of digital data 1-6 . This is primarily attributed to its ultra-high storage density, which is currently estimated to be in the hundreds of petabytes per gram DNA 7 . The attractiveness of DNA as a data storage medium is additionally bolstered by its durability, longevity and energy efficiency compared to counterpart storage mediums; both analog and digital 8,9 . However, for storing a meaningful volume of digital data, the synthesis of many unique DNA sequences at long lengths is required. While advances in array-based Oligonucleotide Library Synthesis (OLS) technology have enabled highly multiplexed DNA oligonucleotide synthesis, production in this format still relies on decades old phosphoramidite chemical synthesis methods 10 . Many time-consuming steps of expensive and harsh reactions with the accumulation of toxic by-products greatly limit chemical synthesis as the demand for longer and larger quantities of DNA oligonucleotides increases 11 . 3 Recently, the use of terminal deoxynucleotidyl transferase (TdT), a template-independent polymerase, to synthesize DNA oligonucleotides was shown to be a promising alternative to chemical synthesis [12][13][14] . Because synthesis reactions are performed under aqueous conditions, many limiting aspects of the phosphoramidite chemistry can be circumvented or improved upon. This would be ideal for digital data storage in DNA; however, due to the natural promiscuity of TdT, controlling the enzyme in a sequencespecific manner is challenging [15][16][17] . In order to overcome this challenge, a recent study showed controlled TdT extension activity with apyrase by degrading free nucleotides needed for synthesis 14 .Incubation with optimized ratios of apyrase, TdT and nucleotide over multiple cycles resulted in the successful synthesis of several DNA oligonucleot...

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Section: Spontaneous Quenching Of Reactions By the Diffusion Of Excesmentioning

confidence: 99%

Section: Spontaneous Quenching Of Reactions By the Diffusion Of Excesmentioning

confidence: 99%

Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

Lee

Wiegand

Griswold

et al. 2020

Preprint

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“…Most efforts to use DNA as a data storage medium have involved inserting data either into "naked," molecular DNA or into DNA contained in laboratory strains of E. coli. Between 1999 and 2012, all attempts at recording digital information into DNA were recorded in vivo (27).…”

Section: -D Encoded Dnamentioning

confidence: 99%

In vivomulti-dimensional information-keeping inHalobacterium salinarum

Davis

Bisson‐Filho

Kadyrov

et al. 2020

Preprint

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Shortage of raw materials needed to manufacture components for silicon-based digital memory storage has led to a search for alternatives, including systems for storing texts, images, movies and other forms of information in DNA. Use of DNA as a medium for storage of 3-D information has also been investigated. However, two problems have yet to be addressed: first, storage of 3-D information in DNA has used objects and coding schemes which require large volumes of data; second, the medium used for DNA information-keeping has been inconsistent with qualities needed for long-term data storage. Here, we address these problems. First, we created in vivo DNA-encoded digital archives holding precise specifications for 3-and 4-dimensional figures with unprecedented efficiency. Second, we have demonstrated more robust and longer-lasting information-carriers than earlier repositories for DNA-based data archives by inserting digital information into the halophile, Halobacterium salinarum, an extremophilic archaeon. We then embedded Information-keeping halophiles into crystalline mineral salts in which similar organisms have been shown to persist in stasis for hundreds of millions of years. We propose that digital information archives composed in 3 or more dimensions may be inserted into halophilic organisms and preserved intact for indefinite periods of time.

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“…DNA-based information storage continues to gain momentum with the emergence of highthroughput DNA sequencing (sequencing-by-synthesis) and synthesis (array-based synthesis); these technologies enable vast amounts of text and visual (1)(2)(3) information to be encoded, stored, and decoded. DNA data storage offers unique advantages over mainstream storage methods like magnetic tape and hard disk drives, including higher physical density and longer retention lifetimes (4). This is particularly useful for archival storage, where current access speeds and read/write costs are not an issue.…”

Section: Introductionmentioning

confidence: 99%

Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands

Doroschak

Zhang

Queen

et al. 2020

Preprint

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Molecular tagging is an approach to labeling physical objects using DNA or other molecules that can be used in cases where methods like RFID tags and QR codes are not suitable. No molecular tagging method exists that is inexpensive, fast and reliable to decode, and usable outside a lab setting to create or read tags. To address this, we present Porcupine, an end-user molecular tagging system that features DNA-based tags readable within seconds using a portable nanopore device. Porcupine's digital bits are represented by the presence or absence of distinct, nanopore-orthogonal DNA strands, which we call molecular bits (molbits). We classify molbits directly from the raw nanopore signal, avoiding basecalling. To extend the tag's shelf life, decrease readout time, and make tags robust to environmental contamination, molbits are prepared for readout during tag assembly and can be stabilized by dehydration. The result is an extensible, real time, high accuracy tagging system that includes a novel approach to developing nanopore-orthogonal barcodes. One sentence summaryPorcupine lets end-users label physical objects with custom DNA tags, without requiring a lab to create or read tags, and offers rapid readout using nanopore sequencing.

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Molecular digital data storage using DNA

Cited by 411 publications

References 61 publications

Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

Photon-directed Multiplexed Enzymatic DNA Synthesis for Molecular Digital Data Storage

In vivomulti-dimensional information-keeping inHalobacterium salinarum

Porcupine: Rapid and robust tagging of physical objects using nanopore-orthogonal DNA strands

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