High density DNA data storage library via dehydration with digital microfluidic retrieval

Newman, Sharon; Stephenson, Ashley; Willsey, Max; Nguyen, Bichlien H.; Takahashi, Christopher N.; Strauß, Karin; Ceze, Luís

doi:10.1038/s41467-019-09517-y

Cited by 102 publications

(85 citation statements)

References 18 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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“…Additionally, practical DNA storage system must move out of biochemical test tube to build device by highly integrating all related biochemical processes. Prototypes of DNA storage hardware have already been proposed with high density DNA material in microfluidic device( 29, 30 ). We contend that besides some crucial features of iDR make it more fit for hardware construction.…”

Section: Discussionmentioning

confidence: 99%

Low-Bias Amplification for Robust DNA Data Readout

Gao

Chen

Hao

et al. 2020

Preprint

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11In DNA data storage, the huge sequence complexity is challenging repeatable and efficient 12 information reading. Here, we demonstrated that biased amplification is serious matter for stable 13 information retrieve from synthetic oligo pool comprising over ten thousand strands encoding over 14 2.85 MB digital information. Therefore, we adapted isothermal DNA amplification as a new 15 biochemical framework, termed as isothermal DNA reading (iDR) for low biased manipulation of 16 DNA pool with huge sequence complexity. iDR was built to work in a priming-free and error-17 spreading proof manner and achieved low-biased amplification. Finally, we demonstrated that 18 immobilized DNA materials read by iDR is able to stably read data deeply and repeatedly, the first 19 reported sustainable DNA storage system. Necessary amount of sequencing reads for perfect 20 2 oligos retrieve significantly decreased. These advanced features enable the iDR chemical 21 framework being ideal alternative for manipulating the huge sequence complexity and building 22 the sustainable and efficient DNA storage "hardware". 23 24 3 Introduction: 25 In DNA data storage, technology originally developed for bioengineering approach including array 26 oligo synthesis, PCR and DNA sequencing were integrated to construct the "hardware" for DNA 27 storage 1-5 . Array synthesized DNA oligo pool comprising of from thousands up to millions of oligo 28 strands with several hundred bases in length has been utilized in many applications, e.g., probe 29 blend, DNA origami assembly, and genome synthesis 1 . Because of both the location on microchip 30 and DNA sequence context, the copy number for each oligo strand from array synthesis is distinct 5 . 31Furthermore, the sheer number of synthesized oligos from array on microchip is very small, 32 roughly from 10 5 to 10 12 at the concentration of femtomolar depending on the synthesis platform 6, 33 7 . Generally, amount of DNA materials, over a few hundred nanograms, at the concentration of 34 micromolar is necessary for high quality DNA sequencing covering all oligos in the pool on 35 commercial DNA sequencing platform, e.g., Illumina 8 . Therefore, amplification is crucial to boost 36 the signal for the subsequent DNA sequencing for stably reading data. 37The oligo pool size for DNA data storage is much larger at least several orders of magnitude than 38 that in other bioengineering applications 9-11 . The unevenness of copy number generated a huge 39 complexity that caused serious problem for DNA molecule retrieval and data decoding 4, 5, 12, 13 . 40 Thus far, in reported systems the information reading was achieved by PCR amplification and 41 NGS, but the copy number unevenness originally stemmed from microchip synthesis was further 42 skewed by highly biased amplification process 5, 12 . Therefore, more amplified DNA materials was 43 necessary to fetch the minor oligo strands from the skewed oligo pool. The length and sequence 44 context, GC content and secondary structure of DNA molecule are well...

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“…Beyond the specific capabilities enabled by DORIS, one of the greatest benefits we envision DORIS providing is compatibility with future miniaturized and automated devices 31,32 . In particular, DORIS can operate with no temperature cycling and functions at or close to room temperature for all steps.…”

Section: Doris Represents a Proof Of Principle Framework For How Inclmentioning

confidence: 99%

Dynamic DNA-based information storage

Lin

Tuck

Keung

2019

Preprint

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Technological leaps are often driven by key innovations that transform the underlying architectures of systems. Current DNA storage systems largely rely on polymerase chain reaction, which broadly informs how information is encoded, databases are organized, and files are accessed. Here we show that a hybrid 'toehold' DNA structure can unlock a fundamentally different, dynamic DNA-based information storage system architecture with broad advantages.This innovation increases theoretical storage densities and capacities by eliminating non-specific DNA-DNA interactions common in PCR and increasing the encodable sequence space. It also provides a physical handle with which to implement a range of in-storage file operations. Finally, it reads files non-destructively by harnessing the natural role of transcription in accessing information from DNA. This simple but powerful toehold structure lays the foundation for an information storage architecture with versatile capabilities.

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High density DNA data storage library via dehydration with digital microfluidic retrieval

Cited by 102 publications

References 18 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

Low-Bias Amplification for Robust DNA Data Readout

Dynamic DNA-based information storage

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