Driving the scalability of DNA-based information storage systems

Tomek, Kyle J.; Volkel, Kevin; Simpson, Alex; Hass, Austin G.; Indermaur, Elaine W.; Tuck, James; Keung, Albert J.

doi:10.1101/591594

Cited by 8 publications

(8 citation statements)

References 15 publications

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“…al reported an emulsion-PCR based random-access technique 12 , which can also be used for sub-file level random access if reasonable partition rules and primers are designed.…”

Section: Discussionmentioning

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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“…al reported an emulsion-PCR based random-access technique 12 , which can also be used for sub-file level random access if reasonable partition rules and primers are designed.…”

Section: Discussionmentioning

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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“…We envisioned that toeholds could be multipurpose structures serving as file addresses as well as molecular 'handles' for file operations. As future DNA databases would be comprised of upwards of 10 15 distinct strands 21 , we first asked if toeholds could be created in a high throughput and parallelized manner. We began with 160 bp ssDNA strands with a common 23 bp sequence inset 20 bp from the 3' end ( Figure 1C, Table S1, Figure 2A).…”

Section: Toehold Structures Can Be Efficiently Created In 'One-pot' Rmentioning

confidence: 99%

“…The creation of toehold strands is simple and high throughput, it is compatible with existing file system architectures including hierarchical addresses 11,21 , and it facilitates scaling of capacity. While the need to include the T7 promoter in every strand does occupy valuable data payload space, it is a worthwhile tradeoff; while the T7 promoter decreases data density and capacity in a linear fashion, it improves both metrics exponentially by allowing many sequences to appear in the data payload that normally would have to be avoided in PCR-based systems (or conversely by allowing the full set of mutually 'good', non-conflicting primers to be used) 11,21 . Future work may assess how DORIS and other physical innovations may alter and reduce the stringency of encoding and error correction algorithms and subsequently benefit system density and capacity.…”

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

confidence: 99%

Dynamic DNA-based information storage

Lin

Tuck

Keung

2019

Preprint

Self Cite

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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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“…Recent works have examined various aspects of DNA storage, including error correction [1,5,10,11,12], random access [4,5,13], novel synthesis techniques [14,15] and analysis of the fundamental limits [16,17,18]. While initial works used Illumina sequencing which provides highly accurate short reads, there is growing interest in the use of nanopore sequencing [19] because it is a portable, real-time and low-cost platform that also supports long reads.…”

Section: Introductionmentioning

confidence: 99%

Overcoming High Nanopore Basecaller Error Rates for DNA Storage Via Basecaller-Decoder Integration and Convolutional Codes

Chandak

Neu

Tatwawadi

et al. 2019

Preprint

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As magnetization and semiconductor based storage technologies approach their limits, bio-molecules, such as DNA, have been identified as promising media for future storage systems, due to their high storage density (petabytes/gram) and long-term durability (thousands of years). Furthermore, nanopore DNA sequencing enables high-throughput sequencing using devices as small as a USB thumb drive and thus is ideally suited for DNA storage applications. Due to the high insertion/deletion error rates associated with basecalled nanopore reads, current approaches rely heavily on consensus among multiple reads and thus incur very high reading costs. We propose a novel approach which overcomes the high error rates in basecalled sequences by integrating a Viterbi error correction decoder with the basecaller, enabling the decoder to exploit the soft information available in the deep learning based basecaller pipeline. Using convolutional codes for error correction, we experimentally observed 3x lower reading costs than the state-of-the-art techniques at comparable writing costs.The code, data and Supplementary Material is available at https://github.com/shubhamchandak94/nanopore_ dna_storage.

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Driving the scalability of DNA-based information storage systems

Cited by 8 publications

References 15 publications

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

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

Dynamic DNA-based information storage

Overcoming High Nanopore Basecaller Error Rates for DNA Storage Via Basecaller-Decoder Integration and Convolutional Codes

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