Demonstration of End-to-End Automation of DNA Data Storage

Takahashi, Christopher N.; Nguyen, Bichlien H.; Strauß, Karin; Ceze, Luís

doi:10.1038/s41598-019-41228-8

Cited by 91 publications

(56 citation statements)

References 16 publications

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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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Section: Discussionmentioning

confidence: 99%

Low-Bias Amplification for Robust DNA Data Readout

Gao

Chen

Hao

et al. 2020

Preprint

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“…In their work they focused on increasing the throughput of nanopore sequencing by assembling and sequencing together fragments of 24 short DNA strands. Recent studies also presented an end-to-end demonstration of DNA storage [51], the use of LDPC codes for DNAbased storage [10], a computer systems prospective on molecular processing and storage [9], and lastly, the work of Tabatabaei et al [50] which uses existing DNA strands as punch cards to store information.…”

Section: Dna Storage and Dna Errorsmentioning

confidence: 99%

Reconstruction Algorithms for DNA-Storage Systems

Sabary

Yucovich

Shapira

et al. 2020

Preprint

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In the trace reconstruction problem a length-n string x yields a collection of noisy copies, called traces, y1, …, yt where each yi is independently obtained from x by passing through a deletion channel, which deletes every symbol with some fixed probability. The main goal under this paradigm is to determine the required minimum number of i.i.d traces in order to reconstruct x with high probability. The trace reconstruction problem can be extended to the model where each trace is a result of x passing through a deletion-insertion-substitution channel, which introduces also insertions and substitutions. Motivated by the storage channel of DNA, this work is focused on another variation of the trace reconstruction problem, which is referred by the DNA reconstruction problem. A DNA reconstruction algorithm is a mapping which receives t traces y1, …, yt as an input and produces , an estimation of x. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm’s estimation. For the deletion channel case, the problem is referred by the deletion DNA reconstruction problem and the goal is to minimize the Levenshtein distance .In this work, we present several new algorithms for these reconstruction problems. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for the shortest common supersequence and the longest common subsequence problems, in order to decode the original sequence. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data as well as on data from previous DNA experiments and are shown to outperform all previous algorithms.

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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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Demonstration of End-to-End Automation of DNA Data Storage

Cited by 91 publications

References 16 publications

Low-Bias Amplification for Robust DNA Data Readout

Low-Bias Amplification for Robust DNA Data Readout

Reconstruction Algorithms for DNA-Storage Systems

Dynamic DNA-based information storage

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