DNA-Based Storage: Trends and Methods

Yazdi, S. M. Hossein Tabatabaei; Kiah, Han Mao; García-Ruiz, Eva; Ma, Jian; Zhao, Huimin; Milenković, Olgica

doi:10.1109/tmbmc.2016.2537305

Cited by 210 publications

(118 citation statements)

References 81 publications

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“…In this work we presented the concept of composite DNA, which leverages properties of current DNA synthesis and sequencing processes, to potentially attain higher density DNA based storage systems. Composite DNA schemes can be combined with other approaches to increase capacity and fidelity of DNA based storage systems such as orthogonal base pair systems 22 , efficient coding 8,11,25,26 and random access approaches 7,8,12,27,28 . Incorporating composite DNA into future DNA based storage systems will require further investment in several directions.…”

Section: Discussionmentioning

confidence: 99%

Improved DNA based storage capacity and fidelity using composite DNA letters

Anavy

Vaknin

Atar

et al. 2018

Preprint

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DNA, with its remarkable density and long-term stability, is an appealing potential next generation data storage medium, most notably for long-term archiving. Megabyte scale DNA based storage was first reported in 2012. The Shannon information capacity of DNA was recently demonstrated, using fountain codes, to be ~1.57 bit per synthesized position.However, synthesis and sequencing technologies process multiple nominally identical molecules in parallel, leading to significant information redundancies. We introduce composite DNA alphabets, using mixed DNA base types, to leverage this redundancy, enabling higher density. We develop encoding and decoding for composite DNA based storage, including error correction. Using current DNA synthesis technologies, we code 6.4Megabyte data into composite DNA, achieving ~25% increase in capacity as compared to literature. We further demonstrate, on smaller scales, how flexible synthesis leads to 2.7 fold increased capacity per synthesized position. Composite DNA can thus reduce costs for DNA based storage and can also serve in other applications.DNA based data storage systems are particularly appealing due to the high information capacityof DNA compared to current state of the art storage media. Storing digital information on DNA involves encoding the information into a sequence over the DNA alphabet (i.e. "A", "C", "G" and "T"), producing synthetic DNA molecules with the desired sequence, and storing the synthetic

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Section: Discussionmentioning

confidence: 99%

Improved DNA based storage capacity and fidelity using composite DNA letters

Anavy

Vaknin

Atar

et al. 2018

Preprint

View full text Add to dashboard Cite

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“…All existing DNA-based data recording architectures store user content in synthetic DNA oligos (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and retrieve desired information via next-generation (e.g., HiSeq and MiSeq) or nanopore sequencing technologies (6). Although DNA sequencing can be performed routinely and at low cost, de novo synthesis of DNA strands with a predetermined content is a major bottleneck (15); DNA synthesis protocols add one nucleotide per cycle and are inherently slow and prohibitively expensive compared to existing optical and magnetic writing mechanisms.…”

Section: Main Textmentioning

confidence: 99%

DNA Punch Cards: Storing Data on Native DNA Sequences via Nicking

Tabatabaei

Wang

Athreya

et al. 2019

Preprint

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Synthetic DNA-based data storage systems (1-11) have received significant attention due to the promise of ultrahigh storage density. However, all proposed systems suffer from high cost, read-write latency and error-rates that render them impractical. One means to avoid synthesizing DNA is to use readily available native DNA. As native DNA content is fixed, one may adopt an alternative recording strategy that modifies the DNA topology to encode desired information.Here, we report the first macromolecular storage paradigm in which data is written in the form of "nicks (punches)" at predetermined positions on the sugar-phosphate backbone of native dsDNA.The platform accommodates parallel nicking on multiple "orthogonal" genomic DNA fragments, paired nicking and disassociation for creating "toehold" regions that enable single-bit random access and strand displacement. As a proof of concept, we used the multiple-turnover programmable restriction enzyme Pyrococcus furiosus Argonaute (12) to punch files into the PCR

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“…This is due to the side reactions such as depurination and inefficient addition of nucleotides that results in unwanted substitution and indels (insertion/deletion) errors, which greatly affects the overall quality of the synthesized product. Therefore purification steps utilizing polyacrylamide gel electrophoresis and high performance liquid chromatography are essential to remove erroneous sequences upon generating the intended DNA sequences [109].…”

Section: De Novo Synthesis Of Antibody Genesmentioning

confidence: 99%

“…However, this approach promotes higher error rates due to the lack of error elimination during hybridization [112]. Also, target diversity can be introduced at the regions where the overlapping oligo fragments hybridizes [109].…”

Section: De Novo Synthesis Of Antibody Genesmentioning

confidence: 99%