Robust direct digital-to-biological data storage in living cells

Yim, Sung Sun; McBee, Ross M.; Song, Alan M.; Huang, Yiming; Sheth, Ravi U.; Wang, Harris H.

doi:10.1038/s41589-020-00711-4

Cited by 65 publications

(56 citation statements)

References 56 publications

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“…Chen et al (2021) encoded the information in a synthetic yeast artificial chromosome with four autonomously replicating sequences and maintained good stability during yeast replication. Yim et al (2021) used electrical signals to regulate redox reactions in cells, thus causing changes in plasmid copy number, and then used it to control the trapping frequency of different sequences by Cas proteins and to achieve one-step storage of data in cells. Hao et al (2020) assembled a large oligo pool into vector plasmids based on homology and introduced them into bacterial cells for mixed culture, then combining the advantages of in vivo cell systems and in vitro data storage mediated by oligo pools to achieve high-fidelity replication of DNA molecules at low cost.…”

Section: Recent Progress Of Data Storage In Dnamentioning

confidence: 99%

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Song

Deng²,

Gong³

et al. 2021

Front. Bioeng. Biotechnol.

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Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications. Among them, de novo genome synthesis and DNA data storage are striking. However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements, which is a challenge to be met by the phosphoramidite chemistry. Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge. In this review, we first summarize the status of large-scale oligonucleotide synthesis technologies including the basic methodology and large-scale synthesis approaches, with special focus on the emerging enzymatic methods. Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.

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Section: Recent Progress Of Data Storage In Dnamentioning

confidence: 99%

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Song

Deng²,

Gong³

et al. 2021

Front. Bioeng. Biotechnol.

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“…Molecular recording strategies write information into DNA by altering existing DNA sequences (5) or adding new sequences (6). For example, systems have been developed that use methods including differential CRISPR spacer acquisition (5,7,8), enzymatic synthesis (9)(10)(11) and others (1,8,12). By connecting these DNA modifications to a user input (in the case of data storage) or environmental signal of interest (in the case of recording events), these strategies enable post hoc recovery of signal dynamics over time by DNA sequencing.…”

Section: Introductionmentioning

confidence: 99%

Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

Bhan

Castinado

Glaser

et al. 2021

Preprint

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Employing DNA as a high-density data storage medium has paved the way for next-generation digital storage and biosensing technologies. However, the multipart architecture of current DNA-based recording techniques renders them inherently slow and incapable of recording fluctuating signals with sub-hour frequencies. To address this limitation, we developed a simplified system employing a single enzyme, terminal deoxynucleotidyl transferase (TdT), to transduce environmental signals into DNA. TdT adds nucleotides to the 3 prime ends of single-stranded DNA (ssDNA) in a template-independent manner, selecting bases according to inherent preferences and environmental conditions. By characterizing TdT nucleotide selectivity under different conditions, we show that TdT can encode various physiologically relevant signals like Co2+, Ca2+, Zn2+ concentrations and temperature changes in vitro. Further, by considering the average rate of nucleotide incorporation, we show that the resulting ssDNA functions as a molecular ticker tape. With this method we accurately encode a temporal record of fluctuations in Co2+ concentration to within 1 minute over a 60-minute period. Finally, we engineer TdT to allosterically turn off in the presence of physiologically relevant concentration of calcium. We use this engineered TdT in concert with a reference TdT to develop a two-polymerase system capable of recording a single step change in Ca2+ signal to within 1 minute over a 60-minute period. This work expands the repertoire of DNA-based recording techniques by developing a novel DNA synthesis-based system that can record temporal environmental signals into DNA with minutes resolution.

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“…They can be used to provide rapid oscillatory gene expression (22), as well as spatial gradients of gene expression across cells immobilised in hydrogels (26). Already, electrogenetic systems capable of performing digital-to-biological data storage (27) and electrically-controlled in vivo insulin delivery (28) have been developed. Despite these advances, electrogenetics remains an emerging field, with the development of new systems being hindered by a lack of effective and standardised tools, whether they be electrochemical apparatus, redox inducers or genetic parts.…”

Section: Introductionmentioning

confidence: 99%

A modular toolset for electrogenetics

Lawrence

Yin

Bombelli

et al. 2021

Preprint

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Synthetic biology research and its industrial applications rely on the deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and an electrode), allowing for the direct integration of electronics with complex biological processes for a variety of new applications. However, the use of electrogenetic systems is limited by poor activity, tunability and standardisation. Here, we have developed a variety of genetic and electrochemical tools that facilitate the design and vastly improve the performance of electrogenetic systems. We developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We then constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Finally, we demonstrated electrochemical activation of gene expression in aerobic conditions utilising a novel, modular bioelectrochemical device. This toolset provides researchers with all the elements needed to design and build optimised electrogenetic systems for specific applications.

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Robust direct digital-to-biological data storage in living cells

Cited by 65 publications

References 56 publications

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities

Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis

A modular toolset for electrogenetics

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