DNA stability: a central design consideration for DNA data storage systems

Matange, Karishma; Tuck, James; Keung, Albert J.

doi:10.1038/s41467-021-21587-5

Cited by 130 publications

(108 citation statements)

References 66 publications

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“…The area of scientific research devoted to the development of DNA storage systems has become important due to the widespread application of DNA macromolecules [ 9 ]. Preservation of nucleic acid-based drugs from enzymatic degradation in the bloodstream is considered an important point [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding

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Shiabiev

et al. 2021

IJMS

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A convenient method for the synthesis of the first generation PAMAM dendrimers based on the thiacalix[4]arene has been developed for the first time. Three new PAMAM-calix-dendrimers with the macrocyclic core in cone, partial cone, and 1,3-alternate conformations were obtained with high yields. The interaction of the obtained compounds with salmon sperm DNA resulted in the formation of the associates of the size up to 200 nm, as shown by the UV-Vis spectroscopy, DLS, and TEM. It was demonstrated by the CD method that the structure of the DNA did not undergo significant changes upon binding. The PAMAM-calix-dendrimer based on the macrocycle in cone conformation stabilized DNA and prevented its degradation.

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Section: Introductionmentioning

confidence: 99%

PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding

Mostovaya

Padnya

Shiabiev

et al. 2021

IJMS

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“…Medical application of oligonucleotides and DNA shows the importance of developing protection and storage systems preventing enzymatic digestions of biopolymers and their target delivery and release in target tissues [9]. Chemical encapsulation via multiple noncovalent interactions is considered as one of the most promising issues in this area of research [10].…”

Section: Introductionmentioning

confidence: 99%

Electrochemical Sensing of Interactions between DNA and Charged Macrocycles

et al. 2021

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In this work, we investigated aggregation of native DNA and thiacalix[4]arene derivative bearing eight terminal amino groups in cone configuration using various redox probes on the glassy carbon electrode. It was shown that sorption transfer of the aggregates on the surface of the electrode covered with carbon black resulted in changes in electrostatic interactions and diffusional permeability of the surface layer. Such changes alter the signals of ferricyanide ion, methylene green and hydroquinone as redox probes to a degree depending on their specific interactions with DNA and own charge. Inclusion of DNA in the surface layer was independently confirmed by scanning electron microscopy, electrochemical impedance spectroscopy and experiments with doxorubicin as a model intercalator. Thermal denaturing of DNA affected the charge separation on the electrode interface and the signals of redox probes. Using hydroquinone, less sensitive to electrostatic interactions, made it possible to determine from 10 pM to 1.0 nM doxorubicin (limit of detection 3 pM) after 10 min incubation. Stabilizers present in the commercial medications did not alter the signal. The DNA sensors developed can find future application in the assessment of the complexes formed by DNA and macrocycles as delivery agents for small chemical species.

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“…The DNA data storage channel is a complex channel with types of errors. Most previous studies have focused on substitution and indel errors 28,30,36,[45][46][47][48] . In practice, however, DNA breaks and rearrangements occur frequently during the preservation of DNA molecules and PCR-based data copying, threatening the robustness of DNA data storage.…”

Section: Design Of Dbgps: a De Novo Assembly-based Strand Reconstruct...mentioning

confidence: 99%

Robust retrieval of data stored in DNA by de Bruijn graph-basedde novostrand assembly

Song

Geng

Gong

et al. 2020

Preprint

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High density and long-term features make DNA data storage a potential media. However, DNA data channel is a unique channel with unavoidable ‘data reputations’ in the forms of multiple error-rich strand copies. This multi-copy feature cannot be well harnessed by available codec systems optimized for single-copy media. Furthermore, lacking an effective mechanism to handle base shift issues, these systems perform poorly with indels. Here, we report the efficient reconstruction of DNA strands from multiple error-rich sequences directly, utilizing a De Bruijn Graph-based Greedy Path Search (DBG-GPS) algorithm. DBG-GPS can take advantage of the multi-copy feature for efficient correction of indels as well as substitutions. As high as 10% of errors can be accurately corrected with a high coding rate of 96.8%. Accurate data recovery with low quality, deep error-prone PCR products proved the high robustness of DBG-GPS (314Kb, 12K oligos). Furthermore, DBG-GPS shows 50 times faster than the clustering and multiple alignment-based methods reported. The revealed linear decoding complexity makes DBG-GPS a suitable solution for large-scale data storage. DBG-GPS’s capacity with large data was verified by large-scale simulations (300 MB). A Python implementation of DBG-GPS is available at https://switch-codes.coding.net/public/switch-codes/DNA-Fountain-De-Bruijn-Decoding/git/files.

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DNA stability: a central design consideration for DNA data storage systems

Cited by 130 publications

References 66 publications

PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding

PAMAM-calix-dendrimers: Synthesis and Thiacalixarene Conformation Effect on DNA Binding

Electrochemical Sensing of Interactions between DNA and Charged Macrocycles

Robust retrieval of data stored in DNA by de Bruijn graph-basedde novostrand assembly

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