Oligo replication advantage driven by GC content and Gibbs free energy

Qiao, Hongyan; Gao, Yanmin; Liu, Qian; Wei, Yanan; Li, Jiaojiao; Wang, Zhaoguan; Qi, Hao

doi:10.1007/s10529-022-03295-2

Cited by 5 publications

(2 citation statements)

References 28 publications

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“…The effect of secondary structure on DNA replication may be secondary to Gibbs free energy and GC content. [ 48 ] This was also confirmed by the significantly decreased coverage of these two sequences in the master pool without adsorption on cellulose paper (Figure 4f). Therefore, when designing DNA oligo pool in the future, choosing DNA sequences with higher GC content and absolute value of Gibbs free energy may improve the data stability.…”

Section: Resultssupporting

confidence: 56%

Sustainable DNA Data Storage on Cellulose Paper

et al. 2023

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DNA is a promising material for high density and long‐term archival data storage. In addition to algorithms for encoding digital information into DNA sequences, the DNA writing (chemical synthesis) and reading (DNA sequencing), the preservation of DNA mixtures with high sequence diversity is another critical issue for sustainable, long‐term, and large‐scale DNA data storage. Here, this work demonstrates a method for low‐cost, convenient and sustainable DNA data storage on cellulose paper. A DNA pool comprising thousands of sequences, in which archival data are encoded, is conveniently stored on a cellulose paper with a calculated density as high as 15 TB per mm3 through electrostatic adsorption. This work demonstrates that these digitally encoded DNA pools can be stable for years on the cellulose paper after drying even when directly exposed to air. Furthermore, the reversible electrostatic adsorption enables repeated loading/retrieval of DNA on/off cellulose paper. Therefore, this sustainable DNA preservation on cellulose paper through the convenient electrostatic adsorption exhibits a great advantage in terms of storage capacity and cost that is crucial for practical systems to achieve large‐scale and long‐time data storage.

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Section: Resultssupporting

confidence: 56%

Sustainable DNA Data Storage on Cellulose Paper

et al. 2023

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“…Likewise, Z‐containing oligo probes exhibited better selectivity and higher binding affinity when hybridizing with the target DNA (Chollet & Kawashima, 1988). Therefore, the nucleotide base Z holds significant potential for applications that are critically dependent on the stability of DNA hybridization, such as genotyping (Bai et al, 2014; Gao et al, 2022), targeted therapy (Wang et al, 2012), biosensing (Sadat Mousavi et al, 2020), drug delivery (Hu et al, 2018), and DNA amplification (Qiao et al, 2022), and so forth. In a previous study (Gao et al, 2022), we demonstrated that specially designed toehold blockers facilitated the detection of low‐frequency single nucleotide variation (SNV) in an isothermal genotyping assay.…”

Section: Introductionmentioning

confidence: 99%

2,6‐diaminopurine (Z)‐containing toehold probes improve genotyping sensitivity

Kang,

Liu,

Zhang

et al. 2023

Biotech & Bioengineering

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Abstract2,6‐diaminopurine (Z), a naturally occurring noncanonical nucleotide base found in bacteriophages, enhances DNA hybridization by forming three hydrogen bonds with thymine (T). These distinct biochemical characteristics make it particularly valuable in applications that rely on the thermodynamics of DNA hybridization. However, the practical use of Z‐containing oligos is limited by their high production cost and the challenges associated with their synthesis. Here, we developed an efficient and cost‐effective approach to synthesize Z‐containing oligos of high quality based on an isothermal strand displacement reaction. These newly synthesized Z‐oligos are then employed as toehold‐blockers in an isothermal genotyping assay designed to detect rare single nucleotide variations (SNV). When compared with their counterparts containing the standard adenine (A) base, the Z‐containing blockers significantly enhance the accuracy of identifying SNV. Overall, our innovative methodology in the synthesis of Z‐containing oligos, which can also be used to incorporate other unconventional and unnatural bases into oligonucleotides, is anticipated to be adopted for diverse applications, including genotyping, biosensing, and gene therapy.

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A digital twin for DNA data storage based on comprehensive quantification of errors and biases

Gimpel,

Stark,

Heckel

et al. 2023

Nat Commun

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Archiving data in synthetic DNA offers unprecedented storage density and longevity. Handling and storage introduce errors and biases into DNA-based storage systems, necessitating the use of Error Correction Coding (ECC) which comes at the cost of added redundancy. However, insufficient data on these errors and biases, as well as a lack of modeling tools, limit data-driven ECC development and experimental design. In this study, we present a comprehensive characterisation of the error sources and biases present in the most common DNA data storage workflows, including commercial DNA synthesis, PCR, decay by accelerated aging, and sequencing-by-synthesis. Using the data from 40 sequencing experiments, we build a digital twin of the DNA data storage process, capable of simulating state-of-the-art workflows and reproducing their experimental results. We showcase the digital twin’s ability to replace experiments and rationalize the design of redundancy in two case studies, highlighting opportunities for tangible cost savings and data-driven ECC development.

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Oligo replication advantage driven by GC content and Gibbs free energy

Cited by 5 publications

References 28 publications

Sustainable DNA Data Storage on Cellulose Paper

Sustainable DNA Data Storage on Cellulose Paper

2,6‐diaminopurine (Z)‐containing toehold probes improve genotyping sensitivity

A digital twin for DNA data storage based on comprehensive quantification of errors and biases

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