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Accelerating DNA computing via freeze-thaw cycling.

ABSTRACT: DNA computing harnesses the immense potential of DNA molecules to enable sophisticated and transformative computational processes but is hindered by low computing speed. Here, we propose freeze-thaw cycling as a simple yet powerful method for high-speed DNA computing without complex procedures. Through iterative cycles, we achieve a substantial 20-fold speed enhancement in basic strand displacement reactions. This acceleration arises from the utilization of eutectic ice phase as a medium, temporarily increasing the effective local concentration of molecules during each cycle. In addition, the acceleration effect follows the Hofmeister series, where kosmotropic anions such as sulfate (SO₄^2-) reduce eutectic phase volume, leading to a more notable enhancement in strand displacement reaction rates. Leveraging this phenomenon, freeze-thaw cycling demonstrates its generalizability for high-speed DNA computing across various circuit sizes, achieving up to a remarkable 120-fold enhancement in reaction rates. We envision its potential to revolutionize molecular computing and expand computational applications in diverse fields.

SUBMITTER: Zhu Y

PROVIDER: S-EPMC10456841 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Accelerating DNA computing via freeze-thaw cycling.

Zhu Yun Y Xiong Xiewei X Cao Mengyao M Li Li L Fan Chunhai C Pei Hao H

Science advances 20230825 34

DNA computing harnesses the immense potential of DNA molecules to enable sophisticated and transformative computational processes but is hindered by low computing speed. Here, we propose freeze-thaw cycling as a simple yet powerful method for high-speed DNA computing without complex procedures. Through iterative cycles, we achieve a substantial 20-fold speed enhancement in basic strand displacement reactions. This acceleration arises from the utilization of eutectic ice phase as a medium, tempor ...[more]

PMID: 37624882

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Project description:Although the presence of live microbes in utero remains under debate, newborn gastrointestinal bacteria are undoubtedly important to infant health. Measuring bacteria in meconium is an ideal strategy to understand this issue; however, the low efficiency of bacterial DNA extraction from meconium has limited its utilization. This study aims to improve the efficiency of bacterial DNA extraction from meconium, which generally has low levels of microflora but high levels of PCR inhibitors in the viscous matrix. The research was approved by the ethical committee of the Xiamen Maternity and Child Health Care Hospital, Xiamen, China. All the mothers delivered naturally, and their newborns were healthy. Meconium samples passed by the newborns within 24 h were collected. Each sample was scraped off of a sterile diaper, transferred to a 5-ml sterile tube, and stored at -80°C. For the assay, a freeze-thawing sample preparation protocol was designed, in which a meconium-InhibitEX buffer mixture was intentionally frozen 1-3 times at -20°C, -80°C, and (or) in liquid nitrogen. Then, DNA was extracted using a commercial kit and sequenced by 16S rDNA to verify the enhanced bacterial DNA extraction efficiency. Ultimately, we observed the following: (1) About 30 mg lyophilized meconium was the optimal amount for DNA extraction. (2) Freezing treatment for 6 h improved DNA extraction at -20°C. (3) DNA extraction efficiency was significantly higher with the immediate thaw strategy than with gradient thawing at -20°C, -80°C, and in liquid nitrogen. (4) Among the conditions of -20°C, -80°C, and liquid nitrogen, -20°C was the best freezing condition for both improving DNA extraction efficiency and preserving microbial species diversity in meconium, while liquid nitrogen was the worst condition. (5) Three freeze-thaw cycles could markedly enhance DNA extraction efficiency and preserve the species diversity of meconium microflora. We developed a feasible freeze-thaw pretreatment protocol to improve the extraction of microbial DNA from meconium, which may be beneficial for newborn bacterial colonization studies.

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Accelerating DNA computing via freeze-thaw cycling.

Publications

Accelerating DNA computing via freeze-thaw cycling.

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