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Sequence-specific eDNA extraction using hydrophobic magnetic ionic liquids attached with oligonucleotide strand
Analytica Chimica Acta ( IF 5.7 ) Pub Date : 2022-11-14 , DOI: 10.1016/j.aca.2022.340612
Yao Chen 1 , Yani Ma 1 , Feixia Peng 1 , Xueqin Ding 1
Affiliation  

Isolation of high-purity nucleic acids, especially sequence-specific DNA, from complex samples is critical to the downstream nucleic acid analysis. In this work, an oligonucleotide strand-attached magnetic ionic liquid (OSMIL) was designed and prepared for DNA extraction. The attached oligonucleotide strand has a sequence complementary to that of a specific DNA to be extracted. The OSMIL has good hydrophobicity and magnetic response properties. At the extraction temperature, OSMIL was in a liquid state, which was favorable for maximizing the adsorption of DNA; while at the separation temperature, OSMIL was in a solid state (with an average particle size of 897 nm) and could be attracted by an external magnet in 3s, which was favorable for the separation and recovery of DNA. The sequence-specific DNA extraction process with OSMIL is simple and fast. After extraction, the DNA-enriched OSMILs were quickly attracted and separated by an external magnetic field. The extracted DNA was evaluated by a NanoDrop (wavelength detection at 260–280 nm) and the OSMIL can be recycled and reused. The enrichment factor was 0.81. Through single-factor experimental analysis, the effects of OSMIL extraction volume, thermal excitation temperature, thermal excitation time, pH, and other factors on the DNA extraction process were systematically investigated. The RSD of repeatability experiment was 1.19% (n = 3), showing the method has good repeatability. The extraction method presented here has been shown to extract DNA with specific sequences from mixtures containing DNA of different sequences and from mixtures containing proteins, respectively. In addition, the OSMIL has been applied to extract target environmental DNA with specific sequences from different water environments with high extraction efficiency. In the long run, OSMIL has great potential for identifying existing organisms in environmental samples or exploring unknown organisms.



中文翻译:

使用附有寡核苷酸链的疏水磁性离子液体进行序列特异性 eDNA 提取

从复杂样品中分离高纯度核酸,尤其是序列特异性 DNA,对于下游核酸分析至关重要。在这项工作中,设计并制备了一种用于 DNA 提取的寡核苷酸链附着磁性离子液体 (OSMIL)。连接的寡核苷酸链的序列与要提取的特定 DNA 的序列互补。OSMIL 具有良好的疏水性和磁响应特性。在提取温度下,OSMIL呈液态,有利于最大限度地吸附DNA;而在分离温度下,OSMIL呈固态(平均粒径897 nm),可在3s内被外接磁铁吸附,有利于DNA的分离回收。使用 OSMIL 进行的序列特异性 DNA 提取过程简单且快速。提取后,富含 DNA 的 OSMIL 被外部磁场迅速吸引和分离。提取的 DNA 通过 NanoDrop(在 260–280 nm 的波长检测)进行评估,并且 OSMIL 可以回收和重复使用。富集因子为 0.81。通过单因素实验分析,系统考察了OSMIL提取体积、热激发温度、热激发时间、pH等因素对DNA提取过程的影响。重复性实验的RSD为1.19%(系统考察了OSMIL提取体积、热激发温度、热激发时间、pH等因素对DNA提取过程的影响。重复性实验的RSD为1.19%(系统考察了OSMIL提取体积、热激发温度、热激发时间、pH等因素对DNA提取过程的影响。重复性实验的RSD为1.19%(n  = 3),表明该方法具有良好的重复性。这里介绍的提取方法已被证明可以分别从含有不同序列 DNA 的混合物和含有蛋白质的混合物中提取具有特定序列的 DNA。此外,OSMIL已被应用于从不同的水环境中提取具有特定序列的目标环境DNA,提取效率高。从长远来看,OSMIL在识别环境样本中的现有生物或探索未知生物方面具有巨大的潜力。

更新日期:2022-11-14
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