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An efficient extraction method for short single-stranded DNA from agarose gels in aptamer screening

文献类型： 外文期刊

作者： Pu, Chunmin 1 ; Liao, Xiaoyan 1 ; Shi, Xianming 3 ; Cui, Yan 3 ; Bai, Yalong 2 ; Chen, Lili 1 ;

作者机构： 1.Univ South China, Coll Publ Hlth, Hengyang Med Sch, Dept Publ Hlth Lab Sci, 28 Changsheng West Rd, Hengyang 421001, Hunan, Peoples R China

2.Shanghai Acad Agr Sci, Inst Agrifood Stand & Testing Technol, 1000 Jinqi Rd, Shanghai 201403, Peoples R China

3.Shanghai Jiao Tong Univ, MOST USDA Joint Res Ctr Food Safety, Sch Agr & Biol, State Key Lab Microbial Metab, Shanghai 200240, Peoples R China

关键词： Short single-stranded DNA; DNA extraction; Amino-modified magnetic particles; Aptamer; Agarose gel

期刊名称：INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES （ 影响因子：8.2； 五年影响因子：7.8 ）

ISSN： 0141-8130

年卷期： 2023 年 252 卷

页码：

收录情况： SCI

摘要： With the rapid advancements in aptamer screening, the efficient extraction of short single-stranded DNA (ssDNA) from agarose gel has become a new requirement. However, the currently available products are primarily designed for double-stranded DNA (dsDNA) and exhibit limited efficacy when applied to the extraction of short ssDNA. In this study, we successfully developed a novel method based on amino-modified silica-coated magnetic particles (ASMPs) for the extraction of short ssDNA from agarose gel. The gel slices containing short ssDNA were subjected to centrifugation in a spin column/centrifugation tube assembly with silica wool, followed by the adsorption using ASMPs. Subsequently, reagents containing phosphate groups were employed to desorb ssDNA from the surface of ASMPs. Through optimization of each step, we realized remarkable efficiency in the extraction of short ssDNA. To assess the efficacy of our method, we utilized it in aptamer screening. The results demonstrated that our method outperformed three commercially available DNA gel extraction products (Q-kit, Skit, and V-kit). The relative recovery rates of all methods were as follows: M-dNTP (100.00 %) > M-BB (63.38 %) >Q-kit (46.64 %) >S-kit (15.98 %) >V-kit (0.38 %). The results strongly suggest that the developed method holds promise for short ssDNA extraction from agarose gel.

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