Development of DNA Extraction Kit Based on Silica-Coated Magnetic Nanoparticles for Formalin-Fixed and Paraffin-Embedded Cancer Tissues

Nguyen Thi Huyen, Le Duc Linh, Pham Thi Thu Huong, Nguyen Minh Hieu, Nguyen Hoang Nam, Tran Thi My, Nguyen Hoa Anh, Phan Tuan Nghia, Nguyen Thi Van Anh

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Published Mar 15, 2016

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HUYEN, Nguyen Thi et al. Development of DNA Extraction Kit Based on Silica-Coated Magnetic Nanoparticles for Formalin-Fixed and Paraffin-Embedded Cancer Tissues. VNU Journal of Science: Natural Sciences and Technology, [S.l.], v. 32, n. 1S, mar. 2016. ISSN 2588-1140. Available at: <https://js.vnu.edu.vn/NST/article/view/3558>. Date accessed: 21 nov. 2024.
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Vol 32 No 1S
Section
Review Articles

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Abstract

Abstract: The aim of this study is to develop a kit for the extraction of DNA from formalin fixed paraffin embedded (FFPE) tissues using silica-coated magnetic nanoparticles Fe3O4@SiO2 (MagSi nano) and suitable buffers. We selected the best version of synthesized MagSi nano (code M1) and optimised buffers including Lysis Buffer (code LB2) and Binding Buffer (code BB2) for extracting DNA from FFPE tissues with highest DNA recovery (84 - 103 ng/ml) and good purity (A260/A280 around 1.8 - 2.0). Using the MagPure FFPE DNA nano kit based on the selected MagSi nano and the optimised LB2 + BB2 buffers, we successfully performed extraction of DNA from FFPE tissues of colon and nasopharyngeal carcinoma patients. The extracted DNAs from FFPE colon cancer tissues could be used as templates for downstream amplifying and sequencing Braf bio marker gene, and the extracted DNAs from nasopharyngeal cancer tissues could be used as templates for downstream detection of Epstein-Barr virus (EBV) using real-time Taqman PCR. In sum, the MagPure FFPE DNA nano kit is potential for extraction of DNA from FFPE tissues, and need to be further developed to improve DNA recovery yield for application in diagnostics of cancers using molecular biology. 

Keywords: Silica-coated magnetic nanoparticles Fe3O4@SiO2, DNA extraction, FFPE cancer tissue, PCR, DNA sequencing.

References

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