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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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.


[1] Ahmad-Neiad P, Duda A, Sucker A, Werner M, et al. (2015), “Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks”, Clinical Chemistry and Laboratory Medicine, 53(12), pp. 1972-34.
[2] McSherry E. A., McGoldrick A., Kay E. W, Hopkins A. M., Gallagher W. M., Dervan P. A. (2007), “Formalin-Fixed Paran-Embedded Clinical Tissues Show Spurious Copy Number Changes in Array-CGH Proles”, Clin Genetics, 72, pp. 441 - 447.
[3] Shi S. R, Datar R., Liu C, Wu L, Zhang Z, Cote R. J, Taylor C. R. (2004), “DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat induced retrieval in alkaline solution”, Histochem Cell Biol, 122, pp. 211 - 218.
[4] Boom R., Sol C. J. A, Beld M, Weel J, Goudsmit J, Dillen P. W. V. (1999), “Improved Silica-Guanidiniumthiocyanate DNA Isolation Procedure Base on Selective Binding of Bovine Alpha-Casein to Silica Particles”, J Clinic Microbiol, 37, pp. 615-619.
[5] Boom R., Sol C. J. A., R, Heijtink R. Wertheim- van Dillen P. M. E, Van Der Noordaa J. (1991), “Rapid purification of Hepatitis B virus DNA from serum”, J Clinic Microbiol, 29, pp. 1804 - 1811.
[6] Boom R, Sol C. J. A, Salimans M. M. M, Jansen C. L, Wertheim P. M. E. (1990), “Rapid and simple method for purification of nucleic acids”, J Clinic Microbiol, 28, pp. 495 - 503.
[7] Esser K. H, Marx W. H, Lisowsky T. (2006), “MaxXbond: first regeneration system for DNA binding silicamatrices”, Nature methods, 3,
pp. 1 - 2.
[8] Berensmeier S. (2006), “Magnetic particles for the separation and purification of nucleic acid”, Applied Microbiology and Biotechnology, 73, pp. 495 - 504.
[9] Kathryn A. M, Chris S. S, Robin F. B. T, Charles A. H. J., “Driving Force for DNA Adsorption to Silica in Perchlorate Solutions”, J. Colloid and Interface Sci 181 (1996) 635.
[10] Pham T. T, Dao V. Q, Nguyen M. H, Nguyen T. S, Nguyen H. N, Nguyen T. V. A, Nguyen H. H, Phan T. N, Nguyen H. L. (2012), “DNA Purification of Epstein Barr virus by silica-coated magnetic nanoparticles for application in PCR detection of the virus”. VNU Journal of Science: Natural Sciences and Technology, 28, pp. 195.
[11] Nguyen T. H, Dao V. Q, Nguyen H. N, Nguyen H. L, Tran T. V. K., Nguyen T. V. A. (2014), “Efficient purification of DNA from blood cells using silica- coated magnetic nanoparticles and suitable buffers”, VNU Journal of Science: Natural Sciences and Technology, 30 (3S),
pp. 158 - 166.
[12] Vu M. H, Dao V. Q, Chu T. N. M., Phan T. N, Nguyen T. V. A. (2014), “Development and evaluation of DNA purification kit based on silica-coated magnetic nanoparticles for PCR product and DNA separated on agarose-gel”, VNU Journal of Science: Natural Sciences and Technology, 30 (3S), pp. 175 - 183.
Dao V.Q, Nguyen M. H, Pham T. T, Nguyen H. N, Nguyen H. H, Nguyen T. S, Phan T. N, Nguyen T. V. A, Tran T. H, Nguyen H. L. (2013), “Synthesis of silica-coated magnetic nanoparticles and application in the detection of pathogenic viruses”, Journal of Nanomaterials, 60, pp. 3940.