Fumed silica-coated magnetic particles: DNA extraction application
DOI:
https://doi.org/10.24193/subbbiol.2025.1.01Keywords:
DNA extraction, fumed silica, magnetiteAbstract
Tetraethyl orthosilicate (TEOS) is widely used for preparing magnetic particles in DNA extraction kits, but it poses toxicity and safety concerns. To address this issue, we developed magnetic particles using fumed silica as a safer alternative to TEOS for magnetite particle preparation for DNA extraction. The method effectively extracts DNA from various biological matrices, including urine, serum, saliva, sputum, whole blood, and plasma, without detectable inhibitors. The extracted DNA is suitable for downstream molecular applications such as qPCR and sequencing. The proposed magnetic particles with fumed silica not only reduce chemical hazards but also provide a safer, efficient, and reliable method for routine DNA extraction in molecular biology laboratories.
Article history: Received 15 January 2025; Revised 03 March 2025;
Accepted 11 March 2025; Available online 25 June 2025
References
Al-Shuhaib, M.B.S. & Hashim, H.O. (2023). Mastering DNA chromatogram analysis in Sanger sequencing for reliable clinical analysis. J. Genet. Eng. Biotechnol. 21, 115. https://doi.org/s43141-023-00587-6
Al-Soud, W.A. & Rådström, P. J. (2001). Purification and Characterization of PCR-Inhibitory Components in Blood Cells. Clin. Microbiol. 39, 2, 485-493. https://doi.org/10.1128/JCM.39.2.485-493.2001
Alghuthaymi, M. (2020). Magnetic-silica nanoshell for extraction of fungal genomic DNA from Rhizopus oryzae. Biointerface Res. Appl. Chem. 10, 2, 4972-4976. https://doi.org/0.33263/BRIAC102.972976
Booth, C.S., Pienaar, E., Termaat, J.R., Whitney, S.E., Louw, T.M., & Viljoen, H.J. (2010). Efficiency of the Polymerase Chain Reaction. Chem. Eng. Sci. 65, 17, 4996-5006 (2010) https://doi.org/10.1013/j.ces.2010.05.046
Crossley, B.M., Bai, J., Glaser, A., Maers, R., Porter, E., Killian, M.L, Clement, T., & Toohey-Kurth, K. (2020). Guidelines for Sanger sequencing and molecular assay monitoring. J. Vet. Diagn. Invest. 32, 6, 767-775. https://doi.org/10.1177/1040638720905833
Dzeranov, A., Bondarenko, L., Pankratov, D., Dzhardimalieva, G., Jorobekova, S., Saman, D., & Kydralieva, K. (2023). Impact of Silica-Modification and Oxidation on the Crystal Structure of Magnetite Nanoparticles. Magnetochemistry. 2023, 9, 18. https://doi.org/10.3390/magnetochemistry9010018
Fan, Q., Guan, Y., Zhang, Z., Xu, G., Yang, Y., & Guo, C. (2019). A new method of synthesis well-dispersion and dense Fe3O4@SiO2 magnetic nanoparticles for DNA extraction. Chem. Phys. Lett. 715, 7-13. https://doi.org/10.1016/j.cplett.2018.11.001
Firoozeh, F., Neshan, A., Khaledi, A., Zibaei, M., Amiri, A., Sobhani, A., Badmasti, F., & Nikbin, V.S. (2023). Evaluation of the effect of magnetic nanoparticles on extraction of genomic DNA of Escherichia coli. Polym. Bull. 80, 3153-3163. https://doi.org/10.1007/s00289-022-04196-0
Flörke, O.W., Graetsch, H.A., Brunk, F., Benda, L., Paschen, S., Bergna, H.E., Roberts, W.O., Welsh, W.A., Libanati, C., Ettlinger, M., Kerner, D., Maier, M., Meon, W., Schmoll, R., Gies, H., & Schiffmann, D. (2012). Silica.Ullmann’s encyclopedia of industrial chemistry. Wiley, Weinheim. https://doi.org/10.1002/14356007.a23_583
Louw, T.M., Booth, C.S., Pienaar, E., TerMaat, J.R., Whitney, S.E., & Viljoen, H.J. (2011). Experimental Validation of a Fundamental Model for PCR Efficiency. Chem. Eng. Sci. 66, 1783-1789. https://doi.org/10.1016/j.ces.2011.01.029
Munch, M.M., Chambers, L.C., Manhart, L.E., Domogala, D., Lopez, A., Fredricks, D.N., & Srinivasan, S. (2019). Optimizing Bacterial DNA Extraction in Urine. PLoS One. 14, 9, e0222962. https://doi.org/10.1371/journal.pone.0222962
Nguyen, L.T., Le, N.T., Ta, H.K.T., & Nguyen, K.D. (2022). Isolation of DNA from Arthrospira platensis and whole blood using magnetic nanoparticles (Fe3O4@OA and Fe3O4@OA@SiO2). J. Anal. Sci. Technol. 13, 1, 28. https://doi.org/10.1186/s40543-022-00337-2
Nybo, K. (2011). qPCR Efficiency Calculations. Biotechniques, 51, 401-402. https://doi.org/10.2144/000113776
Reed, J.L., Walker, Z.J., Basu, D., Allen, V., Nicol, M.P., Kelso, D.M., & McFall, S. (2016). Highly Sensitive Sequence Specific qPCR Detection of Mycobacterium tuberculosis Complex in Respiratory Specimens. Tuberculosis. 101, 114-124. https://doi.org/10.1016/j.tube.2016.09.002.
Thangaraj, B., Jia, Z., Dai, L., Liu, D., & Du, W. (2019). Effect of silica coating on Fe3O4 magnetic nanoparticles for lipase immobilization and their application for biodiesel production. Arab. J. Chem. 12, 8, 4694-4706. https://doi.org/10.1016/j.arabjc.2013.09.004
Tjoa, S.E.E., Mudasir, M., Suharyadi, E., & Daryono, B.S. (2025). DNA extraction procedure based on magnetite nanoparticle: A Plackett-Burman design optimization. Res. J. Biotech. 20, 3, 1-7. https://doi.org/10.25303/203rjbt0107
Torres-Rodríguez, J., Soto, G., Medina, J.L., Portillo-López, A., Hernández-López, E.L., Viveros, E.V., Galindo, J.T.E., Tiznado, H., Flores, D., & Muñoz-Muñoz, F. (2019). Cobalt–zinc ferrite and magnetite SiO2 nanocomposite powder for magnetic extraction of DNA. J. Sol-Gel Sci. Technol. 91, 33-43. https://doi.org/10.1007/s10971-019-05017-z
Waiblinger, H. & Grohmann, L. (2014). Guidelines for validation of DNA extraction methods applied in subsequent PCR analysis of food and feed products for the presence of genetically modified material. J. Verbrauch. Lebensm. 9, 183-190. https://doi.org/10.1007/s00003-014-0862-3
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000). A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 1-2, 203-214. https://doi.org/10.1089/10665270050081478
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