Development of Magnetic-Silica Particles and In-house Buffers Kit for SARS-CoV-2 and CDV RNA Extraction

Ahadi Damar Prasetya(1*), Muflikhah Muflikhah(2), Wildan Zakiah Lubis(3), Andon Insani(4), Grace Tjungirai Sulungbudi(5), Mujamilah Mujamilah(6), Uus Saepulloh(7)

(1) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(2) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(3) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(4) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(5) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(6) Research Center for Radiation Detection and Nuclear Analysis Technology, Research Organization for Nuclear Energy, National Research and Innovation Agency, South Tangerang 15314, Indonesia
(7) Primate Research Center, Bogor Agricultural University, Bogor 16151, Indonesia
(*) Corresponding Author


Since the end of 2019, COVID-19 pandemic caused by the novel SARS-CoV-2 has become a serious problem for the world. Accurate and rapid techniques in testing and tracing are needed to control the virus spreading. Molecular diagnostics through gene amplification techniques, especially PCR, still become the gold standard for SARS-CoV-2 detection, which requires the first step of RNA extraction and purification. The limitations of commercial RNA extraction-purification kits during the pandemic caused a big problem in testing and tracing, especially for developing countries. A simple RNA extraction-purification kit based on magnetic-silica (MAGSi) beads and non-guanidine in-house buffers for RNA virus extraction-purification has been developed. Two types of MAGSi beads with different magnetic nanoparticles (MNPs) content were synthesized through a modified Stöber’s method using the sonication technique. The PCR result shows that both the MAGSi beads and the buffer can be used as a kit for RNA extraction-purification, tested for SARS-CoV-2 and Canine Distemper Virus. Further study shows that MAGSi-1 has better RNA extraction ability, and a higher concentration of RNA has been extracted. This is likely because of the smaller particle size distribution (50–1,500 nm distribution) and higher magnetization (20.2 emu/g) of MAGSi-1 compared to MAGSi-2 with 100–1,700 nm size distribution and 14.2 emu/g magnetization.


buffer kit; Canine Distemper Virus; magnetic-silica; RNA extraction; SARS-CoV-2

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[1] WHO, 2020, WHO Coronavirus (COVID-19) Dashboard with Vaccination Data,, accessed March 14, 2022.

[2] Yüce, M., Filiztekin, E., and Özkaya, K.G., 2021, COVID-19 diagnosis: A review of current methods, Biosens. Bioelectron., 172, 112752.

[3] Khandia, R., Singhal, S., Alqahtani, T., Kamal, M.A., El-Shall, N.A., Nainu, F., Desingu, P.A., and Dhama, K., 2022, Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic, Environ. Res., 209, 112816.

[4] Chang K.P., Lin Z.Y., Hung M.C., and Hsieh B.S., 2011, Effects of Irradiation on Chitosan-coated Nanoparticles for Hyperthermia, Adv. Mater. Res., 311-313, 419–431.

[5] Namagerdi, A.A., Ciani, F., d’Angelo, D., Napolitano, F., Avallone, L., Napolitano, F., and Avallone, L., 2022, Covid-19, environment, clinicopathologic features, laboratory findings and diagnosis, treatment, vaccines, animals, and cancer, Ann. Res. Oncol., 2 (1), 34–54.

[6] Cheng, M.P., Papenburg, J., Desjardins, M., Kanjilal, S., Quach, C., Libman, M., Dittrich, S., and Yansouni, C.P., 2020, Diagnostic testing for severe acute respiratory syndrome–related Coronavirus 2, Ann. Intern. Med., 172 (11), 726–734.

[7] Morehouse, Z.P., Samikwa, L., Proctor, C.M., Meleke, H., Kamdolozi, M., Ryan, G.L., Chaima, D., Ho, A., Nash, R.J., and Nyirenda, T.S., 2021, Validation of a direct-to-PCR COVID-19 detection protocol utilizing mechanical homogenization: A model for reducing resources needed for accurate testing, PLoS One, 16 (8), e0256316.

[8] Colbert, A.J., Lee, D.H., Clayton, K.N., Wereley, S.T., Linnes, J.C., and Kinzer-Ursem, T.L., 2022, PD-LAMP smartphone detection of SARS-CoV-2 on chip, Anal. Chim. Acta, 1203, 339702

[9] Nyaruaba, R., Mwaliko, C., Hong, W., Amoth, P., and Wei, H., 2021, SARS-CoV-2/COVID-19 laboratory biosafety practices and current molecular diagnostic tools, J. Biosaf. Biosecur., 3 (2), 131–140.

[10] Das, D., Hsieh, H.C., Chen, C.S., Chen, W.L., and Chuang, H.S., 2022, Ultrafast and sensitive screening of pathogens by functionalized Janus microbeads-enabled rotational diffusometry in combination with isothermal amplification, Small Sci., 2 (5), 2200010.

[11] Shin, J.H., 2013, “Nucleic Acid Extraction Techniques” in Advanced Techniques in Diagnostic Microbiology, Eds. Tang, Y.W., and Stratton, C.W., Springer US, Boston, MA, 209–225.

[12] Ambrosi, C., Prezioso, C., Checconi, P., Scribano, D., Sarshar, M., Capannari, M., Tomino, C., Fini, M., Garaci, E., Palamara, A.T., De Chiara, G., and Limongi, D., 2021, SARS-CoV-2: Comparative analysis of different RNA extraction methods, J. Virol. Methods, 287, 114008.

[13] Klein, S., Müller, T.G., Khalid, D., Sonntag-Buck, V., Heuser, A.M., Glass, B., Meurer, M., Morales, I., Schillak, A., Freistaedter, A., Ambiel, I., Winter, S.L., Zimmermann, L., Naumoska, T., Bubeck, F., Kirrmaier, D., Ullrich, S., Barreto Miranda, I., Anders, S., Grimm, D., Schnitzler, P., Knop, M., Kräusslich, H.G., Dao Thi, V.L., Börner, K., and Chlanda, P., 2020, SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP, Viruses, 12 (8), 863.

[14] Haile, S., Nikiforuk, A.M., Pandoh, P.K., Twa, D.D.W., Smailus, D.E., Nguyen, J., Pleasance, S., Wong, A., Zhao, Y., Eisler, D., Moksa, M., Cao, Q., Wong, M., Su, E., Krzywinski, M., Nelson, J., Mungall, A.J., Tsang, F., Prentice, L.M., Jassem, A., Manges, A.R., Jones, S.J.M., Coope, R.J., Prystajecky, N., Marra, M.A., Krajden, M., and Hirst, M., 2022, Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents, J. Virol. Methods, 299, 114339.

[15] He, H., Li, R., Chen, Y., Pan, P., Tong, W., Dong, X., Chen, Y., and Yu, D., 2017, Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections, Sci. Rep., 7 (1), 45199.

[16] Setyawan, H., Fajaroh, F., Widiyastuti, W., Winardi, S., Lenggoro, I.W., and Mufti, N., 2012, One-step synthesis of silica-coated magnetite nanoparticles by electrooxidation of iron in sodium silicate solution, J. Nanopart. Res., 14 (4), 807.

[17] Majidi, S., Zeinali Sehrig, F., Farkhani, S.M., Soleymani Goloujeh, M., and Akbarzadeh, A., 2016, Current methods for synthesis of magnetic nanoparticles, Artif. Cells, Nanomed., Biotechnol., 44 (2), 722–734.

[18] Stöber, W., Fink, A., and Bohn, E., 1968, Controlled growth of monodisperse silica spheres in the micron size range, J. Colloid Interface Sci., 26 (1), 62–69.

[19] Mahajan, R., Suriyanarayanan, S., and Nicholls, I.A., 2021, Improved solvothermal synthesis of γ-Fe2O3 magnetic nanoparticles for SiO2 coating, Nanomaterials, 11 (8), 1889.

[20] Sharafi, Z., Bakhshi, B., Javidi, J., and Adrangi, S., 2018, Synthesis of silica-coated iron oxide nanoparticles: Preventing aggregation without using additives or seed pretreatment, Iran. J. Pharm. Res., 17 (1), 386–395.

[21] Asab, G., Zereffa, E.A., and Abdo Seghne, T., 2020, Synthesis of silica-coated Fe3O4 nanoparticles by microemulsion method: Characterization and evaluation of antimicrobial activity, Int. J. Biomater., 2020, 4783612.

[22] Pham, X.H., Kyeong, S., Jang, J., Kim, H., Kim, J., Jung, S., Lee, Y.S., Jun, B.H., and Chung, W.J., 2016, Facile method for preparation of silica coated monodisperse superparamagnetic microspheres, J. Nanomater., 2016, 1730403.

[23] Bui, T.Q., Ngo, H.T.M., and Tran, H.T., 2018, Surface-protective assistance of ultrasound in synthesis of superparamagnetic magnetite nanoparticles and in preparation of mono-core magnetite-silica nanocomposites, J. Sci.: Adv. Mater. Devices, 3 (3), 323–330.

[24] Harris, M.T., Brunson, R.R., and Byers, C.H., 1990, The base-catalyzed hydrolysis and condensation reactions of dilute and concentrated TEOS solutions, J. Non-Cryst. Solids, 121 (1), 397–403.

[25] Cihlář, J., 1993, Hydrolysis and polycondensation of ethyl silicates. 1. Effect of pH and catalyst on the hydrolysis and polycondensation of tetraethoxysilane (TEOS), Colloids Surf., A, 70 (3), 239–251.

[26] Mohammed, M.A.A., Chen, Z., Li, K., and Zhang, B., 2022, The study of Fe3O4@SiO2-NH2 nano-magnetic composite modified by glutaraldehyde to immobilized penicillin G acylase, Turk. J. Chem., 46 (1), 103–115.

[27] Ndiritu, W., Cawthorn, R.J., and Kibenge, F.S.B., 1994, Use of proteinase K in the excystation of Sarcocystis cruzi sporocysts for in vitro culture and DNA extraction, Vet. Parasitol., 52 (1), 57–60.

[28] Shehadul Islam, M., Aryasomayajula, A., and Selvaganapathy, P.R., 2017, A review on macroscale and microscale cell lysis methods, Micromachines, 8 (3), 83.

[29] Farrell, R.E., 2017, “Chapter 3 - RNA Isolation Strategies” in RNA Methodologies (Fifth Edition), Academic Press, Cambridge, MA, US, 75–115.

[30] Davies, K., Arnold, U., Buczkowski, H., Burton, C., Welch, S.R., Green, N., Strachan, R., Beetar-King, T., Spencer, P., Hettiarachchi, N., Hannah, M.J., Jones, M., Cane, P.A., Bruce, C.B., Woodford, N., Roberts, A.D.G., and Killip, M.J., 2021, Virucidal efficacy of guanidine-free inactivants and rapid test buffers against SARS-CoV-2, Sci. Rep., 11 (1), 23379.

[31] Sun N., Deng, C., Liu, Y., Zhao, X., Tang, Y., Liu, R., Xia, Q., Yan, W., and Ge, G., 2014, Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: Application to viral nucleic acid extraction from serum, J. Chromatogr. A, 1325, 31–39.

[32] Shin, J.H., 2018, “Nucleic Acid Extraction and Enrichment” in Advanced Techniques in Diagnostic Microbiology: Volume 1: Techniques, Eds. Tang, Y.W., and Stratton, C.W., Springer International Publishing, Cham, Germany, 273–292.

[33] Gjerde, D.T., Hoang, L., and Hornby, D., 2009, RNA Purification and Analysis: Sample Preparation, Extraction, Chromatography, Wiley-VCH, Weinheim, Germany.

[34] Digigow, R.G., Dechézelles, J.F., Dietsch, H., Geissbühler, I., Vanhecke, D., Geers, C., Hirt, A.M., Rothen-Rutishauser, B., and Petri-Fink, A., 2014, Preparation and characterization of functional silica hybrid magnetic nanoparticles, J. Magn. Magn. Mater., 362, 72–79.

[35] Tiwari, A.P., Satvekar, R.K., Rohiwal, S.S., Karande, V.A., Raut, A.V., Patil, P.G., Shete, P.B., Ghosh, S.J., and Pawar, S.H., 2015, Magneto-separation of genomic deoxyribose nucleic acid using pH responsive Fe3O4@silica@chitosan nanoparticles in biological samples, RSC Adv., 5 (11), 8463–8470.

[36] Zhang, Z.C., Yuan, C., and Wan, Q.H., 2007, Surface modification of magnetic silica microspheres and its application to the isolation of plant genomic nucleic acids, Chin. J. Anal. Chem., 35 (1), 31–36.

[37] Chen, W.Y., Matulis, D., Hu, W.P., Lai, Y.F., and Wang W.H., 2020, Studies of the interactions mechanism between DNA and silica surfaces by isothermal titration calorimetry, J. Taiwan Inst. Chem. Eng., 116, 62–66.

[38] Wu, J., Wang, H., Zhu, A., and Long, F., 2018, Adsorption kinetics of single-stranded DNA on functional silica surfaces and its influence factors: An evanescent-wave biosensor study, ACS Omega, 3 (5), 5605–5614.

[39] Morel, A.L., Nikitenko, S.I., Gionnet, K., Wattiaux, A., Lai-Kee-Him, J., Labrugere, C., Chevalier, B., Deleris, G., Petibois, C., Brisson, A., and Simonoff, M., 2008, Sonochemical approach to the synthesis of Fe3O4@SiO2 core−shell nanoparticles with tunable properties, ACS Nano, 2 (5), 847–56.

[40] Fuentes-García, J.A., Carvalho Alavarse, A., Moreno Maldonado, A.C., Toro-Córdova, A., Ibarra, M.R., and Goya, G.F., 2020, Simple sonochemical method to optimize the heating efficiency of magnetic nanoparticles for magnetic fluid hyperthermia, ACS Omega, 5 (41), 26357–26364.

[41] Ali Dheyab, M., Abdul Aziz, A., and Jameel, M.S., 2021, Recent advances in inorganic nanomaterials synthesis using sonochemistry: A comprehensive review on iron oxide, gold and iron oxide coated gold nanoparticles, Molecules, 26 (9), 2453.

[42] Oberacker, P., Stepper, P., Bond, D.M., Höhn, S., Focken, J., Meyer, V., Schelle, L., Sugrue, V.J., Jeunen, G.J., Moser, T., Hore, S.R., von Meyenn, F., Hipp, K., Hore, T.A., and Jurkowski, T.P., 2019, Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation, PLoS Biol., 17 (1), e3000107.

[43] Prasetya, A.D., Muflikhah, M., Lubis, W.Z., Arif, M.F., Sulungbudi, G.T., Mujamilah, M., and Insani, A., 2023, Synthesis method variations effects on magnetic-silica particles characteristics and its potential for nucleic acid adsorption, AIP Conf. Proc., 2902 (1), 080005.

[44] Anonymous, 2020, User Guide: MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit, Thermo Fisher Scientific Inc., Waltham, MA, US.

[45] Zhang, L., Shao, H.P., Zheng, H., Lin, T., and Guo, Z.M., 2016, Synthesis and characterization of Fe3O4@SiO2 magnetic composite nanoparticles by a one-pot process, Int. J. Miner. Metall. Mater., 23 (9), 1112–1118.

[46] Ding, H., Zhao, Y., Duan, Q., Wang, J., Zhang, K., Ding, G., Xie, X., and Ding, C., 2017, Efficient removal of phosphate from aqueous solution using novel magnetic nanocomposites with Fe3O4@SiO2 core and mesoporous CeO2 shell, J. Rare Earths, 35 (10), 984–994.

[47] Prasetya A.D., Fisli, A., Sulungbudi, G.T., Richtiara, G.C., Muslih, M.R., Mujamilah, M., Wildan, Z.L., Firda, Y., 2021, Effect of magnetic and silica ratio on the synthesis of magnetic mesoporous silica particles, AIP Conf. Proc., 2381 (1), 020060.

[48] Wang, J., Shah, Z.H., Zhang, S., and Lu, R., 2014, Silica-based nanocomposites via reverse microemulsions: Classifications, preparations, and applications, Nanoscale, 6 (9), 4418–4437.

[49] Ab Rahman, I., and Padavettan, V., 2012, Synthesis of silica nanoparticles by sol-gel: Size-dependent properties, surface modification, and applications in silica-polymer nanocomposites—A review, J. Nanomater., 2012, 132424.

[50] Ta, T.K.H., Trinh, M.T., Long, N.V., Nguyen, T.T.M., Nguyen, T.L.T., Thuoc, T.L., Phan, B.T., Mott, D., Maenosono, S., Tran-Van, H., and Le, V.H. 2016, Synthesis and surface functionalization of Fe3O4-SiO2 core-shell nanoparticles with 3-glycidoxypropyltrimethoxysilane and 1,1′-carbonyldiimidazole for bio-applications, Colloids Surf., A, 504, 376–383.

[51] Lee, A.H.F., Gessert, S.F., Chen, Y., Sergeev, N.V., and Haghiri, B., 2018, Preparation of iron oxide silica particles for Zika viral RNA extraction, Heliyon, 4 (3), e00572.

[52] Dahdouh, E., Lázaro-Perona, F., Romero-Gómez, M.P., Mingorance, J., and García-Rodriguez, J., 2021, Ct values from SARS-CoV-2 diagnostic PCR assays should not be used as direct estimates of viral load, J. Infect., 82 (3), 414–451.

[53] Dang, F., Enomoto, N., Hojo, J., and Enpuku, K., 2010, Sonochemical coating of magnetite nanoparticles with silica, Ultrason. Sonochem., 17 (1), 193–199.


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