Abstract
Isolation of deoxyribonucleic acid is an important step in the molecular diagnostics of microorganisms. A high quality of isolated deoxyribonucleic acid is necessary for deoxyribonucleic acid amplification by the polymerase chain reaction. The conventional deoxyribonucleic acid isolation using phenol–chloroform extraction and deoxyribonucleic acid precipitation in ethanol is time-consuming and requires the use of toxic phenol. Magnetic separation techniques using magnetic solid particles are one of modern methods to speed up the nucleic acids isolation. The aim of this work was to use two different types of magnetic particles for solid-phase deoxyribonucleic acid extraction. The amounts of deoxyribonucleic acid in separation mixtures were measured using ultraviolet spectrophotometry. The first experimental conditions were tested on chicken erythrocytes deoxyribonucleic acid. Phosphate buffer (pH 7, 7.6 and 8) was used for the adsorption of deoxyribonucleic acid on magnetic particles. Tested values of pH have no effects on deoxyribonucleic acid adsorption. It was shown that approximately almost one half of deoxyribonucleic acid was adsorbed to the particles. A number of different elution conditions (temperature, time and pH value of elution buffer) were investigated to determine their effect on elution efficiency. It was shown that only a small fraction of the bound DNA was released at 22 °C, while the release was more effective as the temperature was increased also the amount of elution deoxyribonucleic acid was more effective when time was increased. The higher amounts of deoxyribonucleic acid were eluted with TE buffer pH 9.0. Second, bacterial deoxyribonucleic acid was tested. This deoxyribonucleic acid eluted from the particles was in polymerase chain reaction ready quality.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Babic M, Horák D, Trchová M et al (2008) Poly(l-lysine)-modified iron oxide nanoparticles for stem cell labeling. Bioconjug Chem 19:740–750. https://doi.org/10.1021/bc700410z
Berensmeier S (2006) Magnetic particles for the separation and purification of nucleic acids. Appl Microbiol Biotechnol 73:495–504
Bitar A, Ahmad NM, Fessi H, Elaissari A (2012) Silica-based nanoparticles for biomedical applications. Drug Discov Today 17:1147–1154. https://doi.org/10.1016/j.drudis.2012.06.014
Borlido L, Azevedo AM, Roque ACA, Aires-Barros MR (2013) Magnetic separations in biotechnology. Biotechnol Adv 31:1374–1385. https://doi.org/10.1016/j.biotechadv.2013.05.009
Demkin VV, Koshechkin SI, Slesarev A (2017) A novel real-time PCR assay for highly specific detection and quantification of vaginal lactobacilli. Mol Cell Probes 32:33–39. https://doi.org/10.1016/j.mcp.2016.11.006
Desjardins PR, Conklin DS (2011) Microvolume quantitation of nucleic acids. Curr Protoc Mol Biol 93:1–4. https://doi.org/10.3791/2565
Ghaemi M, Absalan G (2014) Study on the adsorption of DNA on Fe3O4 nanoparticles and on ionic liquid-modified Fe3O4 nanoparticles. Microchim Acta 181:45–53. https://doi.org/10.1007/s00604-013-1040-5
Haarman M, Knol J (2006) Quantitative real-time PCR analysis of fecal lactobacillus species in infants receiving a prebiotic infant formula. Appl Environ Microbiol 72:2359–2365. https://doi.org/10.1128/AEM.72.4.2359
Hola K, Markova Z, Zoppellaro G et al (2015) Tailored functionalization of iron oxide nanoparticles for MRI, drug delivery, magnetic separation and immobilization of biosubstances. Biotechnol Adv 33:1162–1176. https://doi.org/10.1016/j.biotechadv.2015.02.003
Horák D, Španová A, Tvrdíková J, Rittich B (2011) Streptavidin-modified magnetic poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) microspheres for selective isolation of bacterial DNA. Eur Polym J 47:1090–1096. https://doi.org/10.1016/j.eurpolymj.2011.02.007
Horák D, Kučerová J, Korecká L et al (2012) New monodisperse magnetic polymer microspheres biofunctionalized for enzyme catalysis and bioaffinity separations. Macromol Biosci 12:647–655. https://doi.org/10.1002/mabi.201100393
Kang K, Choi J, Nam JH et al (2009) Preparation and characterization of chemically functionalized silica-coated magnetic nanoparticles as a DNA separator. J Phys Chem B 113:536–543
Kazemi Ashtiani M, Zandi M, Shokrollahi P et al (2018) Surface modification of poly(2-hydroxyethyl methacrylate) hydrogel for contact lens application. Polym Adv Technol 29:1227–1233. https://doi.org/10.1002/pat.4233
Kramer MF, Coen DM (2006) Enzymatic amplification of DNA by PCR: standard procedures and optimization. Curr Protoc Mol Biol 37:A.3 K.1–A.3 K.15. https://doi.org/10.1002/0471142956.cya03ks37
Křížová J, Španová A, Rittich B, Horák D (2005) Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation. J Chromatogr A 1064:247–253. https://doi.org/10.1016/j.chroma.2004.12.014
Liang G, Zhang P, Li H et al (2012) An efficient strategy for unmodified nucleotide-mediated dispersion of magnetic nanoparticles, leading to a highly sensitive MRI-based mercury ion assay. Anal Chim Acta 726:73–78. https://doi.org/10.1016/j.aca.2012.03.024
Liébana S, Brandão D, Cortés P et al (2016) Electrochemical genosensing of Salmonella, Listeria and Escherichia coli on silica magnetic particles. Anal Chim Acta 904:1–9. https://doi.org/10.1016/j.aca.2015.09.044
Liu H, Li S, Liu L et al (2010) An integrated and sensitive detection platform for biosensing application based on Fe@Au magnetic nanoparticles as bead array carries. Biosens Bioelectron 26:1442–1448. https://doi.org/10.1016/j.bios.2010.07.078
Liu M, Hu P, Zhang G et al (2015) Copy number variation analysis by ligation-dependent PCR based on magnetic nanoparticles and chemiluminescence. Theranostics 5:71–85. https://doi.org/10.7150/thno.10117
Macková H, Horák D, Trachtová Š et al (2012) The use of magnetic poly(N-isopropylacrylamide) microspheres for separation of DNA from probiotic dairy products. J Colloid Sci Biotechnol 1:235–240. https://doi.org/10.1166/jcsb.2012.1018
Prodělalová J, Rittich B, Španová A et al (2004) Isolation of genomic DNA using magnetic cobalt ferrite and silica particles. J Chromatogr A 1056:43–48. https://doi.org/10.1016/j.chroma.2004.08.090
Rahman MM, Elaissari A (2011) Temperature and magnetic dual responsive microparticles for DNA separation. Sep Purif Technol 81:286–294. https://doi.org/10.1016/j.seppur.2011.07.030
Rittich B, Španová A (2013) SPE and purification of DNA using magnetic particles. J Sep Sci 36:2472–2485. https://doi.org/10.1002/jssc.201300331
Rittich B, Španová A, Šálek P et al (2009) Separation of PCR-ready DNA from dairy products using magnetic hydrophilic microspheres and poly (ethylene glycol)–NaCl water solutions. J Magn Magn Mater 10:1667–1670. https://doi.org/10.1016/j.jmmm.2009.02.110
Rychlik W, Spencer WJ, Rhoads RE (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 18(21):6409–6412
Savo Sardaro ML, Levante A, Bernini V et al (2016) The spxB gene as a target to identify Lactobacillus casei group species in cheese. Food Microbiol 59:57–65. https://doi.org/10.1016/j.fm.2016.05.004
Schrader C, Schielke A, Ellerbroek L, Johne R (2012) PCR inhibitors–occurrence, properties and removal. J Appl Microbiol 113:1014–1026. https://doi.org/10.1111/j.1365-2672.2012.05384.x
Shan Z, Wu Q, Wang X et al (2010) Bacteria capture, lysate clearance, and plasmid DNA extraction using pH-sensitive multifunctional magnetic nanoparticles. Anal Biochem 398:120–122. https://doi.org/10.1016/j.ab.2009.11.006
Smerkova K, Dostalova S, Vaculovicova M et al (2013) Investigation of interaction between magnetic silica particles and lambda phage DNA fragment. J Pharm Biomed Anal 86:65–72. https://doi.org/10.1016/j.jpba.2013.07.039
Sun N, Deng C, Liu Y et al (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. https://doi.org/10.1016/j.chroma.2013.11.059
Tanaka T, Sakai R, Kobayashi R et al (2009) Contributions of phosphate to DNA adsorption/desorption behaviors on aminosilane-modified magnetic nanoparticles. Langmuir 25:2956–2961. https://doi.org/10.1021/la8032397
Trachtová Š, Zapletalová H, Španová A et al (2015) The evaluation of magnetic polymethacrylate-based microspheres used for solid phase DNA micro-extraction. Chromatography 2:156–166. https://doi.org/10.3390/chromatography2020156
Trachtová Š, Španová A, Horák D et al (2016) Real-time polymerase chain reaction as a tool for evaluation of magnetic poly(Glycidyl methacrylate)-based microspheres in molecular diagnostics. Curr Pharm Des. https://doi.org/10.2174/1381612822666151228105006
Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63:3741–3751
Xu L, Guo C, Wang F et al (2011) A simple and rapid harvesting method for microalgae by in situ magnetic separation. Bioresour Technol 102:10047–10051. https://doi.org/10.1016/j.biortech.2011.08.021
Xu J, Sun J, Wang Y et al (2014) Application of iron magnetic nanoparticles in protein immobilization. Molecules 19:11465–11486. https://doi.org/10.3390/molecules190811465
Acknowledgements
The financial support of internal Grant no. FCH-S-18-5334 and Academy of Sciences of the Czech Republic are gratefully acknowledged for magnetic particles provision and cooperation. We are obliged to Mrs. Lenka Burdějová for her kind language revision.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Konečná, J., Romanovská, D., Horák, D. et al. Optimalization of deoxyribonucleic acid extraction using various types of magnetic particles. Chem. Pap. 73, 1247–1255 (2019). https://doi.org/10.1007/s11696-018-00675-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11696-018-00675-9