Skip to main content
SpringerLink
Log in

Evaluation of the effect of magnetic nanoparticles on extraction of genomic DNA of Escherichia coli

  • Original Paper
  • Published:
Polymer Bulletin Aims and scope Submit manuscript

Abstract

The initial step in molecular biology and genetic engineering fields are the finding of optimal methods for the extraction of the genomic DNA from microorganisms and cells. There are several methods for the extraction of bacterial DNA and the use of magnetic nanoparticles is a novel method for the isolation of nucleic acid. In the present study, the synthesized magnetic nanoparticles were used to extract the genomic DNA of Escherichia coli. In this study, the naked (Fe3O4) and coated (Fe3O4/SiO2; Fe3O4/SiO2/TiO2) magnetic nanoparticles were synthesized by precipitation methods. The purity of the product was assessed using energy-dispersive x-ray spectroscopy (EDS) and x-ray crystallography. The morphology and size of specimens were observed via field emission scanning electron microscopy (FESEM). The efficacy of the synthesized nanoparticles in genomic DNA extraction from Escherichia coli strain ATCC25922 was compared. The quality of the resulting DNA was analyzed by NanoDrop spectrophotometer, agarose gel electrophoresis, and PCR assays. According to the findings of SEM, the size of Fe3O4/SiO2/TiO2 magnetic nanoparticles was about 43.25 nm (Fe3O4/SiO2/TiO2). XRD analysis showed that the product nanoparticles were synthesized without impurities. The extraction results also showed that the purity and concentration of extracted genomic DNA by coated magnetic nanoparticles in comparison with naked magnetic nanoparticles were higher. In addition, the use of 0.4 mg of nanoparticles and 80% polyethylene glycol were optimal conditions for achieving a higher quality of DNA. According to the obtained results, the coated magnetic nanoparticles Fe3O4/SiO2/TiO2 can be used to extract genomic DNA of high quality from gram-negative bacteria.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Vesty A, Biswas K, Taylor MW, Gear K, Douglas RG (2017) Evaluating the impact of DNA extraction method on the representation of human oral bacterial and fungal communities. PloS one 12(1):e0169877

    Article  PubMed  PubMed Central  Google Scholar 

  2. Mocan T, Matea CT, Pop T, Mosteanu O, Buzoianu AD, Puia C et al (2017) Development of nanoparticle-based optical sensors for pathogenic bacterial detection. J nanobiotechnol 15(1):1–14

    Article  Google Scholar 

  3. Akbari M, Aetemady A, Firoozeh F, Yaseliani M (2017) Synthesis of AgO–TiO2 nanocomposite through a simple method and its antibacterial activities. J Mater Sci: Mater Electron 28(14):10245–10249

    CAS  Google Scholar 

  4. Neamati F, Firoozeh F, Saffari M, Zibaei M (2015) Virulence genes and antimicrobial resistance pattern in uropathogenic Escherichia coli isolated from hospitalized patients in Kashan, Iran. Jundishapur J Microbiol 8(2):23–28

    Google Scholar 

  5. Blount ZD (2015) The natural history of model organisms: The unexhausted potential of E. coli. Elife 4:e05826

    Article  PubMed  PubMed Central  Google Scholar 

  6. Tan SC, Yiap BC (2009) DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol 12(4):161–172

    Google Scholar 

  7. Abdel-Latif A, Osman G (2017) Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13(1):1–9

    Article  PubMed  PubMed Central  Google Scholar 

  8. Gong R, Li S (2014) Extraction of human genomic DNA from whole blood using a magnetic microsphere method. Int J Nanomed 9:3781

    Article  CAS  Google Scholar 

  9. Rohland N, Hofreiter M (2007) Comparison and optimization of ancient DNA extraction. Biotechniques 42(3):343–352

    Article  CAS  PubMed  Google Scholar 

  10. Danthanarayana AN, Manatunga DC, De Silva RM, Chandrasekharan NV, Nalin De Silva K (2018) Magnetofection and isolation of DNA using polyethyleneimine functionalized magnetic iron oxide nanoparticles. Royal Soc open sci 5(12):181369

    Article  CAS  Google Scholar 

  11. Wierucka M, Biziuk M (2014) Application of magnetic nanoparticles for magnetic solid-phase extraction in preparing biological, environmental and food samples. TrAC, Trends Anal Chem 59:50–58

    Article  CAS  Google Scholar 

  12. Saiyed Z, Ramchand C, Telang S (2008) Isolation of genomic DNA using magnetic nanoparticles as a solid-phase support. J Phys: Condens Matter 20(20):204153

    CAS  PubMed  Google Scholar 

  13. Jeevanandam J, Barhoum A, Chan YS, Dufresne A, Danquah MK (2018) Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations. Beilstein J Nanotechnol 9(1):1050–1074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhu N, Ji H, Yu P, Niu J, Farooq M, Akram MW et al (2018) Surface modification of magnetic iron oxide nanoparticles. Nanomaterials 8(10):810

    Article  PubMed  PubMed Central  Google Scholar 

  15. Rahnama H, Sattarzadeh A, Kazemi F, Ahmadi N, Sanjarian F, Zand Z (2016) Comparative study of three magnetic nano-particles (FeSO4, FeSO4/SiO2, FeSO4/SiO2/TiO2) in plasmid DNA extraction. Anal Biochem 513:68–76

    Article  CAS  PubMed  Google Scholar 

  16. Wei Y, Han B, Hu X, Lin Y, Wang X, Deng X (2012) Synthesis of Fe3O4 nanoparticles and their magnetic properties. Proced Eng 27:632–637

    Article  CAS  Google Scholar 

  17. Abbas M, Rao BP, Islam MN, Naga S, Takahashi M, Kim C (2014) Highly stable-silica encapsulating magnetite nanoparticles (Fe3O4/SiO2) synthesized using single surfactantless-polyol process. Ceram Int 40(1):1379–1385

    Article  CAS  Google Scholar 

  18. Farnleitner AH, Kreuzinger N, Kavka GG, Grillenberger S, Rath J, Mach RL (2000) Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the β-D-glucuronidase gene. Appl Environ Microbiol 66(4):1340–1346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Cortes-Chosan D, Griffits R (2014) Methods for extracting genomic DNA from whole blood samples: current perspectives. J. Biorepository Sci App Med 2:1–9

    Google Scholar 

  20. Min JH, Woo M-K, Yoon HY, Jang JW, Wu JH, Lim C-S et al (2014) Isolation of DNA using magnetic nanoparticles coated with dimercaptosuccinic acid. Anal Biochem 447:114–118

    Article  CAS  PubMed  Google Scholar 

  21. Yoza B, Matsumoto M, Matsunaga T (2002) DNA extraction using modified bacterial magnetic particles in the presence of amino silane compound. J Biotechnol 94(3):217–224

    Article  CAS  PubMed  Google Scholar 

  22. Frerix A, Schönewald M, Geilenkirchen P, Müller M, Kula M-R, Hubbuch J (2006) Exploitation of the coil− globule plasmid DNA transition induced by small changes in temperature, pH salt, and poly (ethylene glycol) compositions for directed partitioning in aqueous two-phase systems. Langmuir 22(9):4282–4290

    Article  CAS  PubMed  Google Scholar 

  23. Zhou Z, Kadam US, Irudayaraj J (2013) One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles. Anal Biochem 442(2):249–252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

Not applicable.

Author information

Author notes

  1. Farzaneh Firoozeh and Ala Amiri contributed equally to this work.

Authors and Affiliations

  1. Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran

    Farzaneh Firoozeh

  2. Evidence- Based Phytotherapy and Complementary Medicine Research Center, Alborz University of Medical Sciences, Karaj, Iran

    Farzaneh Firoozeh & Mohammad Zibaei

  3. Department of Biomedical Engineering, Faculty of New Sciences and Technology, University of Tehran, Tehhran, Iran

    Abed Neshan

  4. Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Science, P.O. Box 87155.111, 87154, Kashan, Iran

    Azad Khaledi

  5. Department of Parasitology and Mycology, School of Medicine, Alborz University of Medical Sciences, Karaj, 3149779453, Iran

    Mohammad Zibaei

  6. Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran

    Ala Amiri

  7. Social Determinants of Health Research Center, Kashan University of Medical Science, Kashan, Iran

    Ali Sobhani

  8. Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran

    Farzad Badmasti & Vajihe Sadat Nikbin

Authors
  1. Farzaneh Firoozeh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Abed Neshan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Azad Khaledi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mohammad Zibaei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ala Amiri
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ali Sobhani
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Farzad Badmasti
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Vajihe Sadat Nikbin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Azad Khaledi or Mohammad Zibaei.

Ethics declarations

Conflicts of interest

All authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Firoozeh, F., Neshan, A., Khaledi, A. et al. Evaluation of the effect of magnetic nanoparticles on extraction of genomic DNA of Escherichia coli. Polym. Bull. 80, 3153–3163 (2023). https://doi.org/10.1007/s00289-022-04196-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00289-022-04196-0

Keywords

Search

Navigation