Skip to main content
SpringerLink
Log in

Rapid, cost-effective DNA quantification via a visually-detectable aggregation of superparamagnetic silica-magnetite nanoparticles

  • Research Article
  • Published:
Nano Research Aims and scope Submit manuscript

Abstract

DNA and silica-coated magnetic particles entangle and form visible aggregates under chaotropic conditions with a rotating magnetic field, in a manner that enables quantification of DNA by image analysis. As a means of exploring the mechanism of this DNA quantitation assay, nanoscale SiO2-coated Fe3O4 (Fe3O4@SiO2) particles are synthesized via a solvothermal method. Characterization of the particles defines them to be ∼200 nm in diameter with a large surface area (141.89 m2/g), possessing superparamagnetic properties and exhibiting high saturation magnetization (38 emu/g). The synthesized Fe3O4@SiO2 nanoparticles are exploited in the DNA quantification assay and, as predicted, the nanoparticles provide better sensitivity than commercial microscale Dynabeads® for quantifying DNA, with a detection limit of 4 kilobase-pair fragments of human DNA. Their utility is proven using nanoparticle DNA quantification to guide efficient polymerase chain reaction (PCR) amplification of short tandem repeat loci for human identification.

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

Similar content being viewed by others

References

  1. Penn, S. G.; He, L.; Natan, M. J. Nanoparticles for bioanalysis. Curr. Opin. Chem. Biol. 2003, 7, 609–615.

    Article  Google Scholar 

  2. Pankhurst, Q. A.; Connolly, J.; Jones, S. K.; Dobson, J. Applications of magnetic nanoparticles in biomedicine. J. Phys. D: Appl. Phys. 2003, 36, R167–R181.

    Article  Google Scholar 

  3. Willner, I.; Katz, E. Magnetic control of electrocatalytic and bioelectrocatalytic processes. Angew. Chem. Int. Ed. 2003, 42, 4576–4588.

    Article  Google Scholar 

  4. Xu, C. J.; Xu, K. M.; Gu, H. W.; Zhong, X. F.; Guo, Z. H.; Zheng, R. K.; Zhang, X. X.; Xu, B. Nitrilotriacetic acid-modified magnetic nanoparticles as a general agent to bind histidine-tagged proteins. J. Am. Chem. Soc. 2004, 126, 3392–3393.

    Article  Google Scholar 

  5. Perez, J. M.; O’Loughin, T.; Simeone, F. J.; Weissleder, R.; Josephson, L. DNA-based magnetic nanoparticle assembly acts as a magnetic relaxation nanoswitch allowing screening of DNA-cleaving agents. J. Am. Chem. Soc. 2002, 124, 2856–2857.

    Article  Google Scholar 

  6. Laurent, S.; Forge, D.; Port, M.; Roch, A.; Robic, C.; Vander Elst, L.; Muller, R. N. Magnetic iron oxide nanoparticles: Synthesis, stabilization, vectorization, physicochemical characterizations, and biological applications. Chem. Rev. 2008, 108, 2064–2110.

    Article  Google Scholar 

  7. Frey, N. A.; Peng, S.; Cheng, K.; Sun, S. H. Magnetic nanoparticles: Synthesis, functionalization, and applications in bioimaging and magnetic energy storage. Chem. Soc. Rev. 2009, 38, 2532–2542.

    Article  Google Scholar 

  8. Huang, S.-H.; Juang, R.-S. Biochemical and biomedical applications of multifunctional magnetic nanoparticles: A review. J. Nanopart. Res. 2011, 13, 4411–4430.

    Article  Google Scholar 

  9. Gupta, A. K.; Gupta, M. Synthesis and surface engineering of iron oxide nanoparticles for biomedical applications. Biomaterials 2005, 26, 3995–4021.

    Article  Google Scholar 

  10. Suh, S. K.; Yuet, K.; Hwang, D. K.; Bong, K. W.; Doyle, P. S.; Hatton, T. A. Synthesis of nonspherical superparamagnetic particles: In situ coprecipitation of magnetic nanoparticles in microgels prepared by stop-flow lithography. J. Am. Chem. Soc. 2012, 134, 7337–7343.

    Article  Google Scholar 

  11. Drmota, A.; Drofenik, M.; Koselj, J.; Žnidaršič, A. Microemulsion method for synthesis of magnetic oxide nanoparticles. In Microemulsions-An Introduction to Properties and Applications. Najjar, R., Ed.; InTech: Croatia, 2012; pp 191–214.

    Google Scholar 

  12. Okoli, C.; Sanchez-Dominguez, M.; Boutonnet, M.; Järås, S.; Civera, C.; Solans, C.; Kuttuva, G. R. Comparison and functionalization study of microemulsion-prepared magnetic iron oxide nanoparticles. Langmuir 2012, 28, 8479–8485.

    Article  Google Scholar 

  13. Lee, J.; Lee, Y.; Youn, J. K.; Na, H. B.; Yu, T.; Kim, H.; Lee, S.-M.; Koo, Y.-M.; Kwak, J. H.; Park, H. G., et al. Simple synthesis of functionalized superparamagnetic magnetite/silic core/shell nanoparticles and their application as magnetically separable high-performance biocatalysts. Small 2008, 4, 143–152.

    Article  Google Scholar 

  14. Deng, H.; Li, X. L.; Peng, Q.; Wang, X.; Chen, J. P.; Li, Y. D. Monodisperse magnetic single-crystal ferrite microspheres. Angew. Chem. Int. Ed. 2005, 44, 2782–2785.

    Article  Google Scholar 

  15. Cheng, C. M.; Wen, Y. H.; Xu, X. F.; Gu, H. C. Tunable synthesis of carboxyl-functionalized magnetite nanocrystal clusters with uniform size. J. Mater. Chem. 2009, 19, 8782–8788.

    Article  Google Scholar 

  16. Ge, J. P.; Hu, Y. X.; Biasini, M.; Beyermann, W. P.; Yin, Y. D. Superparamagnetic magnetite colloidal nanocrystal clusters with uniform size. Angew. Chem. Int. Ed. 2007, 46, 4342–4345.

    Article  Google Scholar 

  17. Si, S. F.; Li, C. H.; Wang, X.; Yu, D. P.; Peng, Q.; Li, Y. D. Magnetic monodisperse Fe3O4 nanoparticles. Cryst. Growth Des. 2005, 5, 391–393.

    Article  Google Scholar 

  18. Wang, X.; Zhuang, J.; Peng, Q.; Li, Y. D. A general strategy for nanocrystal synthesis. Nature 2005, 437, 121–124.

    Article  Google Scholar 

  19. Jia, X.; Chen, D. R.; Jiao, X. L.; Zhai, S. M. Environmentally-friendly preparation of water-dispersible magnetite nanoparticles. Chem. Commun. 2009, 968–970.

    Google Scholar 

  20. Wang, J.; Yao, M.; Xu, G. J.; Cui, P.; Zhao, J. T. Synthesis of monodisperse nanocrystals of high crystallinity magnetite through solvothermal process. Mater. Chem. Phys. 2009, 113, 6–9.

    Article  Google Scholar 

  21. Beaven, G. H.; Holiday, E. R.; Johnson, E. A. Optical properties of nucleic acids and their components. In The Nucleic Acids. Volume 1. Chargaff, E., Davidson, J. N., Eds.; New York: Academic Press, 1955; pp 493–553.

    Google Scholar 

  22. Ahn S. J.; Costa, J.; Emanuel J. R. PicoGreen quantitation of DNA: Effective evaluation of samples pre- or post-PCR. Nucl. Acids Res., 1996, 24, 2623–2625.

    Article  Google Scholar 

  23. Sanchez J. L.; Storch, G. A. Multiplex, quantitative, real-time PCR assay for cytomegalovirus and human DNA. J. Clin. Microbiol. 2002, 40, 2381–2386.

    Article  Google Scholar 

  24. Leslie, D. C.; Li, J. Y.; Strachan, B. C.; Begley, M. R.; Finkler, D.; Bazydlo, L. A.; Barker, N. S.; Haverstick, D. M.; Utz, M.; Landers, J. P. New detection modality for label-free quantification of DNA in biological samples via superparamagnetic bead aggregation. J. Am. Chem. Soc. 2012, 134, 5689–5696.

    Article  Google Scholar 

  25. Li, J. Y.; Liu, Q.; Alsamarri, H.; Lounsbury, J. A.; Haversitick, D. M.; Landers, J. P. Label-free DNA quantification via a’ pipette, aggregate and blot’ (PAB) approach with magnetic silica particles on filter paper. Lab Chip 2013, 13, 955–961.

    Article  Google Scholar 

  26. Melzak, K. A.; Sherwood, C. S.; Turner, R. F. B.; Haynes, C. A. Driving forces for DNA adsorption to silica perchlorate solutions. J. Colloid. Interface Sci. 1996, 181, 635–644.

    Article  Google Scholar 

  27. Luger, K.; Mäder, A. W.; Richmond, R. K.; Sargent, D. F.; Richmond, T. J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 1997, 389, 251–260.

    Article  Google Scholar 

  28. Rivetti, C.; Codeluppi, S. Accurate length determination of DNA molecules visualized by atomic force microscopy: Evidence for a partial B- to A-form transition on mica. Ultramicroscopy 2001, 87, 55–66.

    Article  Google Scholar 

  29. Brunauer, S.; Emmett, P. H.; Teller, E. Adsorption of gases in multimolecular layers. J. Am. Chem. Soc. 1938, 60, 309–319.

    Article  Google Scholar 

  30. Dodson, M. H.; McClelland-Brown, E. Magnetic blocking temperatures of single-domain grains during slow cooling. J. Geophys. Res.: Solid Earth 1980, 85, 2625–2637.

    Article  Google Scholar 

  31. Andersen, J. Quantification of DNA by slot-blot analysis. MethodsMol. Biol. 1998, 98, 33–38.

    Google Scholar 

  32. Breadmore, M. C.; Wolfe, K. A.; Arcibal, I. G.; Leung, W. K.; Dickson, D.; Giordano, B. C.; Power, M. E.; Ferrance, J. P.; Feldman, S. H.; Norris, P. M., et al. Microchip-based purification of DNA from biological samples. Anal. Chem. 2003, 75, 1880–1886.

    Article  Google Scholar 

  33. Lounsbury, J. A.; Coult, N.; Miranian, D. C.; Cronk, S. M.; Haverstick, D. M.; Kinnon, P.; Saul, D. J.; Landers, J. P. An enzyme-based DNA preparation method for application to forensic biological samples and degraded. Forensic Sci. Int.: Genet. 2012, 6, 607–615.

    Article  Google Scholar 

  34. Golenberg, E. M.; Bickel, A.; Weihs, P. Effect of highly fragmented DNA on PCR. Nucl. Acids Res. 1996, 24, 5026–5033.

    Article  Google Scholar 

  35. Ginoza, W.; Zimm, B. H. Mechanisms of inactivation of deoxyribonucleic acids by heat. Proc. Natl. Acad. Sci. 1961, 47, 639–652.

    Article  Google Scholar 

  36. Lindahl, T.; Nyberg, B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 1974, 13, 3405–3410.

    Article  Google Scholar 

  37. Liu, J.; Sun, Z. K.; Deng, Y. H.; Zou, Y.; Li, C. Y.; Guo, X. H.; Xiong, L. Q.; Gao, Y.; Li, Fu. Y.; Zhao, D. Y. Highly water-dispersible biocompatible magnetite particles with low cytotoxicity stabilized by citrate groups. Angew. Chem. Int. Ed. 2009, 48, 5875–5879.

    Article  Google Scholar 

  38. Deng, Y. H.; Qi, D. W.; Deng, C. H.; Zhang, X. M.; Zhao, D. Y. Superparamagnetic high-magnetization microspheres with an Fe3O4@SiO2 core and perpendicularly aligned mesoporous SiO2 shell for removal of microcystins. J. Am. Chem. Soc. 2008, 130, 28–29.

    Article  Google Scholar 

  39. Masters, J. R.; Thomson, J. A.; Daly-Burns, B.; Reid, Y. A.; Dirks, W. G.; Packer, P.; Toji, L. H.; Ohno, T.; Tanabe, H.; Arlett, C. F. et al. Short tandem repeat profiling provides an international reference standard for human cell lines. Proc. Natl. Acad. Sci. 2001, 98, 8012–8017.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Virginia, McCormick Road, P. O. Box 400319, Charlottesville, Virginia, 22904, USA

    Qian Liu, Jingyi Li, Ibrahim Tora & James P. Landers

  2. Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia, 22908, USA

    James P. Landers

  3. Department of Mechanical Engineering, University of Virginia, Charlottesville, Virginia, 22904, USA

    James P. Landers

  4. Center for Microsystems for the Life Sciences, University of Virginia, Charlottesville, Virginia, 22904, USA

    Qian Liu, Jingyi Li & James P. Landers

  5. Department of Materials Science & Engineering, University of Virginia, P. O. Box 400745, 395 McCormick Road, Charlottesville, Virginia, 22904-4745, USA

    Hongxue Liu & Jiwei Lu

  6. Department of Chemical Engineering, University of Virginia, 123 Engineers’ Way, Charlottesville, Virginia, 22904, USA

    Matthew S. Ide, Robert J. Davis & David L. Green

Authors
  1. Qian Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jingyi Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hongxue Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ibrahim Tora
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Matthew S. Ide
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jiwei Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Robert J. Davis
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. David L. Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. James P. Landers
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to James P. Landers.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Q., Li, J., Liu, H. et al. Rapid, cost-effective DNA quantification via a visually-detectable aggregation of superparamagnetic silica-magnetite nanoparticles. Nano Res. 7, 755–764 (2014). https://doi.org/10.1007/s12274-014-0436-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12274-014-0436-9

Keywords

Search

Navigation