Skip to main content
SpringerLink
Log in

Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?

  • Research Protocol
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

An automated nucleic acid extraction procedure with magnetic particles originally designed for isolation of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from animal tissues was tested for plant material. We isolated genomic DNA and total RNA from taxonomically diverse plant species representing conifers (Scots pine), broad-leaved trees (silver birch and hybrid aspen), dwarf shrubs (bilberry), and both monocotyledonous (regal lily) and dicotyledonous (Saint John’s wort, round-leaved sundew, and tobacco) herbaceous plants. Buffers developed for DNA extraction were successfully used in addition to manufacturer’s extraction kits. The quality of RNA was appropriate for many applications, but the quality of DNA was not always sufficient for polymerase chain reaction (PCR) amplification. However, we could strikingly improve the quality by eliminating the adherent compounds during the extraction or later in the PCR phase. Our results show that the use of the procedure could be extended to diverse plant species. This procedure is especially suitable for small sample sizes and for simultaneous processing of many samples enabling large-scale plant applications in population genetics, or in the screening of putative transgenic plants.

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.

Similar content being viewed by others

References

  1. Do, N. and Adams, R. P. (1991) A simple technique for removing plant polysaccharide contaminants from DNA. Biotechniques 10, 162–166.

    PubMed  CAS  Google Scholar 

  2. Demeke, T. and Adams, R. P. (1992) The effects of plant polysaccharides and buffer additives on PCR. Biotechniques 12, 332–334.

    PubMed  CAS  Google Scholar 

  3. John, M. E. (1992) An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res. 20, 2381.

    Article  PubMed  CAS  Google Scholar 

  4. Levi, A., Galau, G. A., and Wetzstein, H. Y. (1992) A rapid procedure for the isolation of RNA from high-phenolic-containing tissue of pecan. HortSci. 27, 1316–1318.

    CAS  Google Scholar 

  5. Chang, S., Puryear, J., and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Reptr. 11, 113–116.

    CAS  Google Scholar 

  6. Rogers, S. O. and Benedich, A. J. (1994) Extraction of total cellular DNA from plants, algae and fungi. In Plant Molecular Biology Manual. Gelvin, S. B. and Schilerpoort, R. A., eds., Kluwer Academic, Dordrecht, The Netherlands, pp. D1, 1–8.

    Google Scholar 

  7. Kim, C. S., Lee, C. H., Shin, J. S., Chung, Y. S., and Hyung, N. I. (1997) A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucleic Acids Res. 25, 1085, 1086.

    Article  PubMed  CAS  Google Scholar 

  8. Kiefer, E., Heller, W., and Ernst, D. (2000) A simple and efficient protocol for isolation of functional RNA from plant tissues rich in secondary metabolites. Plant Mol. Biol. Reptr. 18, 33–39.

    CAS  Google Scholar 

  9. Rodriques-Pousada, R., Van Montagu, M., and Van der Straeten, D. (1990) A protocol for preparation of total RNA from fruit. Technique 2, 292–294.

    Google Scholar 

  10. Hultman, T., Stahl, S., Hornes, E., and Uhlen, M. (1989) Direct solid phase sequencing of genomic and plasmid DNA using magnetic beads as solid support. Nucleic Acids Res. 18, 5107–5112.

    Article  Google Scholar 

  11. Gelsthorpe, A. R., Gelsthorpe, K., and Sokol, R. J. (1997) Extraction of DNA using monoclonal anti-DNA and magnetic beads. Biotechniques 22, 1080–1082.

    PubMed  CAS  Google Scholar 

  12. Rudi, K., Kroken, M., Dahlberg, O. J., Deggerdal, A., Jakobsen, K. S., and Larsen F. (1997) Rapid, universal method to isolate PCR-ready DNA using magnetic beads. Biotechniques 22, 506–511.

    PubMed  CAS  Google Scholar 

  13. Karrer, E. E., Lincoln, J. E., Hogenhout S., et al. (1995) In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proc. Natl. Acad. Sci. USA 92, 3814–3818.

    Article  PubMed  CAS  Google Scholar 

  14. Heinrich, T., Washer, S., Marshall, J., Jones, M. G., and Potter, R. H. (1997). Subtractive hybridization of cDNA from small amounts of plant tissue. Mol. Biotechnol. 8, 7–12.

    PubMed  CAS  Google Scholar 

  15. Obata, K., Segawa, O., Yakabe, M., et al. (2001) Development of a novel method for operating magnetic particles, Magtration Technology, and its use for automating nucleic acid purification. J. Biosci. Bioeng. 91, 500–503.

    Article  PubMed  CAS  Google Scholar 

  16. Dilwort, E. and Frey, J. (2000) A rapid method for high throughput DNA extraction from plant material for PCR amplification. Plant Mol. Biol. Reptr. 18, 61–64.

    Google Scholar 

  17. Edwards, K., Johnstone, C., and Thompson, C. (1991). A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res. 19, 1349.

    Article  PubMed  CAS  Google Scholar 

  18. Pich, U. and Schubert, I. (1993). Midiprep method for isolation of DNA from plants with a high content of polyphenolics. Nucleic Acids Res. 21, 3328.

    Article  PubMed  CAS  Google Scholar 

  19. Wang, G. L., Wing, R. A., and Paterson, A. H. (1993) PCR amplification from single seeds, facilitating DNA marker-assisted breeding. Nucleic Acids Res. 21, 2527.

    Article  PubMed  CAS  Google Scholar 

  20. Kreike, J. (1990) Genetic analysis of forest tree populations: isolation of DNA from spruce and fir apices. Plant Mol. Biol. 14, 877–879.

    Article  PubMed  CAS  Google Scholar 

  21. McCarthy, P. L., Hansen, J. L., Zemetra, R. S., and Berger, P. H. (2002) Rapid identification of transformed wheat using a half-seed PCR assay. Biotechniques 32, 560–564.

    PubMed  CAS  Google Scholar 

  22. Jaakola, L., Pirttilä, A. M., Halonen, M., and Hohtola, A. (2001) Isolation of high quality RNA from bilberry (Vaccinium myrtillus L.) fruit. Mol. Biotechnol. 19, 201–203.

    Article  PubMed  CAS  Google Scholar 

  23. Pirttilä, A. M., Hirsikorpi, M., Kämäräinen, T., Jaakola, L., and Hohtola, A. (2001) DNA isolation methods for medical and aromatic plants. Plant Mol. Biol. Reptr. 19, 273a-f.

    Article  Google Scholar 

  24. Klopfenstein, N. B., Chun, Y. W., Kim, M. S., and Ahuja, M. R. (1997) Micropropagation, Genetic Engineering, and Molecular Biology of Populus. Rocky Mountain Forest and Range Experiment Station, Fort Collins, CO.

    Google Scholar 

  25. Bradshaw, H. D., Jr., Ceulemans R., Davis, J., and Stettler, R. (2000) Emerging model systems in plant biology: poplar (Populus) as a model forest tree. J. Plant Growth Regul. 19, 306–313.

    Article  CAS  Google Scholar 

  26. Aljanabi, S. M. and Martinez, I. (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25,4692,4693.

    Article  PubMed  CAS  Google Scholar 

  27. Aronen, T. S., Nikkanen, T. O., and Häggman, H. M. (2003) The production of transgenic Scots pine (Pinus sylvestris L.) via the application of transformed pollen in controlled crossing. Transgenic Res. 12, 375–378.

    Article  PubMed  CAS  Google Scholar 

  28. Helariutta, Y., Elomaa, P., Kotilainen, M., Griesbach, R. J., Schröder, J., and Teeri, T. H. (1995) Chalcone synthase-like genes active during corolla development are differentially expressed and encode enzymes with different catalytic properties in Gerbera hybrida (Asteraceae). Plant Mol. Biol. 28, 47–60.

    Article  PubMed  CAS  Google Scholar 

  29. Jaakola, L., Määttä, K., Pirttilä, A. M., Törrönen, R., Kärenlampi, S., and Hohtola, A. (2002) Expression of genes involved in anthocyanin biosynthesis in relation to anthocyanin, proanthocyanidin, and flavonol levels during bilberry fruit development. Plant Physiol. 130, 729–739.

    Article  PubMed  CAS  Google Scholar 

  30. Aronen, T. and Häggman, H. (1995) Differences in Agrobacterium infections in silver birch and Scots pine. Eur. J. For. Path. 25, 197–213.

    Google Scholar 

  31. Piispanen, R., Aronen, T., Chen, X., Saranpää, P., and Häggman, H. (2003). Silver birch (Betula pendula) plants with aux and rol genes show consistent changes in morphology, xylem structure and chemistry. Tree Phys. 23, 721–733.

    CAS  Google Scholar 

  32. Bekesiova, I., Nap, J. P., and Mlynarova, L. (1999) Isolation of high quality DNA and RNA from leaves of the carnivorous plant Drosera rotundifolia. Plant Mol. Biol. Reptr. 17, 269–277.

    Article  CAS  Google Scholar 

  33. Niemi, K. (2002) Ectomycorrhizal fungi and exogenous growth regulators in vegetative propagation of Scots pine (Pinus sylvestris L.). PhD thesis, Kuopio University Publications C. Natural and Environmental Sciences, Finland.

    Google Scholar 

  34. Stulnig, T. M. and Amberger, A. (1994) Exposing contaminating phenol in nucleic acid preparations. Biotechniques 16, 403, 404.

    Google Scholar 

  35. Glasel, J. A. (1995) Validity of nucleic acid purities monitored by 260 nm/280 nm absorbance ratios. Biotechniques 18, 62, 63.

    PubMed  CAS  Google Scholar 

  36. Pikaart, M. J. and Villeponteau, B. (1993) Suppression of PCR amplification by high levels of RNA. Biotechniques 14, 24, 25.

    PubMed  CAS  Google Scholar 

  37. Stewart, C. N. and Via, L. E. (1993) A rapid CTAB DNA isolation technique useful for RAPD finger-printing and other PCR applications. Biotechniques 14, 748–750.

    PubMed  CAS  Google Scholar 

  38. Koonjul, P. K., Brand, W. F., Farrant, J. M., and Lindsey, G. G. (1999) Inclusion of polyvinylpyrrolidone in the polymerase chain reaction reverses the inhibitory effects of polyphenolic contamination of RNA. Nucleic Acids Res. 27, 915, 916.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biology, University of Oulu, PO Box 3000, FIN-90014, Oulu, Finland

    Jaana Vuosku, Laura Jaakola, Soile Jokipii, Katja Karppinen, Terttu Kämäräinen, Veli-Pekka Pelkonen, Anne Jokela, Anja Hohtola & Hely Häggman

  2. Parkano Research Center, Finnish Forest Research Institute, Finland

    Tytti Sarjala

Authors
  1. Jaana Vuosku
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laura Jaakola
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Soile Jokipii
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Katja Karppinen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Terttu Kämäräinen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Veli-Pekka Pelkonen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anne Jokela
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tytti Sarjala
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Anja Hohtola
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hely Häggman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jaana Vuosku.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vuosku, J., Jaakola, L., Jokipii, S. et al. Does extraction of DNA and RNA by magnetic fishing work for diverse plant species?. Mol Biotechnol 27, 209–215 (2004). https://doi.org/10.1385/MB:27:3:209

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1385/MB:27:3:209

Index Entries

Search

Navigation