, Volume 80, Issue 3, pp 420–431 | Cite as

Micro- and nanoparticles of condensed DNA Formed in PCR with Taq polymerase and plasmid DNA as a template

  • V. N. DanilevichEmail author
  • E. A. Vasilenko
  • E. V. Pechnikova
  • O. S. Sokolova
  • E. V. Grishin
Experimental Articles


Formation of micro- and nanoparticles of condensed DNA during PCR with microbial genomic DNA or plasmid DNA as templates was reported previously. Initially, the microparticles were formed using a thermostable KlenTaq polymerase, which is a deletion variant of Taq polymerase. The present work shows that Taq polymerase is also capable of efficient formation of micro- and nanoparticles of condensed DNA in PCR. Electron microscopy revealed a number of morphological types (more than four) of microparticles produced in PCR with different reaction buffers in the presence of Taq polymerase and different plasmid DNAs as a template. In the case of some kinds of amplicons, an increase in the number of thermal cycles was shown to result in production of numerous nanowires and electron-dense spherical nanoparticles. The PCR conditions for preferential formation of discs (or ellipsoids) a few micrometers in diameter and several dozens of nanometers in thickness were determined. The structure of microparticles formed in the presence of Taq polymerase was found to depend on the level of synthesis of single-stranded DNA fragments in PCR. Experiments with nuclease S1 revealed that, along with double-stranded DNAs of the amplicon, micro- and nano-particles contained single-stranded DNA fragments, which were absolutely necessary for their formation. In light of these data, the molecular mechanism of micro- and nanoparticle formation in the course of PCR is discussed.


polymerase chain reaction (PCR) Taq polymerase KlenTaq polymerase DNA condensation microparticles and nanoparticles of condensed DNA epifluorescence microscopy electron microscopy 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Gosule, L.C. and Schellman, J.A., Compact Form of DNA Induced by Spermidine, Nature, 1976, vol. 259, pp. 333–335.PubMedCrossRefGoogle Scholar
  2. 2.
    Chattoraj, D.K., Gosule, L.C., and Schellman, J.A., DNA Condensation with Polyamines. II. Electron Microscopic Studies, J. Mol. Biol., 1978, vol. 121, pp. 327–337.PubMedCrossRefGoogle Scholar
  3. 3.
    Wilson, R.W. and Bloomfield, V.A., Counterion-Induced Condensation of Deoxyribonucleic Acid. A Light-Scattering Study, Biochemistry, 1979, vol. 18, pp. 2192–2196.PubMedCrossRefGoogle Scholar
  4. 4.
    Widom, J. and Baldwin, R.L., Cation-Induced Toroidal Condensation of DNA: Studies with Co3(NH3)6, J. Mol. Biol., 1980, vol. 144, pp. 431–453.PubMedCrossRefGoogle Scholar
  5. 5.
    Plum, G.E., Arscott, P.G., and Bloomfield, V.A., Condensation of DNA by Trivalent Cations. 2. Effects of Cation Structure, Biopolymers, 1990, vol. 30, pp. 631–43.PubMedCrossRefGoogle Scholar
  6. 6.
    Arscott, P.G., Li, A.Z., and Bloomfield, V.A., Condensation of DNA by Trivalent Cations. 1. Effects of DNA Length and Topology on the Size and Shape of Condensed Particles, Biopolymers, 1990, vol. 30, pp. 619–630.PubMedCrossRefGoogle Scholar
  7. 7.
    Arscott, P.G., Ma, S., Wenner, J.R., and Bloomfield, V.A., DNA Condensation by Cobalt Hexaamine (III) in Alcohol-Water Mixture, Biopolymers, 1995, vol. 36, pp. 345–364.PubMedCrossRefGoogle Scholar
  8. 8.
    Ma, C. and Bloomfield, V.A., Condensation of Supercoiled DNA Induced by MnCl2, Biophys. J., 1994, vol. 67, pp. 1678–1681.PubMedCrossRefGoogle Scholar
  9. 9.
    Bloomfied, V.A., Condensation of DNA by Multivalent Cations: Considerations on Mechanism, Biopolymers, 1991, vol. 31, pp. 1471–1481.CrossRefGoogle Scholar
  10. 10.
    Teif, V.B., Ligand-Induced DNA Condensation: Choosing the Model, Biophys. J., 2005, vol. 89, pp. 2574–2587.PubMedCrossRefGoogle Scholar
  11. 11.
    Kornyshev, A.A. and Leikin, S., Electrostatic Interaction between Helical Macromolecules in Dense Aggregates: an Impetus for DNA Poly- and Meso-Morphism, Proc. Natl. Acad. Sci. USA, 1998, vol. 95, no. 23, pp. 13579–13584.PubMedCrossRefGoogle Scholar
  12. 12.
    Danilevich, V.N., Petrovskaya, L.E., and Grishin, E.V., DNA Nano- and Microparticles: New Products of Polymerase Chain Reaction, Doklady AN, 2008, vol. 421, no. 1, pp. 119–122 [Doklady Biochem. Biophys., vol. 421, pp. 168–170].Google Scholar
  13. 13.
    Danilevich, V.N., Barinova, E.S., and Grishin, E.V., Microparticles from Coupled DNA Formed in the Process of Polymerase Chain Reaction, Bioorg. Khim., 2009, vol. 35, no. 2, pp. 226–238 [Russ. J. Bioorg. Chem. (Engl. Transl.), vol. 35, no. 2, pp. 207–218].PubMedGoogle Scholar
  14. 14.
    Danilevich, V.N. and Grishin, E.V., Characteristics of Microspheres Formed in PCR with Bacterial Genomic DNA or Plasmid DNA as Templates, Mikrobiologiya, 2009, vol. 78, no. 3, pp. 369–380 [Microbiology (Engl. Transl.), vol. 78, no. 3, pp. 328–338].Google Scholar
  15. 15.
    Lawyer, F.C., Stoffel, S., Saiki, R.K., Myambo, K., Drummond, R., and Gelfand, D.H., Isolation, Characterization, and Expression in Escherichia coli of the DNA Polymerase Gene from Thermus aquaticus, J. Biol. Chem., 1989, vol. 264, no. 11, pp. 6427–6437.PubMedGoogle Scholar
  16. 16.
    Barnes, W.M., The Fidelity of Taq Polymerase Catalyzing PCR Is Improved by an N-Terminal Deletion, Gene, 1992, vol. 112, no. 1, pp. 29–35.PubMedCrossRefGoogle Scholar
  17. 17.
    Danilevich, V.N., Kadykov, V.A., and Grishin, E.V., Micro- and Nanoparticles of Condensed DNA Formed in a PCR with Yeast Genomic DNA as a Template. Electron Microscopy Data, Bioorg. Khim., 2010, vol. 36, no. 3, pp. 375–386 [Russ. J. Bioorg. Chem. (Engl. Transl.), vol. 36, no. 3, pp. 344—353].PubMedGoogle Scholar
  18. 18.
    Kondrat’eva, T.F., Danilevich, V.N., Ageeva, S.N., and Karavaiko, G.I., Identification of IS Elements in Acidithiobacillus ferrooxidans Strains Grown in a Medium with Ferrous Iron or Adapted to Elemental Sulfur, Arch. Microbiol., 2005, vol. 183, pp. 401–410.PubMedCrossRefGoogle Scholar
  19. 19.
    Maniatis, T., Fritsch, E.F., and Sambrook, J., Molecular Cloning: A Laboratory Manual, Laboratory Press, 1989, pp. 17–38.Google Scholar
  20. 20.
    Danilevich, V.N., Kadykov, V.A., and Grishin, E.V., Condensed DNA Particles Formed in a PCR with Plasmid Templates: An Electron Microscopy Study, Bioorg. Khim., 2010, vol. 36, no. 4, pp. 535–546 [Russ. J. Bioorg. Chem. (Engl. Transl.), vol. 36, no. 4, pp. 497–507].PubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • V. N. Danilevich
    • 1
    Email author
  • E. A. Vasilenko
    • 1
  • E. V. Pechnikova
    • 2
  • O. S. Sokolova
    • 2
  • E. V. Grishin
    • 1
  1. 1.Shemyakin and Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
  2. 2.Shubnikov Institute of CrystallographyRussian Academy of SciencesMoscowRussia

Personalised recommendations