Skip to main content
Biointerphases

Journal for Biophysical Chemistry

Download PDF

Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution

Biointerphases volume 2, pages 80–88 (2007)Cite this article

Abstract

Peptide nucleic acids (PNAs) are mimics of oligonucleotides containing a neutral peptidelike backbone and are able to bind complementary DNA targets with high affinity and selectivity. In order to investigate the effect of the ionic strength of the buffer solution, hybridization experiments with PNAs as (catcher) probes and DNAs as target oligonucleotides were performed in different salt solutions. Surface plasmon field-enhanced fluorescence spectroscopy was employed for real-time monitoring of DNA hybridizations to surface bound PNA. Probes with three different strand lengths were immobilized by self-assembly on the sensor surface. By introducing Cy5-labeled DNA targets the affinity constants, K A=k on (association)/k off (dissociation), were determined for fully complementary (MM0) as well as for single base mismatched (MM1) duplexes. Furthermore, the thermal stability of each duplex was determined by measuring melting curves in solution which was then compared to the kinetic and affinity parameters determined for the surface hybridization reactions. The results indicate that ions do not play a significant role for the PNA/DNA hybridization kinetics at surfaces. However, changes in the configuration of the PNA/DNA duplex due to the ionic strength variations influence the fluorescence yield drastically.

References

  1. D. R. Thévenot, K. Toth, R. A. Dust, and G. S. Wilson, Pure Appl. Chem. 71, 2333 (1999).

    Article  Google Scholar 

  2. S. Löfås, M. Malmqvist, I. Rönnberg, E. Stenberg, B. Liedberg, and I. Lundström, Sens. Actuators B 5, 79 (1991).

    Article  Google Scholar 

  3. R. Cush, J. M. Cronin, W. J. Steward, C. H. Maule, J. Molloy, and N. J. Goddard, Biosens. Bioelectron. 8, 347 (1993).

    Article  CAS  Google Scholar 

  4. A. Bernard and H. R. Bosshard, Eur. J. Biochem. 230, 416 (1995).

    Article  CAS  Google Scholar 

  5. D. J. van den Heuvel, R. P. Kooyman, H. J. W. Drijfhout, and G. W. Welling, Anal. Biochem. 215, 223 (1993).

    Article  Google Scholar 

  6. P. Schuck, Annu. Rev. Biophys. Biomol. Struct. 26, 541 (1997).

    Article  CAS  Google Scholar 

  7. J. H. Lakey and E. M. Raggett, Curr. Opin. Struct. Biol. 8, 119 (1998).

    Article  CAS  Google Scholar 

  8. S. J. Wood, Microchem. J. 47, 330 (1993).

    Article  CAS  Google Scholar 

  9. P. Nilsson, B. Persson, M. Uhlen, and P. A. Nygren, Anal. Biochem. 224, 400 (1995).

    Article  CAS  Google Scholar 

  10. M. Gotoh, Y. Hasegawa, Y. Shinohara, M. Shimizu, and M. Tosu, DNA Res. 2, 285 (1995).

    Article  CAS  Google Scholar 

  11. T. Herne and M. Tarlov, J. Am. Chem. Soc. 119, 8916 (1997).

    Article  CAS  Google Scholar 

  12. K. K. Jensen, H. Ørum, P. E. Nielsen, and B. Norden, Biochemistry 36, 5072 (1997).

    Article  CAS  Google Scholar 

  13. E. Kai, S. Sawata, K. Ikebukuro, T. Iida, T. Houda, and I. Karube, Anal. Chem. 71, 796 (1999).

    Article  CAS  Google Scholar 

  14. D. Piscevic, R. Lawall, M. Veith, M. Liley, Y. Okahata, and W. Knoll, Appl. Surf. Sci. 90, 425 (1995).

    Article  CAS  Google Scholar 

  15. T. Liebermann and W. Knoll, Colloids Surf., A 171, 115 (2000).

    Article  CAS  Google Scholar 

  16. T. Neumann, M.-L. Johansson, D. Kambhampati, and W. Knoll, Adv. Funct. Mater. 12, 575 (2002).

    Article  CAS  Google Scholar 

  17. W. Knoll, M. Liley, D. Piscevic, J. Spinke, and M.-J. Tarlov, Adv. Biophys. 34, 231 (1996).

    Article  Google Scholar 

  18. D. Kambhampati, P.-E. Nielsen, and W. Knoll, Biosens. Bioelectron. 16, 1109 (2001).

    Article  CAS  Google Scholar 

  19. W. Knoll, H. Park, E.-K. Sinner, D. Yao, and F. Yu, Surf. Sci. 570, 30 (2004).

    Article  CAS  Google Scholar 

  20. D. Yao, F. Yu, J. Kim, J. Scholz, P. Nielsen, E. K. Sinner, and W. Knoll, Nucleic Acids Res. 32, 177 (2004).

    Article  Google Scholar 

  21. P.-E. Nielsen, M. Egholm, R.-H. Berg, and O. Buchardt, Science 254, 1497 (1991).

    Article  CAS  Google Scholar 

  22. J. Anastassopoulou, J. Mol. Struct. 651, 19 (2003).

    Article  Google Scholar 

  23. N. M. Luscombe, R. A. Laskowski, and J. M. Thornton, Nucleic Acids Res. 29, 2860 (2001).

    Article  CAS  Google Scholar 

  24. A. K. Todd, A. Adams, J. H. Thorpe, W. A. Denny, L. P. Wakelin, and C. J. Cardin, J. Med. Chem. 25, 536 (1999).

    Article  Google Scholar 

  25. J. Liu, L. Malinina, T. Huynh-Dinh, and J. A. Subirana, FEBS Lett. 438, 211 (1998).

    Article  CAS  Google Scholar 

  26. Y. Gao, M. Sriram, and A. H.-J. Wang, Nucleic Acids Res. 21, 4093 (1993).

    Article  CAS  Google Scholar 

  27. L. Rulisek and Z. Havlas, J. Am. Chem. Soc. 122, 10428 (2000).

    Article  CAS  Google Scholar 

  28. V. Tereshko, C. J. Wilds, G. Minasov, T. P. Prakash, M. A. Maier, A. Howard, Z. Wawrzak, M. Manoharan, and M. Egli, Nucleic Acids Res. 29, 1208 (2001).

    Article  CAS  Google Scholar 

  29. M. Egholm, O. Buchardt, and L. E. A. Christensen, Nature (London) 365, 566 (1993).

    Article  CAS  Google Scholar 

  30. P. E. Nielsen, Curr. Opin. Biotechnol. 10, 71 (1999).

    Article  CAS  Google Scholar 

  31. A. Germini, A. Mezzelani, F. Lesignoli, R. Corradini, R. Marchelli, R. Bordoni, C. Consolandi, and G. De Bellis, J. Agric. Food Chem. 52, 4535 (2004).

    Article  CAS  Google Scholar 

  32. S. Sawata, E. Kai, K. Ikebukuro, T. Iida, T. Honda, and I. Karube, Biosens. Bioelectron. 14, 397 (1999).

    Article  CAS  Google Scholar 

  33. G. Feriotto, R. Corradini, S. Sforza, C. Mischiati, R. Marchelli, and R. Gambari, Lab. Invest. 81, 1415 (2001).

    CAS  Google Scholar 

  34. R. Corradini, G. Feriotto, S. Sforza, R. Marchelli, and R. Gambari, J. Mol. Recognit. 17, 76 (2004).

    Article  CAS  Google Scholar 

  35. W. Knoll, F.-J. Schmitt, and C. H. Klein, International Patent No. WO 92/10757 (1992).

    Google Scholar 

  36. J. Spinke, M. Liley, F. J. Schmitt, H. J. Guder, L. Angermaier, and W. Knoll, J. Chem. Phys. 99, 7012 (1993).

    Article  CAS  Google Scholar 

  37. J. Spinke, M. Liley, H. J. Guder, L. Angermaier, and W. Knoll, Langmuir 9, 1821 (1993).

    Article  CAS  Google Scholar 

  38. T. Liebermann, W. Knoll, P. Sluka, and R. Herrmann, Colloids Surf., A 169, 337 (2000).

    Article  CAS  Google Scholar 

  39. I. Langmuir, J. Am. Chem. Soc. 40, 1361 (1918).

    Article  CAS  Google Scholar 

  40. R. Karlsson, A. Michaelsson, and L. Mattsson, J. Immunol. Methods 145, 229 (1991).

    Article  CAS  Google Scholar 

  41. S. Sforza, G. Haaima, R. Marchelli, and P. E. Nielsen, Eur. J. Org. Chem., 197 (1999).

  42. L. A. Marky and K. J. Breslauer, Biopolymers 26 1901 (1987).

    Article  Google Scholar 

  43. S. Tomac, M. Sarkar, T. Ratilanen, P. Wittung, P. E. Nielsen, B. Nordèn, and A. Graslund, J. Am. Chem. Soc. 118, 5544 (1996).

    Article  CAS  Google Scholar 

  44. U. Giesen, W. Kleider, C. Berding, A. Geiger, H. Orum, and P. E. Nielsen, Nucleic Acids Res. 2, 5004 (1998).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max-Planck-Institute for Polymer Research, Ackermannweg 10, D-55128, Mainz, Germany

    Hyeyoung Park & Wolfgang Knoll

  2. Department of Organic and Industrial Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43100, Parma, Italy

    Andrea Germini, Stefano Sforza, Roberto Corradini & Rosangela Marchelli

Authors
  1. Hyeyoung Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrea Germini
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Stefano Sforza
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Roberto Corradini
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rosangela Marchelli
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wolfgang Knoll
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wolfgang Knoll.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Park, H., Germini, A., Sforza, S. et al. Effect of ionic strength on PNA-DNA hybridization on surfaces and in solution. Biointerphases 2, 80–88 (2007). https://doi.org/10.1116/1.2746871

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1116/1.2746871