Advertisement

Thermodynamics of PNA Interactions with DNA and RNA

  • Tommi Ratilainen
  • Bengt Nordén
Part of the Methods in Molecular Biology book series (MIMB, volume 208)

Abstract

Thermodynamic properties of peptide nucleic acids (PNA) and their complexes with nucleic acids have attracted increasing attention. More detailed thermodynamic information is desired in order to understand and improve the behavior of PNAs in various contexts, e.g., in the design of polymerase chain reaction (PCR) probes and potentially for the use of PNA in therapeutics. The ultimate goal is to predict the thermodynamic properties of PNA-nucleic acid complexes of any sequence. For DNA and RNA thermodynamics, this has been achieved for relatively short (10–30 base pairs) doublestranded complexes (duplexes). These studies have yielded nearest neighbor parameters (ΔH° and ΔS°) for all possible combinations of base pairs in DNA and RNA (1), as well as for single mismatches in DNA (2).

Keywords

Differential Scanning Calorimetry Thermodynamic Parameter Melting Curve Single Strand Peptide Nucleic Acid 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Turner D. H. (1996) Thermodynamics of base-pairing. Curr. Opin. Struct. Biol. 6, 299–304.PubMedCrossRefGoogle Scholar
  2. 2.
    Peyret N., Seneviratne P. A., Allawi H. T., and SantaLucia J. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G, and T·T mismatches. Biochemistry 38, 3468–3477.PubMedCrossRefGoogle Scholar
  3. 3.
    Egholm M., Buchardt O., Christensen L., Behrens C., Freier S. M., Driver D. A., et al. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules. Nature 365, 566–568.PubMedCrossRefGoogle Scholar
  4. 4.
    Tomac S., Sarkar M., Ratilainen T., Wittung P., Nielsen P. E., Nordén B., and Gräslund A. (1996) Ionic effects on the stability and conformation of peptide nucleic acid (PNA) complexes. J. Am. Chem. Soc. 118, 5544–5552.CrossRefGoogle Scholar
  5. 5.
    Ratilainen T., Holmén A., Tuite E., Haaima G., Christensen L., Nielsen P. E., and Nordén B. (1998) Hybridization of peptide nucleic acid. Biochemistry 37, 12,331–12,342.PubMedCrossRefGoogle Scholar
  6. 6.
    Ratilainen T., Holmén A., Tuite E., Nielsen P. E., and Nordén B. (2000) Thermodynamics of sequence-specific binding of PNA to DNA. Biochemistry 39, 7781–7791.PubMedCrossRefGoogle Scholar
  7. 7.
    Eriksson M. and Nielsen P. E. (1996) PNA nucleic acid complexes. Structure, stability and dynamics. Q. Rev. Biophys. 29, 369–394.PubMedCrossRefGoogle Scholar
  8. 8.
    Giesen U., Kleider W., Berding C., Geiger A., Ørum H., and Nielsen P. E. (1998) A formula for thermal stability (Tm) prediction of PNA/DNA duplexes. Nucleic Acids Res. 26, 5004–5006.PubMedCrossRefGoogle Scholar
  9. 9.
    KilsÅ Jensen K., Ørum H., Nielsen P. E., and Nordén B. (1997) Kinetics for hybridization of Peptide Nucleic Acids (PNA) with DNA and RNA studied with the BIAcore technique. Biochemistry 36, 5072–5077.CrossRefGoogle Scholar
  10. 10.
    Marky L. A. and Breslauer K. J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26, 1601–1620.PubMedCrossRefGoogle Scholar
  11. 11.
    Puglisi J. D. and Tinoco J. I. (1989) Absorbance melting curves of RNA. Methods Enzymol. 180, 304–325.PubMedCrossRefGoogle Scholar
  12. 12.
    Noble S. A., Bonham M. A., Bisi J. E., Bruckenstein D. A., Brown P. H., Brown S. C., et al. (1995) Impact of biophysical parameters on the biological assessment of peptide nucleic-acids, antisense inhibitors of gene-expression. Drug Dev. Res. 34, 184–195.CrossRefGoogle Scholar
  13. 13.
    Gildea B. D., Casey S., MacNeill J., Perry-O’Keefe H., Sørensen D., and Coull J. M. (1998) PNA solubility enhancers. Tetrahedr. Lett. 39, 7255–7258.CrossRefGoogle Scholar
  14. 14.
    Sjöback R., Nygren J., and Kubista M. (1995) Absorption and fluorescence properties of fluorescein. Spectroch. Acta Part A 51, L7–L21.CrossRefGoogle Scholar
  15. 15.
    Dawson R. M. C., Elliott D. C., Elliott W. H., and Jones K. M. (1986) Data for Biochemical Research, 3rd ed. Oxford University Press, New York.Google Scholar
  16. 16.
    Holmén A. and Nordén B. (1999) Thermodynamics of PNA-nucleic acid interactions, in Peptide Nucleic Acids: Protocols and Applications (Nielsen P. E., and Egholm M., eds.) Horizon Scientific Press, Wymondham, UK, pp 87–97.Google Scholar
  17. 17.
    Cantor C. R. and Schimmel P. R. (1980) Biophysical Chemistry part 3: The Behaviour of Biological Macromolecules. W. H. Freeman, New York.Google Scholar
  18. 18.
    SantaLucia J., Allawi H. T., and Seneviratne A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562.PubMedCrossRefGoogle Scholar
  19. 19.
    Allawi H. T. and SantaLucia J. (1998) Nearest neighbor thermodynamic parameters for internal GA mismatches in DNA. Biochemistry 37, 2170–2179.PubMedCrossRefGoogle Scholar
  20. 20.
    Bevington P. R. (1969) Data Reduction an Error Analysis for the Physical Sciences. McGraw-Hill, New York.Google Scholar
  21. 21.
    Breslauer K. J., Frank R., Blöcker H., and Marky L. A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746–3750.PubMedCrossRefGoogle Scholar
  22. 22.
    Lundbäck T. and Härd T. (1994) Sequence specific DNA-binding dominated by dehydration. Proc. Natl. Acad. Sci. USA 93, 4754–4759.CrossRefGoogle Scholar
  23. 23.
    Sen S. and Nilsson L. (2001) MD simulations of homomorphous PNA, DNA, and RNA singles strands: Characterization and comparison of conformations and dynamics. J. Am. Chem. Soc. 123, 7414–7422.PubMedCrossRefGoogle Scholar
  24. 24.
    Vesnaver G. and Breslauer K. J. (1991) The contribution of DNA single-stranded order to the thermodynamics of duplex formation. Proc. Natl. Acad. Sci. USA 88, 3569–3573.PubMedCrossRefGoogle Scholar
  25. 25.
    Chakrabarti M. C. and Schwarz F. P. (1999) Thermal stability of PNA/DNA and DNA/DNA duplexes by differential scanning calorimetry. Nucleic Acids Res. 27, 4801–4806.PubMedCrossRefGoogle Scholar
  26. 26.
    Haynie D. T. (1998) in Biocalorimetry: Applications of Calorimetry in the Biological Sciences (Ladbury J. E., and Chowdhry B. Z., eds.), John Wiley & Sons, Chichester, UK, 183–205.Google Scholar
  27. 27.
    Von Hippel P. H. and Schleich T. (1969) Structure and stability of biological macromolecules, in Biological Macromolecules, (Timasheff S. N. and Fasman G., eds.), Marcel Dekker, New York, pp. 417–574.Google Scholar
  28. 28.
    Bloomfield V., and Carpenter I. L. (1993) Biological polyelectrolytes, in Polyelectrolytes; Science and Technology (Hara M., ed.), Marcel Dekker, New York, pp. 77–125.Google Scholar
  29. 29.
    Collins K. D. and Washabaugh M. W. (1985) The Hofmeister effect and the behaviour of water at interfaces. Q. Rev. Biophys. 18, 323–422.PubMedCrossRefGoogle Scholar
  30. 30.
    Record M. T., Jr. (1975) Effects of Na+ and Mg2+ ions on the helixcoil transition of DNA. Biopolymers 14, 2137–2158.CrossRefGoogle Scholar
  31. 31.
    Krakauer H. and Sturtevant J. M. (1968) Heats of the helix-coil transitions of the poly A-poly U complexes. Biopolymers 6, 491–512.PubMedCrossRefGoogle Scholar
  32. 32.
    Record M. T., Jr. (1967) Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH. Biopolymers 5, 975–992.PubMedCrossRefGoogle Scholar
  33. 33.
    Igloi G. L. (1998) Variability in the stability of DNA-peptide nucleic acid (PNA) single-base mismatched duplexes: Real-time hybridization during affinity electrophoresis in PNA-containing gels. Proc. Natl. Acad. Sci. USA 95, 8562–8567.PubMedCrossRefGoogle Scholar
  34. 34.
    Allawi H. T. and SantaLucia J. (1997) Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 36, 10581–10594.PubMedCrossRefGoogle Scholar
  35. 35.
    Aboul-ela F., Koh D., and Tinoco I. J. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 13, 4811–4824.PubMedCrossRefGoogle Scholar
  36. 36.
    Allawi H. T. and SantaLucia J. (1998) Nearest-neighbor thermodynamics of internal A center dot C mismatches in DNA: sequence dependence and pH effects. Biochemistry 37, 9435–9444.PubMedCrossRefGoogle Scholar
  37. 37.
    Gilli P., Ferretti V., Gilli G., and Borea P. A. (1994) Enthalpyentropy compensation in drug-receptor binding. J. Phys. Chem. 98, 1515–1518.CrossRefGoogle Scholar
  38. 38.
    Gelfand C. A., Plum G. E., Grollman A. P., Johnson F., and Breslauer K. J. (1998) The impact of an exocyclic cytosine adduct on DNA duplex properties: significant thermodynamic consequences despite modest lesion-induced structural alterations. Biochemistry 37, 12507–12512.PubMedCrossRefGoogle Scholar
  39. 39.
    Blasko A., Dempcy R. O., Minyat E. E., and Bruice T. C. (1996) Association of short-strand DNA oligomers with guanidinium-linked nucleosides. A kinetic and thermodynamic study. J. Am. Chem. Soc. 118, 7892–7899.CrossRefGoogle Scholar
  40. 40.
    Krug R. R., Hunter W. G., and Grieger R. A. (1976) Enthalpyentropy compensation. 2. Separation of the chemical from the statistical effect. J. Phys. Chem. 80, 2341–2351.CrossRefGoogle Scholar
  41. 41.
    Krug R. R., Hunter W. G., and Grieger R. A. (1976) Enthalpyentropy compensation. 1. Some fundamental statistical problems associated with the analysis of van’t Hoff and Arrhenius data. J. Phys. Chem. 80, 2335–2341.CrossRefGoogle Scholar
  42. 42.
    Chalikian T. V., Völker J., Plum G. E., and Breslauer K. J. (1999) A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques. Proc. Natl. Acad. Sci. USA 96, 7853–7858.PubMedCrossRefGoogle Scholar
  43. 43.
    Rouzina I. and Bloomfield V. A. (1999) Heat capacity effects on the melting of DNA. 1. General aspects. Biophys. J. 77, 3242–3251.PubMedCrossRefGoogle Scholar
  44. 44.
    Rouzina I. and Bloomfield V. A. (1999) Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. Biophys. J. 77, 3252–3255.PubMedCrossRefGoogle Scholar
  45. 45.
    Schwarz F. P., Robinson S., and Butler J. M. (1999) Thermodynamic comparisons of PNA/DNA and DNA/DNA hybridization reactions at ambient temperature. Nucleic Acids Res. 27, 4792–4800.PubMedCrossRefGoogle Scholar
  46. 46.
    Ratilainen T., Lincoln P., and Nordén B. (2001) A simple model for gene-targeting. Biophys. J. 81, 2876–2885.PubMedCrossRefGoogle Scholar
  47. 47.
    Zhong M., Marky L. A., Kallenbach N. R., and Kupke D. W. (1997) Thermodynamics of dT-dT base pair mismatching in linear DNA duplexes and three-arm DNA junctions. Biochemistry 36, 2485–2491.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2002

Authors and Affiliations

  • Tommi Ratilainen
    • 1
  • Bengt Nordén
    • 1
  1. 1.Department of Physical ChemistryChalmers University of TechnologyGöteborgSweden

Personalised recommendations