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Thermal equivalence of DNA duplexes without calculation of melting temperature

Nature Physics volume 2, pages 55–59 (2006)Cite this article

Abstract

The common key to nearly all processes involving DNA is the hybridization and melting of the double helix: from transmission of genetic information and RNA transcription, to polymerase chain reaction and DNA microarray analysis, DNA mechanical nanodevices and DNA computing. Selecting DNA sequences with similar melting temperatures is essential for many applications in biotechnology. We show that instead of calculating these temperatures, a single parameter can be derived from a statistical-mechanics model that conveniently represents the thermodynamic equivalence of DNA sequences. This parameter is shown to order experimental melting temperatures correctly, is much more readily obtained than the melting temperature, and is easier to handle than the numerous parameters of empirical regression models.

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Figure 1: Z ω(Λ) versus Λ order parameter ω.
Figure 2: Maximal ordering parameter ωmax versus temperature.
Figure 3: Experimental melting temperatures T m versus order parameter ωmax1/2.
Figure 4: Calculated regression coefficient a 1.

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References

  1. Prohofsky, E. W. Solitons hiding in DNA and their possible significance in RNA transcription. Phys. Rev. A 38, 1538–1541 (1988).

    Article  ADS  Google Scholar 

  2. Breslauer, K., Frank, R., Blocker, H. & Marky, L. Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA 83, 3746–3750 (1986).

    Article  ADS  Google Scholar 

  3. SantaLucia, J. Jr, Allawi, H. T. & Seneviratne, P. A. Improved nearest-neighbour parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562 (1996).

    Article  Google Scholar 

  4. Owczarzy, R. et al. Predicting sequence dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217–239 (1998).

    Article  Google Scholar 

  5. Owczarzy, R. et al. Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry 43, 3537–3554 (2004).

    Article  Google Scholar 

  6. Pancoska, P., Moravek, Z. & Moll, U. M. Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using eulerian graphs. Nucl. Acids Res. 32, 4630–4645 (2004).

    Article  Google Scholar 

  7. Peyrard, M. & Bishop, A. R. Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett. 62, 2755–2757 (1989).

    Article  ADS  Google Scholar 

  8. Dauxois, T., Peyrard, M. & Bishop, A. R. Entropy-driven DNA denaturation. Phys. Rev. E 47, R44–R47 (1993).

    Article  ADS  Google Scholar 

  9. Dauxois, T. & Peyrard, M. Entropy-driven transition in a one-dimensional system. Phys. Rev. E 51, 4027–4040 (1995).

    Article  ADS  Google Scholar 

  10. Zhang, Y.-L., Zheng, W.-M., Liu, J.-X. & Chen, Y. Z. Theory of DNA melting based on the Peyrard-Bishop model. Phys. Rev. E 56, 7100–7115 (1997).

    Article  ADS  Google Scholar 

  11. Campa, A. & Giansanti, A. Experimental tests of the Peyard-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E 58, 3585 (1998).

    Article  ADS  Google Scholar 

  12. Theodorakopoulos, N., Dauxois, T. & Peyrard, M. Order of the phase transition in models of DNA thermal denaturation. Phys. Rev. Lett. 85, 6–9 (2000).

    Article  ADS  Google Scholar 

  13. Theodorakopoulos, N., Peyrard, M. & MacKay, R. S. Nonlinear structure and thermodynamic instabilities in a one-dimensional lattice system. Phys. Rev. Lett. 93, 258101 (2004).

    Article  ADS  Google Scholar 

  14. Cule, D. & Hwa, T. Denaturation of heterogeneous DNA. Phys. Rev. Lett. 79, 2375–2378 (1997).

    Article  ADS  Google Scholar 

  15. Blake, R. & Delcourt, S. Thermal stability of DNA. Nucl. Acids Res. 26, 3323–3332 (1998).

    Article  Google Scholar 

  16. Wu, P., Nakano, S. & Sugimoto, N. Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation. Eur. J. Biochem. 269, 2821–2830 (2002).

    Article  Google Scholar 

  17. Tikhomirova, A., Taulier, N. & Chalikian, T. V. Energetics of nucleic acid stability: The effect of ΔC P . J. Am. Chem. Soc. 126, 16387–16394 (2004).

    Article  Google Scholar 

  18. Wartell, R. M. & Benight, A. S. Thermal denaturation of DNA molecules: a comparison of theory with experiment. Phys. Rep. 126, 67–107 (1985).

    Article  ADS  Google Scholar 

Download references

Acknowledgements

This work was supported by Research Councils UK through the Basic Technology Programme.

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Authors and Affiliations

  1. School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK

    Gerald Weber, Niall Haslam, Nava Whiteford, Jonathan W. Essex & Cameron Neylon

  2. School of Electronics and Computer Science, University of Southampton, Southampton, SO17 1BJ, UK

    Adam Prügel-Bennett

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  1. Gerald Weber
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Correspondence to Gerald Weber.

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Weber, G., Haslam, N., Whiteford, N. et al. Thermal equivalence of DNA duplexes without calculation of melting temperature. Nature Phys 2, 55–59 (2006). https://doi.org/10.1038/nphys189

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