Melting of DNA Oligomers: Dynamical Models and Comparison with Experimental Results

Journal of Biological Physics

Volumn 24, Issue 2-4, 1999, Pages 141-155

  Campa, A ^a   Giansanti, A ^b  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^b INFM   (Italy)

Author keywords

Dissociation equilibrium; Melting; Non bonded interactions; Nonlinear models; Oligonucleotides; Short duplex DNA

Indexed keywords

EID: 0000738859     PISSN: 00920606     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1005166612156     Document Type: Review

References (27)

1. Uhlmann, E. and Peyman, A.: Antisense oligonucleotides: a new therapeutic principle, Chem. Rev. 90 (1990), 543-584.
2. Doktycz, M.J., Morris, M.D., Dormandy, S.J., Beattie, K.L. and Jacobson, K.B.: Optical melting of 128 octamer DNA duplexes, J. Biol. Chem. 270 (1995), 8439-8445.
3. SantaLucia, J. Jr., Allawi, H.T. and Seneviratne, P.A.: Improved nearest-neighbor parameters for predicting DNA duplex stability, Biochemistry 35 (1996), 3555-3562.
4. Marky, L.A. and Breslauer, K.J.: Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules, Biopolymers 21 (1982), 2185-2194.
5. Owczarzy, R., Vallone, P.M., Gallo, F.J., Paner, T.M., Lane, M.J. and Benight, A.S.: Predicting sequence-dependent melting stability of short duplex DNA oligomers, Biopolymers 44 (1997), 217-239.
6. SantaLucia, J. Jr.: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc. Natl. Acad. Sci. USA 95 (1998), 1460-1465.
7. Gaeta, G., Reiss, C., Peyrard, M. and Dauxois, T.: Simple models of non-linear DNA dynamics, Rivista del Nuovo Cimento 17 (1994), 1-48.
8. Peyrard, M. and Bishop, A.R.: Statistical mechanics of a nonlinear model for DNA denaturation, Phys. Rev. Lett. 62 (1989), 2755-2758.
9. Campa, A. and Giansanti, A.: Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains, Phys. Rev. E 58 (1998), 3585-3588.
10. Poland, D. and Scheraga, H.R.: Theory of helix-coil transition in biopolymers. New York: Academic Press (1970).
11. Wartell, R.M. and Benight, A.S.: Thermal denaturation of DNA molecules: a comparison of theory with experiment, Physics Reports 126 (1985), 67-107.
12. Dauxois, T. and Peyrard, M.: Entropy-driven transition in a one-dimensional system, Phys. Rev. E 51(1995), 4027-4040.
13. Chen, Y.Z. and Prohofsky, E.W.: Sequence and temperature effect on hydrogen bond disruption in DNA determined by a statistical analysis, Eur. Biophys. J. 25 (1996), 9-18.
14. Kool, E.T.: Circular oligonucleotides: new concepts in oligonucleotide design, Annu. Rev. Biophys. Biomol. Struct. 25 (1996), 1-28.
15. Yakushevich, L.V.: The effect of damping, external fields and inhomogeneity on the nonlinear dynamics of biopolymers, Studia Biophys. 121 (1987), 201-207.
16. Yakushevich, L.V.: Nonlinear DNA dynamics: a new model, Phys. Lett. A 136 (1989), 413-417.
17. Salerno, M.: Discrete model for DNA-promoter dynamics, Phys. Rev. A 44 (1991), 5292-5297.
18. Peyrard, M. and Dauxois T.: Role of the base sequence on the dynamics of DNA melting, in R. Gruber and M. Tomassini (eds.), Proc. 6th Joint EPS-APS International Conference on Physics Computing, Geneva: European Physical Society, 1994.
19. Dauxois, T., Peyrard, M. and Bishop, A.R.: Dynamics and thermodynamics of a nonlinear model for DNA denaturation, Phys Rev. E 47 (1993), 684-695.
20. Dauxois, T., Peyrard, M. and Bishop, A.R.: Entropy-driven DNA denaturation, Phys Rev. E 47 (1993), R44-47.
21. Cule, D. and Hwa, T.: Denaturation of heterogeneous DNA, Phys. Rev. Lett. 79 (1997), 2375-2378.
22. Zhang, Y.L., Zheng, W.M., Liu, J.X. and Chen Y.C.: Theory of DNA melting based on the Peyrard-Bishop model, Phys Rev. E 56 (1997), 7100-7115.
23. These temperatures differ by about 40 K, and their exact values depend on the solvent conditions, especially the ionic strength of the solution. This means that in any effective model, dynamical or thermodynamical, the parameters should depend on the solvent conditions.
24. Landau, L.D. and Lifshitz, E.M.: Statistical Physics. Oxford: Pergamon Press, 1980.
25. Bonincontro, A., Matzeu, M., Mazzei, F., Minoprio, A. and Pedone, F.: Influence of defects on the electrophoretic, thermodynamic and dielectric properties of a 21 base pair DNA in solution, Biochim. Biophys. Acta 1171 (1993), 288-294.
26. Barone, F., Matzeu, M., Mazzei, F. and Pedone, F.: Stability and conformation of triplex oligonucleotides formed on defective duplexes, preprint, 1998.
27. Cantor, R.C. and Schimmel, P.R.: Biophysical Chemistry. San Francisco: W. H. Freeman and Company (1980). Vol. III.