Advertisement

Mathematical Model of the Nucleic Acids Conformational Transitions with Hysteresis over Hydration—Dehydration Cycle

Conference paper
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 4)

Abstract

A model of the conformational transitions of the nucleic acid molecule during the water adsorption-desorption cycle is proposed. The nucleic acid-water system is considered as an open system. The model describes the transitions between three main conformations of wet nucleic acid samples: A-, B- and unordered forms. The analysis of kinetic equations shows the non-trivial bifurcation behaviour of the system which leads to the multistability. This fact allows one to explain the hysteresis phenomena observed experimentally in the nucleic acid-water system. The problem of self-organization in the nucleic acid-water system is of great importance for revealing physical mechanisms of the functioning of nucleic acids and for many specific practical fields.

Keywords

Hydration Shell Conformational State Conformational Transition Adsorbed Water Molecule Hysteresis Phenomenon 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Miyazawa, T.: Conformational aspects and biological functions of biomolecules. J. Mol. Struct. 126 (1985) 493–508CrossRefGoogle Scholar
  2. 2.
    Saenger, W.: Prinsiples of nucleic acid structure. Springer-Verlag, Berlin (1984) 584CrossRefGoogle Scholar
  3. 3.
    Goodfellow, J.M., Cruzeiro-Hansson, L., Norberto de Souza, O., Parker, K., Sayle, T., Umrania, Y.: DNA structure, hydration and dynamics. Int. J. of Radiation Biology 66 (1994) 471–478CrossRefGoogle Scholar
  4. 4.
    Zehfus, M.H., Johnson, W.C.: Conformation of P-form DNA. Biopolymers 23 (1984) 1269–1281CrossRefGoogle Scholar
  5. 5.
    Maleyev, V. Ya., Semenov, M. A., Gasan, A.. L, Kashpur, V. A.: Physical propoties of the DNA-water system. Biopysics 38 (1993) 789–811Google Scholar
  6. 6.
    Krumhansl, J.A., Wysin, G.M., Alexander, D.M., Garcia, A., Lohmdahl, P.S., Layane, S.P.: In: Structure and motions: membranes, nucleic acids and proteins. (Clementi, E., Corongin, G., Sarma, M.H., Sarma, R.H., eds) Adenine Press, New York (1985) 407–415Google Scholar
  7. 7.
    Christiansen, P.L., Muto, V.: Nonlinear models of DNA dynamics. Physica D 68 (1993) 93–96zbMATHCrossRefGoogle Scholar
  8. 8.
    Volkov, S.N.: Conformational transitions and the mechanism of transmission of long-range effects in DNA. Preprint ITP-88-12E, Kiev (1988) 22Google Scholar
  9. 9.
    Krumhansl, J.A., Alexander, D.M.: Nonlinear dynamics and conformational exitations in biomolecular materials. In: Structure and dynamics: nucleic acids and proteins. (Clementi, E.; Sarma, R.H., eds) Adenine Press, New York (1983) 61–80Google Scholar
  10. 10.
    Theory of helix-coil transitions in biopolymers. (Poland, D., Scheraga, H.A., eds) Academic Press, New York (1970)Google Scholar
  11. 11.
    Eisenstein, M., Shakked, Z.: Hydrat ion patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248 (1995) 662–678CrossRefGoogle Scholar
  12. 12.
    Wetzel, R., Zirwer, D., Becker, M.: Optical anisotropy of oriented deoxyribonucleic acid films of different water content. Biopolymers 8 (1969) 391–401CrossRefGoogle Scholar
  13. 13.
    Falk, M., Hartman, K.A., Lord, R.C.: Hydration of deoxyribonucleic acid. I. A gravimetric study. J. Am. Chem. Soc. 84 (1962) 3843–3846CrossRefGoogle Scholar
  14. 14.
    Volkov, V.V., Gasan, A.L, Maleev, V.Ya.: The effect of glycerol on hysteresis phenomena in DNA. Preprint IRE-386, Kharkov (1989) 16 (in Russian)Google Scholar
  15. 15.
    Lahajnar, G., Zupancic, I., Rupprecht, A.: Proton NMR relaxation and diffusion study of water sorbed in oriented DNA and hyaluronic acid samples. In: Biophysics of Water (Pranks, F., Mathias, S., eds) Wiley, New York (1982) 231–234Google Scholar
  16. 16.
    Kochoyan, M., Leroy, J.L.: Hydration and solution structure of nucleic acids. Current Opinion in Structural Biology 5 (1995) 329–333CrossRefGoogle Scholar
  17. 17.
    Lindsay, S. M., Lee, S. A., Powell, J. M., Weidlich, T., DeMarko, C., Lewen, G. D., Tao, N. J., Rupprecht, A.: The origin of the A to B transition in DNA fibers and films. Biopolymers 27 (1988) 1015–1043CrossRefGoogle Scholar
  18. 18.
    Ivanov, V.I., Minchenkova, L.E., Minyat, E.E., Schyolkina, A.K.: Cooperative transitions in DNA with no separation of strands. Cold Spring Harbor Symposia on Quantitative Biology 47 (1983) 243–250CrossRefGoogle Scholar
  19. 19.
    Gascoyne, P.R.C., Pethig, R.: Experimental and theoretical aspects of hydration isotherms for biomolecules. J. Chem. Soc. Faradey Trans. 1 (1977) 171–180CrossRefGoogle Scholar
  20. 20.
    Starikov, E.B., Bolbukh, T.V., Semenov M.A.: The study of nucleic acid hydration isotherms. Preprint IRE-359, Kharkov (1987) 19 (in Russian)Google Scholar
  21. 21.
    d’Arcy, R.L., Watt, J.C.: Analysis of sorption isotherm of nonhomogeneous sorbents. Trans. Faraday Soc. 66 (1970) 1236–1245CrossRefGoogle Scholar
  22. 22.
    Nicolis, G., Prigogine, I.: Self-organization in nonequilibrium systems. John Willey & Sons, New York (1977) 512zbMATHGoogle Scholar
  23. 23.
    Hippel, P.H. von, Wang, K.-Y.: Dynamic aspects of native DNA structure: kinetics of the formaldehyde reaction with calf thymus DNA. J. Mol. Biol. 61 (1971) 587–613CrossRefGoogle Scholar
  24. 24.
    Porschke, D., Eigen, M.: Cooperative nonenzymic base recognition. III. Kinetics of the helix-coil transition of the oligoribouridylic oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62 (1971) 361–381CrossRefGoogle Scholar
  25. 25.
    Tolstorukov, M.Ye., Gatash, S.V., Maleev, V.Ya.: Self-organization and nonlinear dynamics of nucleic acid-water system. Special Issue of Int. J. Bif. Chaos (in press)Google Scholar
  26. 26.
    Porschke D.: Elementary steps of base recognition and helix-coil transitions in nucleic acids. Mol. Biol. Biochem. Biophys. 24 (1977) 191–218CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1999

Authors and Affiliations

  1. 1.Chair of Molecular and Applied BiophysicsKharkov State UniversityKharkovUkraine
  2. 2.Biophysics Division, Institute of Radiophysics and ElectronicsNat. Acad. Sci. of UkraineKharkovUkraine

Personalised recommendations