Biopolym. Cell. 2010; 26(5):390-397.
Molecular Biophysics
Application of equilibrium binding model for analysis of conformational transitions in poly(rA)poly(rU) complexes with metal ions
1Blagoi Yu. P., 1Egupov S. A., 1Usenko E. L., 1Gladchenko G. O., 1Sorokin V. A.
  1. B. I. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine
    47, Prospekt Lenina, Kharkiv, Ukraine, 61103


Aim. The study is aimed at generalization of the previous experimental results on the metal ion (Mg2+, Ni2+, Cd2+) effects on conformation transitions in poly(rA)poly(rU). The objective was to find out how the type of a metal ion-polynucleotide complex influences the phase transitions and to estimate the constants (K) of ions binding to polymers of different structures. Methods. The K values were obtained upon theoretical and experimental transition temperature fitting by the least-square method with the root mean square deviation minimized through the procedure of the gradient descent in the multidimensional space. Results. Calculations of diagrams with Mg2+ are shown to permit obtaining satisfactory results if concentration-independent, mean values of constants are used. For Ni2+ and Cd2+ the concentration dependence of K must be taken into account, especially for high ion contents at which compaction of single-stranded poly(rA) emerges. It was revealed that the main factor responsible for the differences in diagrams with Ni2+ and Cd2+ is a significant distinction of their constants of binding to poly(rA) and poly(rU). Conclusions. The model theory of equilibrium binding is capable to describe adequately conformation transitions in polynucleotides in the presence of metal ions.
Keywords: phase diagrams, conformational transitions, metal ions, poly(rA), poly(rU), poly (rA)poly(rU)


[1] Blagoi Yu. P., Sorokin V. A., Bozhko G. Kh., Valeev V. A., Khomenko S. A. Effect of sodium ions and polycation impurities on DNA heat denaturation. Stud. Biophys. 1977; 65, N 1:55–67.
[2] Blagoi Yu.P., Galkin V.L., Gladchenko G.O., Kornilova S.V., Sorokin V.A., Shkorbatov A.G. Metal complexes of nucleic acids in solutions Kiev: Naukova dumka, 1991 272 p .
[3] Sorokin V. A., Valeev V. A., Gladchenko G. O., Degtyar M. V., Blagoi Yu. P. Ni2+ ion effect on conformations of single-, doubleand three-stranded homopolynucleotides containing adenine and uracil. Macromol. Biosci 2001 1, N 5 P. 191–203.
[4] Sorokin V. A., Valeev V. A., Gladchenko G. O., Degtyar M. V., Karachevtsev V. A., Blagoi Yu. P. Mg2+ ion effect on the conformational equilibrium of polyUpolyApolyU and polyApolyU in aqueous solutions Int. J. Biol. Macromol 2003 31, N 4–5:223–233.
[5] Sorokin V. A., Valeev V. A., Gladchenko G. O., Degtyar M. V., Andrus E. A., Karachevtsev V.A., Blagoi Yu. P. Mg2+ and Ni2+ ion effect on stability and structure of triple polyIpolyApolyI helix Int. J. Biol. Macromol 2005 35, N 4:201–210.
[6] Sorokin V. A., Valeev V. A., Usenko E. L., Blagoi Yu. P. Effect of Cd2+ ions on conformational equilibrium of three-stranded polyUpolyApolyU polynucleotide under near-physiological conditions. Biopolym. Cell. 2007; 23, N 5:433–440.
[7] Sorokin V. A., Valeev V. A., Usenko E. L. Ni2+ ion effect on conformational equilibrium of polynucleotides: polyA, polyU, polyA and polyU under conditions close to physiological ones Biopolym. Cell. 2008; 24, N 2:158–170.
[8] Sorokin V. A., Valeev V. A., Usenko E. L., Andrus E. A., Blagoi Yu. P. The nature of different influence of Cd2+ ions on the conformational equilibrium of triple-stranded polyribonucleotides PolyUPolyAPolyU and PolyIPolyAPolyI in aqueous solutions. Biophysics 2007 52, N 6:545–556.
[9] Andrushchenko V., Blagoi Yu. P., van de Sande J. H., Wieser H. Poly(rA)poly(rU) with Ni2+ ions at different temperatures: infrared absorption and vibrational circular dichroism spectroscopy J. Biomol. Struct. Dynam 2002 19, N 5 P. 889–906.
[10] Blagoi Yu. P., Gladchenko G. O., Nafie L. A., Freedman T. B., Sorokin V. A., He Ya. Phase equilibrium in poly(rA)poly(rU) complexes with Cd2+ and Mg2+ ions, studied by ultraviolet, infrared, and vibrational circular dichroism spectroscopy Biopolymers 2005 78, N 5–P. 275–286.
[11] Frank-Kamenetskii M. D. Consideration of helix-coil transition in homopolymers by the most probable distribution method Mol. Biol 1968 2, N 2:408–419.
[12] Frank-Kamenetskii M. D., Karapetyan A. T. To theory of melting of DNA complexes with low-molecular ligands. Mol. Biol (Mosk). 1972; 6, N 4:621–627.
[13] Lazurkin Yu. S., Frank-Kamenetskii M. D., Trifonov E. N. Melting of DNA: Its study and application as a research method Biopolymers 1970 9, N 11:1253–1306.
[14] Cantor C. R., Schimmel P. R. Biophysical Chemistry San Francisco: W. H. Freeman and Company, 1980 Part III 536 p.
[15] Stevens Ch. L., Fensenfeld G. The conversion of two-stranded poly(A+U) to three-stranded poly(A+2U) and polyA by heat. Biopolymers. 1964; 2, N 1:293–314.
[16] Krakauer H. A thermodynamic analysis of the influence of simple mono-and divalent cations on the conformational transitions of polynucleotide complexes Biochemistry 1974 13, N 12:2579–2589.
[17] Klump H. H. Energetics of order/order transition in nucleic acids Can. J. Chem 1988 66, N 4. P. 804–811.
[18] Vesnaver G., Breslauer K. J. The contribution of DNA single-stranded order to the thermodynamics of duplex formation Proc. Natl Acad. Sci. USA 1991 88, N 9:3569–3573.
[19] Wild D. D. Methods of searching for extremum (in Russia) Moscow: Nauka, 1967 268 p.
[20] Blagoi Yu. P., Egupov S. A., Usenko E. L., Sorokin V. A. Effects of different metal cations on conformational transitions in PolyrAPolyrU under concentration and temperature changes Los Alamos National Laboratory eprint ArXiv: 0904.4100 New Mexico, 2009.