Biopolymers and cell. 2007; 23 (5): 433 - 440

Effect of Cd²⁺ ions on conformational equilibrium of three-stranded polyUpolyApolyU polynucleotide under near-physiological conditions

V. A. Sorokin, V. A. Valeev, E. L. Usenko, Yu. P. Blagoi

Cd²⁺ ions effect on the conformational equilibrium of three-stranded polyUpolyApolyU polynucleotide (0.1M Na⁺, pH 7) has been studied by the method of differential UV spectroscopy. It has been revealed that Cd²⁺ ions do not bind heteroatoms of nitrogen bases of polyA and polyU being in triple (A2U) and double (AU) helices and do not change their conformation. The heating of A2U results in two subsequent processes: the first one represents separation of one strand of poly U from A2U i. e. A2U →AU + U transition (3 →2 transition) is realized, and the second one corresponds to more cooperative melting of AU, i. e. 2 →1 (U + A→ U + A + U) transition. The concentration dependences of melting temperatures for these processes have some intersection point (Tm = 60 °C; [Cd²⁺] ~ 3.5·10^–4 M) at which thermal stability of A2U and AU become identical. The theoretical calculations of concentration dependences (T_m)_3→2 revealed that the best agreement between experiment and theory is observed at ΔH_3→2 = 5 kcal/mol·triplet (ΔH – the enthalpy of transition).

Keywords: metal ions, three-stranded polynucleotides, conformational transitions.