The binding of Mg(II) and Ni(II) to synthetic polynucleotides

• Published in: Biophysical chemistry 1987-05, Vol.26 (2), p.193-205
• Main Authors: Diebler, H., Secco, F., Venturini, M.
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Interactions. Associations; Intermolecular phenomena; Kinetics; Magnesium; Metal-ion binding stability; Mg 2; Molecular biophysics; Ni 2; Nickel; Nucleic Acid Conformation; Poly A; Poly C; Poly I; Poly U; Polynucleotide; Polyribonucleotides; Relaxation kinetics
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/0301-4622(87)80022-4

Equilibria and kinetics of the interactions of Mg 2+ and Ni 2+ with poly(U), poly(C) and poly(I) have been investigated at 25°C, an ionic strength of 0.1 M, and pH 7.0 or 6.0. Analogous studies involving poly(A) were reported earlier. All binding equilibria were studied by means of the (usually small) absorbance changes in the ultraviolet range. This technique yields apparent binding constants which are fairly large for the interaction of Ni 2+ with poly(A) ( K = 0.9 × 10 4 M −1) and poly(I) ( K ≈ 2 × 10 4 M −1) but considerably lower for the corresponding Mg 2+ systems, Mg 2+-poly(A) ( K = 2 × 10 3 M −1) and Mg 2+-poly(I) ( K = 280 M −1). Each of the two pyrimidine nucleotides binds both metal ions with about the same strength ( K ≈ 65 M −1 for poly(U) and K near 600 M −1 for poly(C)). In the case of poly(C) the spectral changes deviate from those expected for a simple binding equilibrium. In addition, the binding of Ni 2+ to the four polynucleotides was measured by using murexide as an indicator of the concentration of free Ni 2+. The results obtained by this technique agree or are at least consistent with those derived from the ultraviolet spectra. Complications are encountered in the binding studies involving poly(I), particularly at higher metal ion concentrations, obviously due to the formation of aggregated poly(I) species. Kinetic studies of the binding processes were carried out by the temperature-jump relaxation technique. Measurable relaxation effects of time constants greater than μs were observed only in the systems Ni 2+-poly(A) and Ni 2+- poly(I). Such not-too-fast reaction effects are expected for processes which include inner-sphere substitution steps at Mg 2+ or Ni 2+. The relaxation process in Ni 2+-poly(I) is characterized by (at least) four time constants. Obviously, the complicated kinetics again include reactions of aggregated poly(I). The absence of detectable relaxation effects in all other systems (except Mg 2+-poly(I), the kinetics of which was not investigated) indicates that inner-sphere coordination of the metal ions to specific sites of the polynucleotides (site binding) does not occur to a significant extent. Rather, the metal ions are bound in these systems mainly by electrostatic forces, forming a mobile cloud. The differences in binding strength which are nevertheless observed are attributed to differences in the conformation of the polynucleotides which result in different charge densities.