Ni2+ Ion Effect of Conformations on Single-, Double- and Three-Stranded Homopolynucleotides Containing Adenine and Uracil

Abstract

Differential UV and visible spectroscopy and thermal denaturation were used to study the interaction of Ni2+ ions with adenosine 5′‐monophosphate (AMP), uridine 5′‐monophosphate (UMP), single‐stranded polyadenylic acid (polyA) and polyuridylic (polyU), double‐stranded polyA/polyU (AU) and three‐stranded polyA/2 polyU (A2U). The coil → helix transition observed in polyA, AU and A2U at room temperature is induced by Ni2+ binding to the oxygen atoms of the phosphate groups which belong to the disordered single‐stranded parts of the polynucleotides. Ni2+ ions coordinate with bases only in individual AMP and single‐stranded polyA. This coordination causes disordering of the helical parts of the strands. The disordered single strands form thermally stable compact particles with effective radii of ˜100 Å. Diagrams of the phase equilibrium between single‐, double‐ and three‐stranded conformations as a function of temperature and Ni2+ concentration have been obtained. The melting ranges of A2U and AU differ considerably, mainly due to different enthalpies of their helix–coil transitions. The behaviour of the transition parameters in the presence of Ni2+ ions agrees with the data obtained from the theory of equilibrium binding. The constants of the Ni2+ binding to AU and A2U are found. The effect of Ni2+ ions upon the thermal stability of AU and A2U is connected mainly with their different binding to multi‐stranded helices and polyU. The end of melting of the double‐stranded AU formed due to the A2U → AU + U transition has the character of a second‐order phase transition.

Divalent metal ion effect on helix–coil transition of high molecular weight DNA in neutral and alkaline solutions

“…Considering that the order of magnitude for the radius of gyration of the statistical single-stranded coil is 10 3Å [29], this means that Mg 2+ ions induce the transition of single-stranded melted DNA parts into the compact form. The formation of similar compact particles by single-stranded poly(rA) and poly(rI) in the presence of Ca 2+ , Ni 2+ and Cu 2+ was observed earlier also in neutral solutions [26,30,31]. Fig.…”

“…According to Table 4, n is equal to 3.6 ± 0.2. For the UV-range of wavenumbers the differential spectrum produced solely by the changes in absorption ( A a ) was calculated by the extrapolation method [26]:…”

DNA structural transitions induced by divalent metal ions in aqueous solutions

“…The latter seems to induce the enolization of hypoxanthine and the deprotonation of N 1 , and, as a result, the transition of the four-stranded helix to single-stranded coils. Single-stranded chains form compact particles with an effective radius of about 100Å [41]. On the contrary to the IR spectra of DNA-Cu 2+ and poly(I)-Cu 2+ complexes in the IR spectra of polyphosphate (pP) complexes with Cu 2+ ions increase of the intensities of the absorption bands upon Cu 2+ ion binding was not observed (Fig.…”

DNA conformational equilibrium in the presence of Zn2+ ions in neutral and alkaline solutions

“…Differential UV (DUV) spectra A( ) were measured at room temperature T o = 25 ± 2 • C with a UV-vis spectrophotometer (Carl Zeiss, Jena, Germany) using the four-cuvette scheme [11,13]. The spectra were normalized to DNA concentration as follows:…”