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.