Effects of different metal cations on conformational transitions in PolyrA PolyrU under concentration and temperature changes

TL;DR

This study models how different metal cations influence the conformational transitions of poly rA poly rU, revealing ion-specific effects on molecular structure and stability through phase diagrams and spectroscopic analysis.

Contribution

It introduces a theoretical framework for understanding ion-dependent conformational changes in polynucleotides, incorporating variable binding constants and experimental validation.

Findings

Mg2+ allows accurate phase diagram modeling with steady binding constants.

Ni2+ and Cd2+ require concentration-dependent binding constants due to molecular compaction.

Conformational transition irreversibility is clarified through spectroscopic comparisons.

Abstract

By the theory based on the equilibrium binding model, phase diagrams have been calculated for the poly rA poly rU system in the presence of Mg2+, Ni2+, Cd2+, with Na+ 0.1 M. Binding constants (KA, KU, KAU, KA2U) have been determined, the best agreement with the early experimental results being observed. Calculations of diagrams with Mg2+ are shown to permit obtaining satisfactory results if steady mean constants of ion binding to polynucleotides of all the mentioned structures are used. But in the cases with Ni2+ and Cd2+, constants dependences on ion concentrations must be taken into account, especially with high ion contents in the presence of which compaction of molecules of single-stranded poly A emerges. It has been revealed that the main factor being responsible for differences in diagrams for Ni2+ and Cd2+ is a significant variation of their constants of binding to poly A. Temperature dependences of conformational transitions obtained by UV spectroscopy for low polymer concentrations are compared with those obtained by IR and VCD spectroscopy at high contents of these molecules and, accordingly, metal ions in solution. Differences and peculiarities conditioning irreversibility of the earlier observed disproportional 2->3 transition are clarified.