Stabilisation and nucleic acids binding of a +3 ion: the Aluminium/Cacodylate/RNA system

Metal ions influence the three-dimensional architecture and function of nucleic acids, can induce folding of nucleic acids strands, or even can aid catalytic mechanism in ribozymes. Therefore, investigations of metal ion binding to specific sites, and of the ability to stabilize local motifs or particular non-canonical structures are of primary interest. We have recently found that Mg(II) and Ni(II) cations are able to induce quadruplex and triplexes formation starting from duplex poly(rA)poly(rU) under still unexplored high ions concentrations. We have now extended our research to the study of the less explored class of tervalent metal ions. The interaction between aluminium(III) and poly(rA) nucleic acid, both in the form of single or double strand, has been analysed. The Al3+/poly(rU) system has been also investigated for comparison purposes. At the pH range needed for these experiments (pH = 5 - 7) the stability of Al3+ in solution is guaranteed by the cacodylate buffer that also complexes the metal ion. It is shown that the binding occurs indeed, with features that differ on passing from poly(rA) to poly(rA)poly(rA). The fast process of the metal ion binding to RNA is studied by means of the initial rate analysis in different reactants conditions and a binding mechanism is proposed. This enables the main binding species to be individuated. In the case of poly(rA) a slow cooperative aggregation of the single strands is found to occur (figure, right), that is favoured by the presence of the aluminium ion. The different binding features will be discussed.