Preliminary thermodynamic and kinetic tests on Al3+ ion interaction with single and double stranded poly(A)

Metal ions influence the three-dimensional architecture and function of nucleic acids. This is known since a long time. Moreover, these ions can also 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.Recently, we have performed a thermodynamic and kinetic analysis on the ability of divalent metal ions (magnesium(II) and nickel(II)) to stabilise non-canonical structures of the synthetic RNA poly(rA)poly(rU) under still unexplored high ions concentrations. We have found that these cations are both able to induce quadruplex and triplexes formation starting from duplex poly(rA)poly(rU). We have now extended our field of research to the study of the less explored class of tervalent metal ions. Preliminary experiments have been made to test the interaction between aluminium(III) and poly(rA) nucleic acid, both in the form of single or double strand. At the pH range needed for these experiments (pH = 5 - 7) the stability of aluminium(III) in solution is guaranteed by the cacodylate buffer that also complexes Al3+. The spectrophotometric titrations show that the binding occurs indeed, with features that differ much on passing from poly(rA) to poly(rA)poly(rA). In the case of poly(rA) cooperative aggregation of the single strands is favoured by the presence of the aluminium ion. On the other hand, quantitative binding of the ion to poly(rA)poly(rA) occurs. A rather complex kinetic behaviour, strongly dependent on pH, has been observed. The slowness of the kinetic effects indicates that Al(III) induces deep conformation changes in poly(rA). The kinetic tests done confirm the occurrence of a slow cooperative process for the single strand. The further analysis of the kinetics of the binding, using fast reaction techniques, will give information of the mechanistic aspects of the process.