Mg(II) and Ni(II) induce aggregation of poly(rA)poly(rU) to either tetra-aggregate or triplex depending on the metal ion concentration

• Mg2 + and Ni2 + at modest concentrations induce formation of RNA triplex.
• Mg2 + and Ni2 + at high concentrations induce formation of RNA tetra-aggregate.
• Nickel is much more effective than magnesium to induce transformations.
• The transitions occur also in the presence of an intercalating dye (coralyne).
• Dye binding affinity to the tetra-aggregate RNA form is enhanced with respect to duplex.

The ability of magnesium(II) and nickel(II) to induce dramatic conformational changes in the synthetic RNA poly(rA)poly(rU) has been investigated. Kinetic experiments, spectrofluorometric titrations, melting experiments and DSC measurements contribute in shedding light on a complex behaviour where the action of metal ions (Na+, Mg2 +, Ni2 +), in synergism with other operators as the intercalating dye coralyne and temperature, all concur in stabilising a peculiar RNA form. Mg2 + and Ni2 + (M) bind rapidly and almost quantitatively to the duplex (AU) to give a RNA/metal ion complex (AUM). Then, by the union of two AUM units, an unstable tetra-aggregate (UAUA(M2)*) is formed which, in the presence of a relatively modest excess of metal, evolves to the UAUM triplex by releasing a single AM strand. On the other hand, under conditions of high metal content, the UAUA(M2)* intermediate rearranges to give a more stable tetra-aggregate (UAUA(M2)). As concerns the role of coralyne (D), it is found that D strongly interacts with UAUA(M2). Also, in the presence of coralyne, the ability of divalent ions to promote the transition of AUD into UAUD is enhanced, according to the efficiency sequence [Ni2 +] ≫ [Mg2 +] ≫ [Na+].

Nickel and magnesium induce stabilisation of non-canonical RNA forms as tetra-aggregates or triplexes, the major form depending on metal ion concentration, temperature and/or presence of intercalating dyes. Mechanism and details of these processes are investigated.Figure optionsDownload as PowerPoint slide