Coralyne induces triplex-to-duplex and duplex-to-triplex transitions in ds-RNA according to a temperature controlled cycle

Over the last few years, non-canonical nucleic acids structures have aroused a great deal of interest due to their involvement in biological processes. In particular, triplex structures have been given paramount importance in therapies based on antigene and antisense strategies. Recently, it has been demonstrated that the fluorescent dye Coralyne chloride (8-methyl-2,3,10,11-tetramethoxydibenzo[a,g]quinolizinium chloride), favours the formation of the poly(A)•2poly(U) triplex from the poly(A)•poly(U) duplex under suitable temperature and dye-to-polymer (CD/CP) conditions.It has been shown that RNA in the poly(A)•poly(U) form diproportionates at 25 ºC in the presence of Coralyne, provided that the duplex (AU) is present in excess, i.e., in a [dye]/[polymer] ratio (CD/CP) less than 0.8. Moreover, melting experiments have shown that, for CD/CP > 0.8, AUD also disproportionates to triplex and single strands provided that the temperature is raised up to about 40 ºC. In this work, spectrophotometric, calorimetric and kinetic analyses of the poly(A)•2poly(U)/Coralyne system have been carried out, that lend further insights into the Coralyne ability to bring about dramatic changes in the RNA structure. The data gathered agree to convey that Coralyne also is able to induce the triplex-to-duplex conversion at room temperature, provided that CD/CP > 1. The results as a whole show that, under excess of dye, the RNA/Coralyne system undergoes a cycle controlled by two key temperatures. At T2, the duplex disproportionates to triplex, whereas at T1 (T2 > T1) the triplex converts to duplex. A cycle operated by a change of the CD/CP ratio can also be devised: at low CD/CP ratio, the duplex disproportionates to triplex whereas, for CD/CP > 1, the triplex converts to duplex.