Binding properties of two ruthenium(II) polypyridyl complexes [Ru(bpy)(dppz-Br)] and [Ru(dmb)(dppz-Br)] with the RNA poly(U)•poly(A)*poly(U) triplex.

Two ruthenium(II) polypyridyl complexes containing different ancillary ligands, [Ru(bpy)(dppz-Br)] (Ru1; bpy = 2,2'-bipyridine dppz-Br = 7-Br-dipyrido[3,2-a,2',3'-c]-phenazine) and [Ru(dmb)(dppz-Br)] (Ru2; dmb = 4,4'-dimethyl-2,2'-bipyridine), have been synthesized and characterized. Binding properties of Ru1 and Ru2 with the RNA poly(U)•poly(A)*poly(U) triplex have been investigated by UV-Vis spectroscopy, fluorescence spectroscopy, viscosity measurements as well as circular dichroism and thermal denaturation. Spectrophotometric studies together with viscosity measurements suggest that both Ru1 and Ru2 bind with the triplex by intercalation mode, and the melting experiments demonstrate that the two complexes can effectively enhance the triplex stabilization. However, results indicate that Ru1 stabilizes the third-strand and Watson-Crick base-paired duplex of the triplex without obvious selectivity. In contrast, Ru2 prefers to bind with the third strand rather than the Watson-Crick base-paired duplex of the triplex to a some extent under the same conditions used in this study, thereby significantly stabilizing the third strand. The obtained results of this study suggest that slight differences in the ancillary ligands bpy and dmb should be the main factor affecting the binding interactions of the two complexes with the triplex.