Effects of the fluorine substituent positions of the intercalating ligands on the binding behavior and third-strand stabilization of two Ru(II) complexes toward poly(U)•poly(A)*poly(U) triplex RNA

Two new Ru(II) polypyridyl complexes [Ru(bpy)2(o-fpip)]2 + (Ru1) and [Ru(bpy)2(p-fpip)]2 + (Ru2) have been synthesized as binder for poly(U)
- poly(A)*poly(U) triplex. Results suggest that the two complexes stabilize the triplex via intercalation. Ru1 somewhat prefers to stabilize the Watson-Crick base pairing duplex strand rather than stabilize the third strand, while Ru2 prefers to exert a rather remarkable stabilization effect on the third strand instead of the template duplex. This observation indicates that the positions of fluorine substituent in the intercalating ligands are able to alter third-strand stabilization.123