Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)]2 + and [Ru(phen)2(ppn)]2 + with triplex RNA: As molecular “light switches” and stabilizers for poly(U)·poly(A)*poly(U) triplex

•Complexes 1 and 2 can serve as molecular “light switches” and stabilizers for poly(U)·poly(A)*poly(U).•The stabilization of third-strand is less than that of the duplex strand by each complex.•The binding of the two complexes with the triplex is favored by the Watson-Crick base-paired duplex.•The effectiveness of complex 2 are more marked.•Results suggest the hydrophobicity of ancillary ligands has a significant effect on the binding.

Stable RNA triplexes play key roles in many biological processes, while triplexes are thermodynamically less stable than the corresponding duplexes due to the Hoogsteen base pairing. To understand the factors affecting the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the binding of [Ru(bpy)2(ppn)]2 + (1, bpy = 2,2′-bipyridine, ppn = 2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2′,3′-h]quinoxaline) and [Ru(phen)2(ppn)]2 + (2, phen = 1,10-phenanthroline) to poly(U)·poly(A)*poly(U) (· denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) has been investigated. The main results obtained here suggest that complexes 1 and 2 can serve as molecular “light switches” and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked, suggesting that the hydrophobicity of ancillary ligands has a significant effect on the two Ru(II) complexes binding to poly(U)·poly(A)*poly(U). This study further advances our knowledge on the binding of RNA triplexes with metal complexes, particularly with octahedral ruthenium polypyridyl complexes.

Graphical abstractComplexes 1 and 2 can serve as molecular “light switches” and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked. Results suggest that the hydrophobicity of ancillary ligands has a significant effect on the binding behaviors.Figure optionsDownload full-size imageDownload as PowerPoint slide