Insight into the intercalating ligands affecting the interactions of ruthenium (II) polypyridyl complexes with RNA poly(A)*poly(U)

A series of ruthenium(II) complexes [Ru(phen)2dppp3]2+ (Ru1, phen = 1,10-phenanthrolline; dppp3 = pyrido [3 ',4 ':5,6]pyrazino[2,3-f][1,10]phenanthroline), [Ru(phen)2dppp2]2+ (Ru2, dppp2 = pyrido[2 ',3 ':5,6]pyrazino [2,3-f][1,10]phenanthroline) and [Ru(phen)2bppp]2+ (Ru3, bppp = 10-bromopyrido[2 ',3 ':5,6]pyrazino-[2,3-f] [1,10]phenanthroline) have been synthesized and characterized that helps to further investigate RNA-complex interactions. The viscosity measurement, UV-vis absorption spectrum study as well as EB (ethidium bromide) fluorescence competition have been explored to prove that the binding modes of Ru1, Ru2 and Ru3 with double -stranded RNA were intercalation, and these binding affinities of Ru1, Ru2 and Ru3 toward poly(A)*poly(U) (where "*" denotes the Watson-Crick base) have followed the order of Ru1 > Ru2 > Ru3. The analysis of thermal denaturation results obtained the identical conclusion and revealed that three complexes have positive roles in the stabilization of RNA base pairs. To my knowledge, this study presents the first Ru(II) polypyridine complexes with the most effective thermal stabilization of RNA poly(A)*poly(U). All results showed the structural effects of complex main ligands in RNA study, in which the RNA-affinities were impacted greatly by the positions of substituents, and the sizes of functional groups were also key factors controlling the interaction between the complexes and double-stranded RNA.