Interaction of ruthenium(II) complexes [Ru(phen)2(o-CNPIP)]2+ and [Ru(phen)2(o-CH3PIP)]2+ with double-stranded RNA poly(rA)•poly(rU) in both dilute and molecular crowding solutions

Double-stranded RNA determines and regulates many biological processes in cells, plays a vital role in cell information transmission and gene regulation, and is a key target for the treatment of certain diseases. Here, we synthesized and characterized two novel ruthenium(II) complexes [Ru(phen) 2 ( o -CNPIP)] 2+ (Ru 1 ) and [Ru(phen) 2 ( o -CH 3 PIP)] 2+ (Ru 2 , phen = 1,10-phenanthroline, o -CNPIP = (2-(4-cyanodipyrido)-imidazo-[4,5- f ][1,10]-phenanthroline, o -CH 3 PIP = 2-(4-methyl)-imidazo-[4,5- f ][1,10]-phenanthroline). The interaction of the two Ru (II) complexes with double-stranded RNA poly(rA)•poly(rU) under dilute solution and molecular crowding conditions was studied by various spectroscopic methods and viscosity measurements. The results of UV–vis absorption spectroscopy and steady-state emission spectroscopy studies show that Ru 1 showed stronger binding and stabilizing ability to poly(rA)•poly(rU) and the binding affinity of Ru 1 and Ru 2 to poly(rA)•poly(rU) was weakened under molecular crowding conditions. Subsequently, the results of circular dichroism spectroscopy studies, thermal denaturation measurements and viscosity measurements also confirmed the results of our UV–vis absorption spectroscopy and steady-state emission spectroscopy studies. The results also showed that the two Ru(II) complexes bind, stabilize and perturb the structure of poly(rA)•poly(rU) by intercalation under dilute solution and molecular crowding conditions. In addition, it was found that the strength of these abilities was closely related to the binding affinity of the Ru(II) complexes to poly(rA)•poly(rU) by comparing the results of these studies. Furthermore, the thermodynamic parameters for the binding of Ru(II) complexes to poly(rA)•poly(rU) under the two conditions indicate that the binding process is spontaneous, is an enthalpy-driven process, and that hydrogen bonding serves as the dominant force. The purpose of this work is to explore the substituent effect of Ru(II) complexes and the effect of solution environment on the ability of Ru(II) complexes to bind and stabilize poly(rA)•poly(rU). Some insights resulting from this work are expected to facilitate the design of highly selective double-stranded RNA binders based on Ru(II) complexes. Interestingly, the phosphorescence intensity of Ru 2 after binding to poly(rA)•poly(rU) is significantly higher than that of Ru 1 under both solution conditions, with even stronger phosphorescence emission observed under molecular crowding conditions. This indicates that Ru 2 possesses the potential to serve as a nucleic acid luminescent probe for nucleic acid imaging in biological cells. To enhance its luminescent properties and specific binding capacity, further structural modification of Ru 2 is essential, which will be one of the key focuses of our future research efforts.