Substituent effects on the interactions of ruthenium(II) polypyridyl complexes [Ru(bpy)2(6-R-dppz)]2+ (R = hydroxy and fluorine) with the RNA triplex poly(rU)·poly(rA) × poly(rU)

Binding properties of a molecular "light switch" ruthenium(II) polypyridyl complex toward double- and triple-helical forms of RNA

To further develop new luminescent probes for RNA, a new ruthenium(II) polypyridyl complex [Ru(dmb)₂dppz-idzo]²⁺ (dmb = 4,4'-dimethyl-2,2'-bipyridine, dppz-idzo = dppz-imidazolone) has been synthesized and characterized in this study. Binding properties of [Ru(dmb)₂dppz-idzo]²⁺ to RNA duplex poly(A) · poly(U) and triplex poly(U) · poly(A) ∗ poly(U) have been explored by spectroscopic techniques and viscometry experiments. The binding modes of [Ru(dmb)₂dppz-idzo]²⁺ to RNA duplex and triplex are intercalation as revealed from spectral titrations and viscosity experiments, while the binding strength of this complex to duplex structure is significantly greater than that of triplex structure. Fluorescence titrations indicate that [Ru(dmb)₂dppz-idzo]²⁺ can act as a molecular "light switch" for both duplex poly(A) · poly(U) and triplex poly(U) · poly(A) ∗ poly(U), while [Ru(dmb)₂dppz-idzo]²⁺ is more sensitive to poly(A) · poly(U) compared to poly(U) · poly(A) ∗ poly(U) and poly(U). Therefore, this complex can distinguish between RNA duplex, triplex and poly(U), and can as luminescent probes for the three RNAs used in this study. In addition, thermal denaturation studies show that [Ru(dmb)₂dppz-idzo]²⁺ is able to significantly increase the Stabilization of RNA duplex and triplex. The results obtained in this study may contribute to further understanding of the binding of Ru(II) complexes with different structural RNAs.

A naked-eye colorimetric molecular "light switch" based on ruthenium(II) polypyridyl complex [Ru(phen)2ttbd]2+ as binder and stabilizer for RNA duplex and triplex

Binding of [Ru(phen)₂ttbd]²⁺ (phen = 1,10-phenanthroline, ttbd = 4-(6-propenylpyrido-[3,2-a]- phenzain-10-yl-benzene-1,2-diamine) to the RNA triplex poly(U-A*U) (herein "-" and "*" refer to the Watson-Crick and Hoogsteen binding, respectively) and the duplex poly(A-U) have been investigated by spectral technology and viscosity method. Analysis of spectral titrations and viscosity experiments as well as melting measurements suggest that [Ru(phen)₂ttbd]²⁺ binds to the studied RNA triplex and duplex through intercalation, while its binding constant toward the triplex is greater than the duplex. Luminescent titrations indicate that [Ru(phen)₂ttbd]²⁺ can act as a molecular "light switch" for the two RNAs and the switch effect can be detected by the naked-eye. Moreover, the "light switch" can be repeatedly cycled off and on by adjusting the pH of the solution, whereas color change in the case of the triplex is more significant compared with the duplex. To our knowledge, [Ru(phen)₂ttbd]²⁺ is the first small molecule capable of serving as a pH-controlled reversible visual molecular "light switch" for both the RNA triplex poly(U-A*U) and duplex poly(A-U). Thermal denaturation experiments suggest that [Ru(phen)₂ttbd]²⁺ can obviously increase the triplex stabilization, while it stabilizing third-strand is more marked in comparison with the template duplex of the triplex, indicating this complex preferentially binds to third-strand. The obtained results may be useful for understanding the binding of Ru(II) polypyridyl complexes to RNAs.

Interaction of arene ruthenium(II) complexes [(η6-C6H6)Ru(L)Cl]PF6 (L = o-fpip and p-fpip) with the RNA triplex poly(U)*poly(A)•poly(U)

To comprehend the binding properties of η⁶-arene Ru(II) complexes with poly(U)*poly(A)•poly(U) triplex, two arene Ru(II) complexes with different fluorine substituent positions, [(η⁶-C₆H₆)Ru(o-fpip)Cl]PF₆ (Ru1,η⁶-C₆H₆ = benzene ring, o-fpip = 2-(2'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline) and [(η⁶-C₆H₆)Ru(p-fpip)Cl]PF₆ (Ru2,η⁶-C₆H₆ = benzene ring, o-fpip = 2-(4'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline), have been synthesized and characterized in this study. The binding of Ru1 and Ru2 with poly(U)*poly(A)•poly(U) triplex has been investigated by viscosity measurement and spectroscopic methods. Analysis of UV-Vis absorption spectral titrations suggests that Ru1 and Ru2 bind to the triplex through an intercalative mode, but the binding affinity of Ru2 is slightly higher than that of Ru1, which is also verified by viscosity and EB (ethidium bromide) competition measurements. Furthermore, the thermal denaturation experiment shows that Ru1 and Ru2 increase the third-strand stabilization to a similar extent. Interestingly, the two complexes have essentially no effect on the stabilization of the template duplex. Considering the structure of Ru1 and Ru2, conceivably besides the intercalation of ligand, the force stabilizing the triplex should also involve covalent binding and electrostatic interaction. The obtained results will contribute to our understanding of the interaction of arene Ru(II) complexes with the poly(U)*poly(A)•poly(U) triplex.