Binding propterties of two Ru(II) polypyridyl complexes containing dppz units and fluorine groups with poly(U)·poly(A) ∗ poly(U) triplex

Interactions of arene ruthenium(II) complexes [η6-(C6H6)Ru(pprip)Cl]+ and [η6-(C6H6)Ru(H2iiP)Cl]+ with RNA triplex poly(U)•poly(A)*poly(U)

Two arene ruthenium(II) complexes [η6-(C6H6)Ru(pprip)Cl]PF6 (Ru1; pprip = 2-(3-phenyl-1H-pyrazol-4-yl)-imidazolo[4,5-f][1,10]phenanthroline) and [η6-(C6H6)Ru(H2iiP)Cl]PF6 (Ru2; H2iiP = 2-(indole-3-yl)-imidazolo[4,5-f][1,10]phenanthroline) have been synthesized and characterized in this work. Binding properties of Ru1 and Ru2 with the triplex RNA poly(U)•poly(A)*poly(U) were investigated by spectrophotometry and spectrofluorometry as well as viscosimetry. Analysis of spectroscopic titrations and viscosity measurements show that the two complexes bind with the triplex through intercalation, while the binding affinity for Ru2 toward the triplex is stronger than that for Ru1. Melting experiments indicate that the stabilizing effects of Ru1 and Ru2 toward the triplex differ from each other. Under the conditions used herein, Ru1 only stabilizes the Hoogsteen base-paired strand (third strand) without affecting stabilization of the Watson-Crick base-paired strand (the template duplex) of the triplex, while Ru2 stabilizes both the template duplex and the third strand. Although the two complexes prefer to stabilizing the third strand rather than the template duplex, the third-strand stabilization effect of Ru2 is stronger than that of Ru1. The obtained results of this work reveal that the planarity of the intercalative ligands plays an important role in the triplex stabilization by arene Ru(II) complexes.

Binding and stabilizating effect of RNA triplex poly(U)⋅poly(A)*poly(U) by enantiomers of ruthenium(II) polypyridyl complex [Ru(bpy)2(dppx)]2

Two chiral ruthenium(II) polypyridyl complexes, Λ-[Ru(bpy)₂(dppx)]²⁺ (bpy = 2,2'-bipyridine, dppx = 7,8-dimethyldipyridophenazine; Λ-1) and Δ-[Ru(bpy)₂(dppx)]²⁺ (Δ-1) have been synthesized and characterized in this work. Interactions of Λ-1 and Δ-1 with the RNA triplex poly(U)⋅poly(A)*poly(U) have been investigated by various biophysical techniques. Spectrophotometric titrations and viscosity measurements suggested that enantiomers Λ-1 and Δ-1 bind with the triplex through intercalation, while the binding strengths of the two enantiomers toward the triplex differed only slightly from each other. Fluorescence titrations showed that although enantiomers Λ-1 and Δ-1 exhibited molecular "light switch" effects toward the triplex, the effect of Δ-1 was more marked. Furthermore, Furthermore, thermal denaturation showed that the two enantiomers have significantly different stabilizing effects on the triplex. The obtained results indicate that the racemic complex [Ru(bpy)₂(dppx)]²⁺ is similar to a non-specific metallointercalator for the triplex investigated in this study, and chiralities of Ru(II) polypyridine complexes have an important influence on the binding and stabilizing effects of enantiomers toward the triplex. Two chiral ruthenium(II) polypyridyl complexes, Λ-[Ru(bpy)₂(dppx)]²⁺ (bpy = 2,2'-bipyridine, dppx = 7,8-dimethyldipyridophenazine; Λ-1) and Δ-[Ru(bpy)₂(dppx)]²⁺ (Δ-1) have been synthesized and characterized in this work. Interactions of Λ-1 and Δ-1 with the RNA triplex poly(U)⋅poly(A)*poly(U) have been investigated by various biophysical techniques. The obtained results indicate that the racemic complex [Ru(bpy)₂(dppx)]²⁺ is similar as a non-specific metallointercalator for the triplex investigated in this study, and chiralities of Ru(II) polypyridine complexes have an important influence on the binding and stabilizing effects of enantiomers toward the triplex.

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.

RNA-binding of Ru(II) complexes [Ru(phen)2(7-OCH3-dppz)]2+ and [Ru(phen)2(7-NO2-dppz)]2+: The former serves as a molecular "light switch" for poly(A)•poly(U)

To further determine the factors that affect the binding properties of ruthenium(II) polypyridine complexes with RNA duplex and to find excellent RNA-binding agents, the binding properties of ruthenium(II) complexes [Ru(phen)₂(7-OCH₃-dppz)]²⁺ (Ru1, phen = 1,10-phenan- throline, 7-OCH₃-dppz = 7-methoxy-dipyrido-[3,2-a,2',3'-c]-phenazine) and [Ru(phen)₂(7-NO₂- dppz)]²⁺ (Ru2, 7-NO₂-dppz = 7-nitro-dipyrido-[3,2-a,2',3'-c]-phenazine) with RNA poly(A)•poly(U) duplex have been investigated by spectroscopic methods and viscosity measurements in this work. The results show that complexes Ru1 and Ru2 bind to poly(A)•poly(U) through intercalation and the binding affinity between Ru2 and poly(A)•poly(U) is greater than that of Ru1. Thermal denaturation experiments suggest that both ruthenium(II) complexes exhibit a significant stabilizing effect on poly(A)•poly(U) duplex. Moreover, fluorescence emission spectra exhibit that, deviating from Ru2, Ru1 exhibits a "light switch" effect for poly(A)•poly(U). This effect can be observed by the naked eye under UV light and adjusted by pH, meaning that Ru1 may act as a reversible pH controlled molecular "light switch". The results obtained in this work will contribute to our understanding of the significant influence of the intercalative ligand substituent effect in the binding process of ruthenium(II) complexes with RNA duplex.

Insight into achirality and chirality effects in interactions of an racemic ruthenium(II) polypyridyl complex and its Δ- and Λ-enantiomers with an RNA triplex

RNA triplexes have a variety of potential applications in molecular biology, diagnostics and therapeutics, while low stabilization of the third strand hinders their practical utilities under physiological conditions. In this regard, achieving the third-strand stabilization by binding small molecules is a promising strategy. Chirality is one of the basic properties of nature. To clarify achirality and chirality effects on the binding and stabilizing effects of RNA triplexes by small molecules, we report for the first time the RNA interactions of an racemic ruthenium(II) polypyridyl complex [Ru(bpy)₂(11-CN-dppz)]²⁺ (rac-Ru1) and its two enantiomers Δ/Λ-[Ru(bpy)₂(11-CN-dppz)]²⁺ (Δ/Λ-Ru1) with an RNA triplex poly(U-A*U) (where "-" represents Watson-Crick base pairing, and "*" denotes Hoogsteen base pairing, respectively) in this work. Research shows that although rac-Ru1 and its two enantiomers Δ/Λ-Ru1 bind to the RNA triplex through the same mode of intercalation, the binding affinity for enantiomer Δ-Ru1 is much higher than that for rac-Ru1 and enantiomer Λ-Ru1. However, compared to enantiomer Λ-Ru1, the binding affinity for rac-Ru1 does not show much of an advantage, which is slightly greater than that for the former. Thermal denaturation measurements reveal both rac-Ru1 and Δ-Ru1 to have a preference for stabilizing the third strand rather than the template duplex of the RNA triplex, while Λ-Ru1 stabilizes the RNA triplex without significant selectivity. Besides, the third-strand stabilizing effects by rac-Ru1 and Δ-Ru1 are not markedly different from each other, but more marked than that by Λ-Ru1. This work shows that the binding properties of the racemic Ru(II) polypyridyl complex with the RNA triplex are not simply an average of its two enantiomers, indicating potentially complicated binding events.

Comparative studies on the binding interaction of two chiral Ru(II) polypyridyl complexes with triple- and double-helical forms of RNA

Two chiral Ru(II) polypyridyl complexes, Δ-[Ru(bpy)₂(6-F-dppz)]²⁺ (Δ-1; bpy = 2,2'-bipyridine, 6-F-dppz = 6-fluorodipyrido[3,2-a:2',3'-c]phenazine) and Λ-[Ru(bpy)₂(6-F-dppz)]²⁺ (Λ-1), have been synthesized and characterized as binders for the RNA poly(U)•poly(A)*poly(U) triplex and poly(A)•poly(U) duplex in this work. Analysis of the UV-Vis absorption spectra and fluorescence emission spectra indicates that the binding of intercalating Δ-1 with the triplex and duplex RNA is greater than that of Λ-1, while the binding affinities of the two enantiomers to triplex structure is stronger than that of duplex structure. Fluorescence titrations show that the two enantiomers can act as molecular "light switches" for triple- and double-helical RNA. Thermal denaturation studies revealed that that the two enantiomers are more stable to Watson-Crick base-paired double strand of the triplex than the Hoogsteen base-paired third strand, but their stability and selectivity are different. For Δ-enantiomer, the increase of the thermal stability of the Watson-Crick base-paired duplex (13 °C) is slightly stronger than of the Hoogsteen base-paired strand (10 °C), displaying no obvious selectivity. However, compared to the Hoogsteen base-paired strand (5 °C), the stability of the Λ-enantiomer to the Watson-Crick base-paired duplex (13 °C) is more significant, which has obvious selectivity. The overall increase in viscosity of the RNA-(Λ-1) system and its curve shape are similar to that of the RNA-(Δ-1) system, suggesting that the binding modes of two enantiomers with RNA are intercalation. The obtained results in this work may be useful for understanding the binding differences in chiral Ru(II) polypyridyl complexes toward RNA triplex and duplex.

A phenolic hydroxyl in the ortho- and meta-positions on the main ligands effect on the interactions of [Ru(phen)2(o-HPIP)]2+ and [Ru(phen)2(m-HPIP)]2+ with the poly(U)·poly(A)*poly(U) triplex

The association of two ruthenium(II) complexes [Ru(phen)₂(o-HPIP)]²⁺ (Ru1; phen = 1,10-phenanthroline, o-HPIP = 2-(2-hydroxyphenyl)-imidazo[4,5-f][1,10] phenanthroline) and [Ru(phen)₂(m-HPIP)]²⁺ (Ru2; m-HPIP = 2-(3-hydroxyphenyl)-imidazo[4,5-f][1,10]phenan- throline) with the RNA poly(U)·poly(A)⁎poly(U) triplex has been investigated by spectrophotometric titrations and melting experiments in this work. All experimental data reveal an intercalative triplex-binding mode of the two complexes, whereas the binding constant for Ru1 is significantly higher than that for Ru2. Circular dichroism spectroscopic investigations show that the two complexes could bind to the chiral environment of the triplex, but the triplex perturbation effects induced by Ru1 are more marked. Thermal denaturation experiments demonstrate that both Ru1 and Ru2 display a large binding preference and stabilizing effect for the third strand over the Watson-Crick base-paired duplex of the triplex. However, the third-strand stabilizing effect of Ru1 is much more effective than that of Ru2. The obtained results suggest that positions of the phenolic group on the main ligands have significant effect on the binding of the two complexes with poly(U)·poly(A)⁎poly(U) triplex.

Synthesis and characterization of chiral Ru(II) polypyridyl complexes and their binding and stabilizing effects toward triple-helical RNA

Two novel chiral Ru(II) complexes, Λ- and Δ-[Ru(bpy)₂(7-CF₃-dppz)]²⁺ (Λ-1 and Δ-1; bpy = 2,2'-bipyridine, 7-CF₃-dppz = 7-trifluoromethyl-dipyrido[3,2-a:2',3'-c]phenazine), were synthesized and characterized in this work. The binding and stabilizing effects of Λ-1 and Δ-1 toward the RNA poly(U)•poly(A)*poly(U) triplex were studied by various biophysical techniques. Absorption spectra and fluorescence quenching indicates that the binding affinity of Δ-1 is slightly higher than that Λ-1. Both enantiomers induce significant positive viscosity changes that are indicative of intercalative binding, whereas changes in the relative viscosities of the triplex are found to be more pronounced with Δ-1. Melting experiments indicate that the triplex stabilization effects of both enantiomers are significantly different from each other. With Λ-1, the stabilization of the Watson-Crick base-paired duplex (the template duplex) of the triplex shows a moderate increase, whereas the stabilization of the Hoogsteen base-paired strand (third-strand) exhibits slight decrease under the same conditions, suggesting Λ-1 prefers to stabilize the template duplex rather than third-strand. In stark contrast to Λ-1, Δ-1 can not only strongly stabilize the template duplex, but also moderately increase the third-strand stabilization, even so, which imply that Δ-1 also prefer to stabilize the template duplex instead of the third-strand. These suggest that the [Ru(bpy)₂(7-CF₃-dppz)]²⁺ is similar as a non-specific metallointercalator the triplex studied in this work. Combined with our recent research, the obtained results further indicate that Δ- enantiomers rather than Λ-ones of Ru(II) polypyridyl complexes usually exhibit stronger binding and stabilizing effects toward the triplex.