An overview on the interaction of phenazinium dye phenosafranine to RNA triple and double helices

Spectroscopic and calorimetric study of the interaction between Nile blue and double-stranded RNA

Nile blue has been widely used in histological staining, fluorescence labeling, and DNA probing, with its intercalation behavior into the DNA helix being well documented. Here, we present a comprehensive investigation to address a current knowledge gap regarding the binding properties of Nile blue to two types of double-stranded RNA (dsRNA): poly(A·U) and poly(I·C), using various biophysical techniques. Absorption and fluorescence spectroscopic studies suggest a significant binding interaction between Nile blue and the two designated dsRNAs, specifically indicating an intercalation binding mode with poly(A·U) and demonstrating a noticeably higher binding affinity compared to poly(I·C). The binding stoichiometry was further determined by Job's plot to be 0.47 for poly(A·U) and 1.0 for poly(I·C). The increased relative viscosity and changes in the circular dichroism (CD) ellipticity of dsRNA after interacting with Nile blue indicate the stacking of Nile blue dyes between the RNA duplexes. These changes suggest a conformational alteration of the dsRNAs and confirm the intercalation mode of binding. The thermal dynamic analysis demonstrates that both binding were favored by negative enthalpy and primarily driven by the hydrophobic effect.

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.

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.

Biophysical insights into the interaction of two enantiomers of Ru(II) complex [Ru(bpy)2(7-CH3-dppz)]2+ with the RNA poly(U-A⁎U) triplex

To determine the factors affecting the stabilization of RNA triple-stranded structure by chiral Ru(II) polypyridyl complexes, a new pair of enantiomers, ∆-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (∆-1; bpy = 2,2'-bipyridine, 7-CH₃-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) and Λ-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (Λ-1), have been synthesized and characterized in this work. Binding properties of the two enantiomers with the RNA poly(U-A⁎U) triplex (where "-" denotes the Watson - Crick base pairing and "⁎" denotes the Hoogsteen base pairing) have been studied by spectroscopy and hydrodynamics methods. Under the conditions used in this study, changes in absorption spectra of the two enantiomers are not very different from each other when bound to the triplex, although the binding affinity of ∆-1 is higher than that of Λ-1. Fluorescence titrations and viscosity experiments give convincing evidence for a true intercalative binding of enantiomers with the triplex. However, melting experiments indicated that the two enantiomers selectively stabilized the triplex. The enantiomer ∆-1 stabilize the template duplex and third-strand of the triplex, while it's more effective for stabilization of the template duplex. In stark contrast to ∆-1, Λ-1 stabilizes the triplex without any effect on the third-strand stabilization, suggesting this one extremely prefers to stabilize the template duplex rather than third-strand. Besides, the triplex stabilization effect of ∆-1 is more marked in comparison with that of Λ-1. The obtained results suggest that substituent effects and chiralities of Ru(II) polypyridyl complexes play important roles in the triplex stabilization. Complexes Λ/Δ-[Ru(bpy)₂(7-CH₃-dppz)]²⁺ (Λ/Δ-1; bpy = 2,2'-bipyridine, 7-CH₃-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) were prepared as stabilizers for poly(U-A ∗ U) triplex. Results suggest the triplex stabilization depends the chiral structures of Λ/Δ-1, indicating that [Ru(bpy)₂(7-CH₃-dppz)]²⁺ is a non-specific intercalator for poly(U-A ∗ U) investigated in this work.

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.

Insights on the interaction of phenothiazinium dyes methylene blue and new methylene blue with synthetic duplex RNAs through spectroscopy and modeling

The ubiquitous influence of double stranded RNAs in biological events makes them imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situations wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of this study is to delve into the interactive pattern of two small molecule phenothiazinium dyes, methylene blue and new methylene blue, with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic and molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules was evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding patterns of the dye molecules within the RNA duplexes. The novelty of the present work lies towards a new contribution of the phenothiazinium dyes in dysfunctioning double stranded RNAs, advancing our knowledge to their potential use as RNA targeted small molecules.

Third-strand stabilizing effects of the RNA poly(U)·poly(A)*poly(U) triplex by a ruthenium(II) polypyridine complex and its hexaarginine peptide conjugate

In this work, a Ru(II) complex [Ru(bpy)₂(pip-CO₂H)]²⁺ (Ru1) and its hexaarginine peptide conjugate [Ru(bpy)₂(pic-Arg₆)]⁸⁺ (Ru2) have been synthesized and characterized. The binding of Ru1 and Ru2 with poly(U)•poly(A)*poly(U) triplex has been studied. Results suggest that Ru1 binds in the surface of the minor groove while Ru2 binds to the minor groove of the triplex. Consequently, the triplex stabilization is barely affected by Ru1, while with Ru2 the triplex stabilizing effect is so strong that that dissociation of the triplex shows an overlapping of both melting processes with the melting temperature increased to a maximum of 56.1 °C at the C_Ru2/C_UAU ratio of 0.05, where ΔT_m1 and ΔT_m2 are 19.6 and 10.1 °C, respectively. Furthermore, the effect of Ru2 stabilizing the third strand at such a low binding ratio of 0.05 is more marked than what obsereved for flavone luteolin and [Ru(bpy)₂(mdpz)]²⁺, which are so far the strongest triplex stabilizers in the reported organic small molecules and metal complexes, respectively. Considering the structure natures of Ru2, conceivably except for electrostatic interaction, the forces stabilizing the triplex should also involve hydrophobic interaction and hydrogen bingding. To our knowledge, this work represents a first example of improving the triplex stabilization by a metallopeptide.

Role of hydroxyl groups in the B-ring of flavonoids in stabilization of the Hoogsteen paired third strand of Poly(U).Poly(A)*Poly(U) triplex

We have reported the interaction of two flavonoids namely quercetin (Q) and morin (M) with double stranded poly(A).poly(U) (herein after A.U) and triple stranded poly(U).poly(A)*poly(U) (herein after U.A*U, dot represents the Watson-Crick and asterisk represents Hoogsteen base pairing respectively) in this article. It has been observed that relative positions of hydroxyl groups on the B-ring of the flavonoids affect the stabilization of RNA. The double strand as well as the triple strand of RNA-polymers become more stabilized in presence of Q, however both the duplex and triplex remain unaffected in presence of M. The presence of catechol moiety on the B-ring of Q is supposed to be responsible for the stabilization. Moreover, after exploiting a series of biophysical experiments, it has been found that, triple helical RNA becomes more stabilized over its parent duplex in presence of Q. Fluorescence quenching, viscosity measurement and helix melting results establish the fact that Q binds with both forms of RNA through the mode of intercalation while M does not bind at all to either forms of RNA.

Third strand stabilization of poly(U)·poly(A)* poly(U) triplex by the naturally occurring flavone luteolin: A multi-spectroscopic approach

Naturally occurring flavonoid luteolin (LTN) was found to interact with double stranded poly(A).poly(U) and triple stranded poly(U)·poly(A)*poly(U) with association constants of the order of 10⁴M^-1. The association was monitored by various spectroscopic and viscometric techniques. Non-cooperative binding was observed for the association of LTN with two different polymorphic forms of RNA. Intercalation mode of binding was confirmed by fluorescence quenching and viscometric experiments. Thermal melting profiles indicated greater stabilization of the Hoogsteen base paired third strand (∼16°C) compared to Watson-Crick double strand (∼5°C) of RNA by LTN. Since the interaction of naturally occurring small molecules with RNA is an active area of research, this study has led to great openings to explore LTN as RNA targeted therapeutic agent.

Biophysical insight into the interaction of the bioflavonoid kaempferol with triple and double helical RNA and the dual fluorescence behaviour of kaempferol

Binding of kaempferol with triple and double helical RNA.