Probing the interaction of spermine and 1-naphthyl acetyl spermine with DNA polynucleotides: a comparative biophysical and thermodynamic investigation

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.

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.

Binding properties of ruthenium(II) complexes [Ru(phen)2(7-R-dppz)]2+ (R = methyl or bromine) toward poly(U)•poly(A) RNA duplex

Two Ru(II) complexes containing different substituents, [Ru(phen)₂(7-CH₃-dppz)]²⁺ (Ru1) and [Ru(phen)₂(7-Br-dppz)]²⁺ (Ru2), have been synthesized in this study. The binding properties of Ru1 and Ru2 with the duplex RNA poly(U)•poly(A) (where "•" denotes the Watson - Crick base pairing) have been researched by biophysical techniques and viscosity measurements. Analysis of spectral titrations and viscosity measurements indicate that Ru1 and Ru2 bind to the duplex via intercalative, and the binding affinity of Ru1 with the duplex is remarkably higher than that of Ru2. Furthermore, fluorescence emission spectra demonstrates that although complexes Ru1 and Ru2 can act as molecular "light switches" for the duplex RNA, alters in fluorescence emission of Ru1 and Ru2 are prominent differences, and the effectiveness of Ru1 is more remarkable compared with that of Ru2. The melting experiments suggest that the duplex RNA stabilizing effects of Ru1 and Ru2 differ from each other, among them, complex Ru1 can obviously enhance the stability of the duplex RNA, while Ru2 has only a slightly stabilizing effect for the duplex RNA, indicating that Ru1 preferentially binds to RNA duplex over Ru2. The obtained results indicate that subtle modifications of the intercalative ligand of Ru(II) polypyridyl complex with either methyl or bromide group have a significant effect on the duplex-binding discrimination.

Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms

Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.

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.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

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.

Binding properties of two ruthenium(II) polypyridyl complexes [Ru(bpy)2(dppz-Br)]2+ and [Ru(dmb)2(dppz-Br)]2+ with the RNA poly(U)•poly(A)*poly(U) triplex

Two ruthenium(II) polypyridyl complexes containing different ancillary ligands, [Ru(bpy)₂(dppz-Br)]²⁺ (Ru1; bpy = 2,2'-bipyridine dppz-Br = 7-Br-dipyrido[3,2-a,2',3'-c]-phenazine) and [Ru(dmb)₂(dppz-Br)]²⁺ (Ru2; dmb = 4,4'-dimethyl-2,2'-bipyridine), have been synthesized and characterized. Binding properties of Ru1 and Ru2 with the RNA poly(U)•poly(A)*poly(U) triplex have been investigated by UV-Vis spectroscopy, fluorescence spectroscopy, viscosity measurements as well as circular dichroism and thermal denaturation. Spectrophotometric studies together with viscosity measurements suggest that both Ru1 and Ru2 bind with the triplex by intercalation mode, and the melting experiments demonstrate that the two complexes can effectively enhance the triplex stabilization. However, results indicate that Ru1 stabilizes the third-strand and Watson-Crick base-paired duplex of the triplex without obvious selectivity. In contrast, Ru2 prefers to bind with the third strand rather than the Watson-Crick base-paired duplex of the triplex to a some extent under the same conditions used in this study, thereby significantly stabilizing the third strand. The obtained results of this study suggest that slight differences in the ancillary ligands bpy and dmb should be the main factor affecting the binding interactions of the two complexes with the triplex.

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

In this work, two Ru(II)-dppz (dppz = dipyrido[3,2-a:2',3'-c]phenazine) complexes containing fluorine substituents, [Ru(bpy)₂(7-F-dppz)]²⁺ (Ru1, bpy = 2,2'-bipyridine, 7-F-dppz = 7-fluorodipyrido[3,2-a:2',3'-c]phenazine) and [Ru(phen)₂(7-F-dppz)]²⁺ (Ru2, phen = 1,10-phenanthroline), have been synthesized and characterized. Binding properties of Ru1 and Ru2 with the RNA poly(U)·poly(A) ∗ poly(U) triplex have been studied by spectroscopic methods and viscosity measurements. The obtained results indicate that the binding differences of the two complexes with the triplex may be attributed to the ancillary ligand effects, implying that the better planarity and greater hydrophobicity of ancillary ligands are advantageous to the π-π stacking interaction between Ru2 and the triplex, thus Ru2 stabilizes the triplex strongly than Ru1. Denaturation of the triplex shows that both Ru1 and Ru2 can not only highly stabilize the template duplex of the triplex, but also significantly stabilize the third strand. Compared with the triplex stabilizing effects for the reported Ru(II)-dppz complexes, thermal melting experiments suggest that the fluorine substituent on the ligand dppz can probably decrease electrostatic repulsion between the three strands of the triplex, thereby Ru1 and Ru2 significantly increase the triplex stabilization. Results obtained from this work further confirm that the substituent electron effect of dppz-based ligands and the planarity and hydrophobicity of ancillary ligands play an important role in the triplex stabilizing effects by Ru(II)-dppz complexes.

Binding properties of chiral ruthenium(II) complexes Λ- and Δ-[Ru(bpy)2dppz-11-CO2Me]2+ toward the triplex RNA poly(U)•poly(A)*poly(U)

Two chiral ruthenium(II) complexes containing ligand dppz-CO₂Me (dppz-11-CO₂Me = dipyrido[3,2-a,2',3'-c]phenazine-11-carboxylic acid methyl ester), Δ-[Ru(bpy)₂dppz-11-CO₂Me]²⁺ (bpy = 2,2'-bipyridine; Δ-1) and Λ-[Ru(bpy)₂dppz-11-CO₂Me]²⁺ (Λ-1), were synthesized and characterized. The binding of the two enantiomers with the triplex RNA poly(U)•poly(A)*poly(U) was carried out by various biophysical techniques. Analysis of the absorption and fluorescence features indicates that the binding strengths of the two enantiomers toward the triplex RNA differ only slightly from each other. The total increase in viscosity and shape of the curves for the triplex RNA with Λ-1 is similar to that with Δ-1, suggesting the binding modes of two enantiomers with the triplex RNA are intercalation. Thermal melting measurements indicate that the stabilization effects clearly depended on the concentrations of Λ-1 and Δ-1. However, the third-strand stabilizing effect of Δ-1 dramatically differs from that of Λ-1 when they interact with the chiral environment of the RNA triple at pH = 7.0 and [Na⁺] = 35 mM. Combined with the CD (CD = circular dichroism) variations of the triplex RNA with either Λ-1 or Δ-1, the reason for their different triplex stabilization effects may originate from the two enantiomers through different orientations intercalating into nucleobases of the triplex. In addition, effects of higher ionic strengths on the triplex stabilization in the absence and presence of the two enantiomers have also been studied. The results presented here may be useful for understanding the binding properties of the triplex RNA with small molecule, particularly chiral ruthenium(II) complexes.

[Ru(bpy)2(7-CH3-dppz)](2+) and [Ru(phen)2(7-CH3-dppz)](2+) as metallointercalators that affect third-strand stabilization of the poly(U)˙poly(A)*poly(U) triplex

Stable RNA triplexes play key roles in many biological processes. However, due to Hoogsteen base pairing, triplexes are thermodynamically less stable than the corresponding duplexes. To understand the factors effecting the stabilization of RNA triplexes by octahedral ruthenium(ii) complexes, two Ru(ii) complexes, [Ru(bpy)2(7-CH3-dppz)](2+) (Ru) and [Ru(phen)2(7-CH3-dppz)](2+) (Ru), have been synthesized and characterized in this work. The interactions of the two Ru(ii) complexes with the poly(U)˙poly(A)*poly(U) triplex are investigated by spectrophotometry, spectrofluorometry, circular dichroism as well as viscometry. The results demonstrate that the two complexes are able to enhance the stability of the RNA triplex and serve as molecular "light switches" for the triplex. However, Ru and Ru affecting the stabilization of the third strand are significantly weaker than that of the Watson-Crick base-paired duplex, suggesting that the binding of the two complexes with the triplex is favored by the Watson-Crick base-paired duplex to a large extent. In addition, considering the nature of Ru and Ru, we presume that their binding differences may be due to different ancillary ligand effects. This study further advances our knowledge on the interaction of RNA triple-stranded structures with metal complexes, particularly with Ru(ii) complexes.

Hybrid pharmacophore approach for bio-relevant di-imines based homobimetallic complexes incorporating functionalized dicarboxylates as co-ligands: Synthesis, spectral and structural activity dependent biological insights (in-vitro DNA and HSA binding, antioxidant and cytotoxicity)

Synthesis of bio-efficient homobimetallic complexes, [Cu₂(L¹)₂(dipic)](NO₃)₂.3H₂O (1), [Zn₂(L¹)₂(dipic)](NO₃)₂.4H₂O (2), [Cu₂(L²)₂(oxa)](NO₃)₂.4H₂O (3) and [Zn₂(L²)₂(oxa)] (NO₃)₂.5H₂O (4) was carried out using Schiff bases [(N¹E,N²E)-N¹,N²-bis(5-chlorothiophen-2-ylmethylene)-4-chlorobenzene-1,2-diamine; L¹] and [(N¹E,N²E)-N¹,N²-bis(5-chlorofuran-2-ylmethylene)-4-chlorobenzene-1,2-diamine; L²] as main ligands and dicarboxylate moieties of 2,6-pyridine dicarboxylic acid (H₂-dipic) and oxalic acid (H₂-oxa) as co-ligands, respectively in order to apprehend their structure activity relationships on the basis of pharmacophore hybrid approach. The stoichiometry, geometry, thermal stability, morphology and crystallite size of the compounds were inferred by analytical, spectral (FT-IR, ¹H NMR and ¹³C NMR and Mass), thermal (TGA/DTA), SEM and XRD studies. In-vitro DNA and HSA binding profiles of complexes were analysed by different biophysical measurements. The absorption study divulged that the observed alterations in the physico-chemical properties of complexes upon binding with DNA connoted their intercalative binding mode while fluorescence quenching mechanism was quantified by using Stern Volmer constant (K_SV)_; 1.73×10⁴ (1), 1.47×10⁴ (2), 5.65×10³ (3) and 3.60×10³M^-1 (4) which discerned that hybrid pharmacophore active metal complexes (1 and 2) exhibited efficient quenching effect with Ct-DNA in comparison to complexes (3 and 4) due to greater planarity and extent of conjugation (π-π interactions). The intercalative binding mode of complexes is further supported by competitive displacement assay by using fluorogenic dyes (EtBr and Hoechst 33258). The results of HSA fluorescence study divulged static quenching of the complexes (1-4) with K_SV values of 7.24×10⁴ (1), 6.03×10⁴ (2), 5.06×10⁴ (3) and 2.85×10⁴ (4) while K_b values; 1.16×10⁵ (1), 2.01×10⁴ (2), 5.84×10³ (3) and 8.60×10² (4) suggested them potent avid binder of HSA. Additionally, comparative estimation of scavenging properties using DPPH, superoxide(O₂^.-), hydroxyl (OH^-) and ABTS method and in-vitro cytotoxicity against different cell lines (MCF-7, HeLa and Hep G2) brought out distinct biopotency of complexes due to diverse structural features and chelation effect.

Polyamine-RNA-membrane interactions: From the past to the future in biology

Biogenic polyamines (PAs), spermine, spermidine and putrescine are widely spread amino acid derivatives, present in living cells throughout the whole evolutionary scale. Their amino groups confer them a marked basic character at the cellular pH. We have tested the interaction of PAs with negatively-charged phospholipids in the absence and presence of nucleic acids (tRNA was mainly used for practical reasons). PAs induced aggregation of lipid vesicles containing acidic phospholipids. Aggregation was detected using both spectroscopic and fluorescence microscopy methods (the latter with giant unilamellar vesicles). PA-liposome complexes were partially disaggregated when nucleic acids were added to the mixture, indicating a competition between lipids and nucleic acids for PAs in a multiple equilibrium phenomenon. Equivalent observations could be made when vesicles composed of oleic acid and 1-decanol (1:1mol ratio) were used instead of phospholipid liposomes. The data could evoke putative primitive processes of proto-biotic evolution. At the other end of the time scale, this system may be at the basis of an interesting tool in the development of nanoscale drug delivery.

Interaction of octahedral ruthenium(II) polypyridyl complex [Ru(bpy)2(PIP)]2+ with poly(U)·poly(A)*poly(U) triplex: Increasing third-strand stabilization of the triplex without affecting the stability of the duplex

Triple-helical RNA are of interest because of possible biological roles as well as the potential therapeutic uses of these structures, while the stability of triplexes is usually weaker than that of the Watson-Crick base pairing duplex strand due to the electrostatic repulsion between three polyanionic strands. Therefore, how to increase the stability of the specific sequences of triplexes are of importance. In this paper the binding of a Ru(II) complex, [Ru(bpy)₂(PIP)]²⁺ (bpy=2.2'-bipyridine, PIP=2-phenyl-1H-imidazo[4,5-f]- [1,10]-phenanthroline), with poly(U)·poly(A)*poly(U) triplex has been investigated by spectrophotometry, spectrofluorometry, viscosimetry and circular dichroism. The results suggest that [Ru(bpy)₂(PIP)]²⁺ as a metallointercalator can stabilize poly(U)·poly(A)*poly(U) triplex (where · denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing),while it stabilizes third-strand with no obvious effect on the duplex of poly(U)·poly(A), reflecting the binding of this complex with the triplex is favored by the Hoogsteen paired poly(U) third strand to a great extent.

Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach

The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNA^Phe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNA^Phe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNA^Phe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNA^Phe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNA^Phe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.

Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)](2+) and [Ru(phen)2(ppn)](2+) with triplex RNA: As molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U) triplex

Stable RNA triplexes play key roles in many biological processes, while triplexes are thermodynamically less stable than the corresponding duplexes due to the Hoogsteen base pairing. To understand the factors affecting the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the binding of [Ru(bpy)2(ppn)](2+) (1, bpy=2,2'-bipyridine, ppn=2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2',3'-h]quinoxaline) and [Ru(phen)2(ppn)](2+) (2, phen=1,10-phenanthroline) to poly(U)·poly(A)*poly(U) (· denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) has been investigated. The main results obtained here suggest that complexes 1 and 2 can serve as molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked, suggesting that the hydrophobicity of ancillary ligands has a significant effect on the two Ru(II) complexes binding to poly(U)·poly(A)*poly(U). This study further advances our knowledge on the binding of RNA triplexes with metal complexes, particularly with octahedral ruthenium polypyridyl complexes.

Experimental and density functional theory (DFT) studies on the interactions of Ru(II) polypyridyl complexes with the RAN triplex poly(U)˙poly(A)*poly(U)

There is renewed interest in investigating triple helices because these novel structures have been implicated as a possible means of controlling cellular processes by endogenous or exogenous mechanisms. Due to the Hoogsteen base pairing, triple helices are, however, thermodynamically less stable than the corresponding duplexes. The poor stability of triple helices limits their practical applications under physiological conditions. In contrast to DNA triple helices, small molecules stabilizing RNA triple helices at present are less well established. Furthermore, most of these studies are limited to organic compounds and, to a far lesser extent, to metal complexes. In this work, two Ru(II) complexes, [Ru(bpy)2(btip)](2+) (Ru1) and [Ru(phen)2(btip)](2+) (Ru2), have been synthesized and characterized. The binding properties of the two metal complexes with the triple RNA poly(U)˙poly(A)*poly(U) were studied by various biophysical and density functional theory methods. The main results obtained here suggest that the slight binding difference in Ru1 and Ru2 may be attributed to the planarity of the intercalative ligand and the LUMO level of Ru(II) complexes. This study further advances our knowledge on the triplex RNA-binding by metal complexes, particularly Ru(II) complexes.

Effect of a Ru(II) polypyridyl complex [Ru(bpy)2(mdpz)]2+ on the stabilization of the RNA triplex poly(U)·poly(A)*poly(U)

There is renewed interest in investigating triplex nucleic acids because triplexes may be implicated in a range of cellular functions. However, the stabilization of triplex nucleic acids is essential to achieve their biological functions. In contrast to triplex DNA, little has been reported concerning the recognition of triplex RNA by transition-metal complexes at present. We report here a ruthenium(ii) polypyridyl complex, [Ru(bpy)2(mdpz)](2+) (bpy = 2,2'-bipyridine; mdpz = 7,7'-methylenedioxyphenyl-dipyrido-[3,2-a:2',3'-c]phenazine), as a sensitive luminescent probe for poly(U)·poly(A)*poly(U), which can strongly stabilize the triplex RNA from 37.5 to 53.1 °C in solution. The main results further advance our knowledge on the triplex RNA-binding by metal complexes, particularly ruthenium(ii) complexes.

Studying non-covalent drug-DNA interactions

Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.

Effect of ancillary ligands on the interaction of ruthenium(II) complexes with the triplex RNA poly(U)·poly(A)*poly(U)

Two new Ru(II) complexes with 1,8-naphthalimide group, [Ru(phen)2(pnip)](2+) (Ru1; phen=1,10-phenanthroline, pnip=2-[N-(p-phenyl)-1,8-napthalimide]imidazo[4',5'-f][1,10]phenanthroline) and [Ru(bpy)2(pnip)](2+) (Ru2; bpy=2,2'-bipyridine), have been synthesized and characterized. The interactions of Ru1 and Ru2 with the triplex RNA poly(U)•poly(A)*poly(U) (where • denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) were studied by various biophysical. Electronic spectra established that the binding affinity for Ru1 was greater than that for Ru2. Fluorescence and viscosity studies gave convincing evidence for a true intercalative binding of both complexes with the RNA triplex. UV melting studies confirmed that the two complexes could stabilize the triplex, whereas the effects of the two complexes on the stability of the Hoogsteen base-paired strand ploy(U) and the Watson-Crick base-paired duplex poly(U)•poly(A) of the triplex were different. In the case of Ru1, the increase of the thermal stability of the Hoogsteen base-paired strand was stronger than that of the Watson-Crick base-paired duplex. However, an opposite effect was observed in the case of Ru2. Circular dichroic studies suggested that the RNA triplex undergoes a conformational transition in the presence of Ru1, whereas the helicity of the RNA triplex still remains A-type in the presence of Ru2. The main results obtained here further advance our knowledge on the interaction of RNA triple-stranded structures with metal complexes, particularly ruthenium(II) complexes.

Interactions of octahedral ruthenium(II) polypyridyl complexes with the RNA triplex poly(U)•poly(A)*poly(U) effect on the third-strand stabilization

Stable triplexes play key roles in many biological processes. Due to the Hoogsteen base pairing, triplexes are, however, thermodynamically less stable than the corresponding duplexes. The poor stabilization of these structures limits their practical applications under physiological conditions. To understand the factors effect on the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the interactions of [RuL2(uip)](2+) {where L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline phen, uip = 2-(5-uracil)-1H-imidazo[4,5-f][1,10]phenanthroline} with the RNA triplex poly(U)•poly(A)*poly(U) are examined by spectrophotometry, spectrofluorometry, circular dichroism, and viscosimetry in this work. The main results obtained here suggest that the third-strand stabilization depends on the hydrophobicity effects of ancillary ligands bpy and phen.

Endogenous polyamine function--the RNA perspective

Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg²⁺) confirming their roles as independent molecular entities which help drive RNA-mediated processes.

Targeting double-stranded RNA with spermine, 1-naphthylacetyl spermine and spermidine: a comparative biophysical investigation

RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.