X-ray crystal structure of rac-[Ru(phen)2dppz]2+ with d(ATGCAT)2 shows enantiomer orientations and water ordering

Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ-[Ru(phen)2 phi]2

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ-[Ru(phen)2 phi]2+ , where phi=9,10-phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2 . The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ-enantiomer and show a high affinity for TA/TA steps and, more generally, TA-rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence.

Array electrochemiluminescence device with ultra-high sensitivity and selectivity for rapid visualized monitoring of trace radon in environment

The World Health Organization has reported radioactive Rn gas as the second leading cause of lung cancer and gives an extreme limit to indoor Radon (Rn) concentration as 100 Bq/m³. To realize rapid and accurate Rn monitoring, we report an efficient visualized electrochemiluminescence (ECL) device for Rn detection with the lowest limit of detection (0.9 Bq/m³/3.6 Bq h m^-3) compared to known Rn detection methods and the shortest measurement time (less than 5 h) among non-pump methods. In detail, an efficient Rn probe is prepared by Au nanoparticles, Pb²⁺ aptamer, as well as NH₂-ssDNA co-reactant and then modified on ITO electrodes to obtain Rn detection devices. With tris(2,2'-bipyridyl)ruthenium(II)chloride (Ru(bpy)₃Cl₂) as an ECL emitter, the devices can exhibit ultra-high sensitivity and selectivity to trace Rn in environment via the ECL quenching caused by ²¹⁰Pb, the relatively stable decay product of Rn. Furthermore, ECL imaging technology can be applied to realize the visualized Rn detection. An efficient up-response ECL detector was also invented to support this detection device to achieve accurate Rn detection in environment. This work reports noble gas ECL detection for the first time and provides an efficient strategy for rapid and accurate monitoring of trace Rn in environment.

Optically Pure Double-Stranded Dinuclear Ir(III) Metallohelices Enabled Chirality-Induced Photodynamic Responses

Investigation on the interactions between enantiomers of chiral drugs and biomolecules can help precisely understand their biological behaviors in vivo and provide insights into the design of new drugs. Herein, we designed and synthesized a pair of optically pure, cationic, double-stranded dinuclear Ir(III)-metallohelices (Λ₂R₄-H and Δ₂S₄-H), and their dramatic enantiomer-dependent photodynamic therapy (PDT) responses were thoroughly studied in vitro and in vivo. Compared to the mononuclear enantiomeric or racemic [Ir(ppy)₂(dppz)][PF₆] (Λ-/Δ-Ir, rac-Ir) that with high dark toxicity and low photocytotoxicity index (PI) values, both of the optically pure metallohelices displayed negligible toxicity in the dark while exhibiting very distinctive light toxicity upon light irradiation. The PI value of Λ₂R₄-H was approximately 428, however, Δ₂S₄-H significantly reached 63,966. Interestingly, only Δ₂S₄-H was found to migrate from mitochondria to nucleus after light irradiation. Further proteomic analysis verified that Δ₂S₄-H activated the ATP-dependent migration process after light irradiation, and subsequently inhibited the activities of the nuclear proteins such as superoxide dismutase 1 (SOD1) and eukaryotic translation initiation factor 5A (EIF5A) to trigger the accumulation of superoxide anions and downregulate mRNA splicing processes. Molecular docking simulations suggested that the interactions between metallohelices and nuclear pore complex NDC1 dominated the migration process. This work presents a new kind of Ir(III) metallohelices-based agent with the highest PDT efficacy, highlights the importance of metallohelices' chirality, and provides inspirations for the future design of chiral helical metallodrugs.

Synthesis, characterization and anticancer properties: A series of highly selective palladium(II) substituted-terpyridine complexes

Ten new palladium(II) complexes [PdCl(L^1-10)]Cl have been synthesized by the reaction of palladium(II) chloride and ten 4'-(substituted-phenyl)-2,2':6',2''-terpyridine ligands bearing hydrogen(L¹), p-hydroxyl(L²), m-hydroxyl (L³), o-hydroxyl (L⁴), methyl (L⁵), phenyl (L⁶), fluoro (L⁷), chloro (L⁸), bromo (L⁹), or iodo (L¹⁰). Their structures were confirmed by FT-IR, ¹H NMR, elemental analysis and/or single crystal X-ray diffraction analysis. Their in vitro anticancer activities were investigated based on five cell lines, including four cancer cell lines (A549, Eca-109, Bel-7402, MCF-7) and one normal cell line (HL-7702). The results show that these complexes possess a strong killing effect on the cancer cells but a weak proliferative inhibition on the normal cells, implying their high inhibitory selectivity for the proliferation of the cancer cell lines. Flow cytometry characterization reveals that these complexes affect cell proliferation mainly in the G0/G1 phase and induce the late apoptotic of the cells. The quantity of palladium(II) ion in extracted DNA was determined by ICP-MS, which proved that these complexes target genomic DNA. And the strong affinity of the complexes with CT-DNA were confirmed by UV-Vis spectrum and circular dichroism (CD). The possible binding modes of the complexes with DNA were further explored by molecular docking. As the concentration of complexes 1-10 gradually increases, the fluorescence intensity of bovine serum albumin (BSA) decreases by a static quenching mechanism.

Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers

Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.

Synthesis, characterization, interactions with the DNA duplex dodecamer d(5'-CGCGAATTCGCG-3')2 and cytotoxicity of binuclear η6-arene-Ru(II) complexes

The novel binuclear η⁶-arene-Ru(II) complexes with the general formula {[(η⁶-cym)Ru(L)]₂(μ-BL)}(PF₆)₄, and their corresponding water soluble {[(η⁶-cym)Ru(L)]₂(μ-BL)}Cl₄, where cym = p-cymene, L = 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen), BL = 4,4'-bipyridine (BL-1), 1,2-bis(4-pyridyl)ethane (BL-2) and 1,3-bis(4-pyridyl)propane (BL-3), were synthesized and characterized. The structure of {[(η⁶-cym)Ru(phen)]₂(μ-BL-1)}(PF₆)₄ was determined by X-ray single crystal methods. The interaction of {[(η⁶-cym)Ru(phen)]₂(μ-BL-i)}Cl₄ (i = 1, 2, 3; (4), (5) and (6) correspondingly) with the DNA duplex d(5'-CGCGAATTCGCG-3')₂ was studied by means of NMR techniques and fluorescence titrations. The results show that complex (4) binds with a K_b = 12.133 × 10³ M^-1 through both intercalation and groove binding, while (5) and (6) are groove binders (K_b = 2.333 × 10³ M^-1 and K_b = 3.336 × 10³ M^-1 correspondingly). Comparison with the mononuclear complex [(η⁶-cym)Ru(phen)(py)]²⁺ reveals that it binds to the d(5'-CGCGAATTCGCG-3')₂ with a K_b value two orders of magnitude lower than (4) (K_b = 0.158 × 10³ M^-1), indicating that for the binuclear complexes both ruthenium moieties participate in the binding. The complexes were found to be cytotoxic against the A2780 and A2780 res. cancer cell line with a selectivity index (SI) in the range of 3.0-5.9.

Ruthenium Polypyridyl Complex Bound to a Unimolecular Chair-Form G-Quadruplex

The DNA G-quadruplex is known for forming a range of topologies and for the observed lability of the assembly, consistent with its transient formation in live cells. The stabilization of a particular topology by a small molecule is of great importance for therapeutic applications. Here, we show that the ruthenium complex Λ-[Ru(phen)₂(qdppz)]²⁺ displays enantiospecific G-quadruplex binding. It crystallized in 1:1 stoichiometry with a modified human telomeric G-quadruplex sequence, GGGTTAGGGTTAGGGTTTGGG (htel21T₁₈), in an antiparallel chair topology, the first structurally characterized example of ligand binding to this topology. The lambda complex is bound in an intercalation cavity created by a terminal G-quartet and the central narrow lateral loop formed by T₁₀–T₁₁–A₁₂. The two remaining wide lateral loops are linked through a third K⁺ ion at the other end of the G-quartet stack, which also coordinates three thymine residues. In a comparative ligand-binding study, we showed, using a Klenow fragment assay, that this complex is the strongest observed inhibitor of replication, both using the native human telomeric sequence and the modified sequence used in this work.

Synthesis, characterisation and biological activity of the ruthenium(II) complexes of the N4-tetradentate (N4-TL), 1,6-di(2'-pyridyl)-2,5-dibenzyl-2,5-diazahexane (picenBz2)

A series of complexes of the type rac-cis-β-[Ru(N₄-T_L)(N₂-bidentates)]²⁺ (where N₄-T_L = 1,6-di(2'-pyridyl)-2,5-dibenzyl-2,5-diazahexane (picenBz₂, N₄-T_L-2) and N₂-bidentates = 1,10-phenanthroline (phen, Ru-2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, Ru-3), 7,8-dimethyl-dipyrido[3,2-a:2',3'-c] phenazine (dppzMe_2,Ru-4), 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline (phenpyrBz, Ru-5), 2-(p-tolyl)-1H-imidazo[4,5-f][1,10]phenanthroline (phenpyrBzMe, Ru-6), 2-(4-nitrophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline (phenpyrBzNO_2,Ru-7), were synthesised and characterised and X-ray crystallography of Ru-5 obtained. The in vitro cytotoxicity assays revealed that Ru-6 was 5, 2 and 19-fold more potent than oxaliplatin, cisplatin, and carboplatin, respectively displaying an average GI₅₀ value of ≈ 0.76 μM against a panel of 11 cancer cell lines.

Synthesis and DNA interaction studies of Ru(II) cell penetrating peptide (CPP) bioconjugates

The synthesis of the first bioconjugates of a set of ruthenium(II) dipyridophenazine complexes with two different cell penetrating peptides (CPPs) is described. The CPPs, an arginine rich TAT-9 (RKKRRQRRR) sequence and the Xentry peptide (LCLRPVG), were synthesized using standard SPPS protocols, and the bioconjugates were obtained by the microwave-assisted coupling of the HOBt/TBTU preactivated metal complexes with the respective peptides on Wang resin. The racemic metal complexes were obtained by modified literature procedures. The bioconjugates were cleaved from the resin, purified by semi-preparative HPLC and characterized by analytical HPLC, high resolution mass spectrometry (HR-MS), and NMR spectroscopy. Despite the bioconjugation of the peptides to the dppz ligand, DNA intercalation was observed by CD spectroscopy, viscometry and the characteristic switch-on fluorescence of this class of compounds. Furthermore, the cellular uptake of the Xentry bioconjugates was confirmed by live cell imaging. Like the parent metal complexes, the bioconjugates show low in vitro cytotoxicity (IC₅₀ > 80 μM), which is similar to the respective metal complexes alone.

Anticancer effect evaluation in vitro and in vivo of iridium(III) polypyridyl complexes targeting DNA and mitochondria

To investigate the antitumor effect of iridium complexes, three iridium (III) complexes [Ir(ppy)₂(dcdppz)]PF₆ (ppy = 2-phenylpyridine, dcdppz = 11,12-dichlorodipyrido[3,2-a:2',3'-c]phenazine) (Ir1), [Ir(bzq)₂(dcdppz)]PF₆ (bzq = benzo[h]quinoline) (Ir2) and [Ir(piq)₂(dcdppz)]PF₆ (piq = 1-phenylisoquinoline) (Ir3) were synthesized and characterized. Geometry optimization, molecular dynamics simulation and docking studies have been performed to further explore the antitumor mechanism. The cytotoxicity of Ir1-3 toward cancer cells was studied by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. The localization of complexes Ir1-3 in the mitochondria, intracellular accumulation of reactive oxygen species (ROS) levels, the changes of mitochondrial membrane potential and morphological changes in apoptosis were investigated. Flow cytometry was applied to quantify fluorescence intensity and determine cell cycle distribution. Western blotting was used to detect the expression of apoptosis-related proteins. The anti-tumor effect of Ir1 in vivo was evaluated. The results showed that Ir1-3 had high cytotoxicity to most tumor cells, especially to SGC-7901 cells with a low IC₅₀ value. Ir1-3 can increase the intracellular ROS levels, reduce the mitochondrial membrane potential. Additionally, the complexes induce an increase of apoptosis-related protein expression, enhance the percentage of apoptosis. The complexes inhibit the cell proliferation at G0/G1 phase. The results obtained from antitumor in vivo indicate that Ir1 can significantly inhibit the growth of tumors with an inhibitory rate of 54.08%. The docking studies show that complexes Ir1-3 interact with DNA through minor-groove intercalation, which increases the distance of DNA base pairs, leading to a change of DNA helix structure. These experimental and theoretical findings indicate that complexes Ir1-3 can induce apoptosis in SGC-7901 cells through the mitochondrial dysfunction and DNA damage pathways, and then exerting anti-tumor activity in vitro and vivo.

Copper chloride complexes with substituted 4'-phenyl-terpyridine ligands: synthesis, characterization, antiproliferative activities and DNA interactions

Eleven copper chloride coordination compounds (1-11) with 4'-(4'-substituted-phenyl)-2,2':6',2''-terpyridine ligands bearing hydrogen (L¹), cyano (L²), p-hydroxyl (L³), m-hydroxyl (L⁴), o-hydroxyl (L⁵), methoxyl (L⁶), iodo (L⁷), bromo (L⁸), chloro (L⁹), fluoro (L¹⁰) or methylsulfonyl (L¹¹) were prepared and characterized by IR spectroscopy, elemental analysis and single crystal X-ray diffraction. Antiproliferative activities against tumor cells were investigated and DNA interactions were studied by circular dichroism spectroscopy and molecular modeling methods. In vitro data demonstrate that all the compounds exhibit higher antiproliferative activities as compared to cisplatin against five human carcinoma cell lines: A549, Bel-7402, Eca-109, HeLa and MCF-7. Compound 6 with methoxyl shows the best anti-proliferation activity. Spectrophotometric results reveal the strong affinity of the compounds for binding with DNA as intercalators and induce DNA conformational transitions. The results of molecular docking studies show that the compounds interact with DNA through π-π stacking, van der Waals forces, hydrophobic interactions and hydrogen bonds. The binding energies between compound 11 and three macromolecules, including DNA duplex, oligonucleotide and DNA-Topo I complex, are the lowest. The binding stability of compounds containing hydroxyl, methoxy and methylsulfonyl groups with biological macromolecules mainly relies on the hydrogen bonds. The ability of a compound to form hydrogen bonds can promote its binding to biological targets, thereby exhibiting high antiproliferative activity.

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.

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.

Bifunctional ruthenium(ii) polypyridyl complexes of curcumin as potential anticancer agents

Ru(ii)-polypyridyl complexes have been widely studied and well established for their antitumor properties. Modifications of the coordination environment around the Ru atom through a proper choice of the ligand can lead to different modes of action and result in greatly improved anticancer efficacy. Herein, two Ru(ii)-polypyridyl complexes of curcumin were synthesized and characterized as potential anticancer agents. In vitro tests indicated that complexes 1 and 2 displayed excellent antiproliferative activity against the tested cancer cell lines, especially complex 2, which exhibited superior cytotoxicity compared to curcumin and cisplatin. Further biological evaluations demonstrated that complexes 1 and 2 can cause cell apoptosis via DNA interaction and MEK/ERK signaling pathway, which is the first example of a Ru(ii)-polypyridyl complex inhibiting the MEK/ERK signaling pathway and DNA intercalation. Overall, this work suggests that coordination with bioactive agents may endow Ru(ii)-polypyridyl complexes with improved pharmaceutical properties and synergistic effects for cancer therapy.

Photoactive metal complexes that bind DNA and other biomolecules as cell probes, therapeutics, and theranostics

Using selected transition metal centres and linking ligand “building blocks” a modular approach to the development of cellular imaging agents and therapeutics is discussed and illustrated with examples from research by the Thomas group.

Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide

Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru(bpy)₂}₂(tpphz)]⁴⁺ (tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine) by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG).d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with Λ Ru^II centers showing a better intercalation fit.

Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz]2+ and [Ru(phen)₂dppz]2+ with a DNA Molecule

[Ru(bpy)₂dppz]²⁺ and [Ru(phen)₂dppz]²⁺ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.

Three thymine/adenine binding modes of the ruthenium complex Λ-[Ru(TAP)2(dppz)]2+ to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography

Λ-[Ru(TAP)₂(dppz)]²⁺ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT).

Spectro-electrochemical Studies on [Ru(TAP)2(dppz)]2+-Insights into the Mechanism of its Photosensitized Oxidation of Oligonucleotides

[Ru(TAP)₂(dppz)]²⁺ (TAP = 1,4,5,8-tetraazaphenanthrene; dppz = dipyrido[3,2- a:2',3'- c]phenazine) is known to photo-oxidize guanine in DNA. Whether this oxidation proceeds by direct photoelectron transfer or by proton-coupled electron transfer is still unknown. To help distinguish between these mechanisms, spectro-electrochemical experiments have been carried out with [Ru(TAP)₂(dppz)]²⁺ in acetonitrile. The UV-vis and mid-IR spectra obtained for the one-electron reduced product were compared to those obtained by picosecond transient absorption and time-resolved infrared experiments of [Ru(TAP)₂(dppz)]²⁺ bound to guanine-containing DNA. An interesting feature of the singly reduced species is an electronic transition in the near-IR region (with λ_max at 1970 and 2820 nm). Density functional and time-dependent density functional theory simulations of the vibrational and electronic spectra of [Ru(TAP)₂(dppz)]²⁺, the reduced complex [Ru(TAP)₂(dppz)]⁺, and four isomers of [Ru(TAP)(TAPH)(dppz)]²⁺ (a possible product of proton-coupled electron transfer) were performed. Significantly, these predict absorption bands at λ > 1900 nm (attributed to a ligand-to-metal charge-transfer transition) for [Ru(TAP)₂(dppz)]⁺ but not for [Ru(TAP)(TAPH)(dppz)]²⁺. Both the UV-vis and mid-IR difference absorption spectra of the electrochemically generated singly reduced species [Ru(TAP)₂(dppz)]⁺ agree well with the transient absorption and time-resolved infrared spectra previously determined for the transient species formed by photoexcitation of [Ru(TAP)₂(dppz)]²⁺ intercalated in guanine-containing DNA. This suggests that the photochemical process in DNA proceeds by photoelectron transfer and not by a proton-coupled electron transfer process involving formation of [Ru(TAP)(TAPH)(dppz)]²⁺, as is proposed for the reaction with 5'-guanosine monophosphate. Additional infrared spectro-electrochemical measurements and density functional calculations have also been carried out on the free TAP ligand. These show that the TAP radical anion in acetonitrile also exhibits strong broad near-IR electronic absorption (λ_max at 1750 and 2360 nm).

In-vivo evaluation of the response of Galleria mellonella larvae to novel copper(II) phenanthroline-phenazine complexes

Herein we report the in-vivo characterisation and metabolic changes in Galleria mellonella larvae to a series of bis-chelate copper(II) phenanthroline-phenazine cationic complexes of [Cu(phen)₂]²⁺ (Cu-Phen), [Cu(DPQ)(Phen)]²⁺ (Cu-DPQ-Phen) and [Cu(DPPZ)(Phen)]²⁺ (Cu-DPPZ-Phen) (where phen = 1,10-phenanthroline, DPQ = dipyrido[3,2-ƒ:2',3'-h]quinoxaline and DPPZ = dipyrido[3,2-a:2',3'-c]phenazine). Our aim was to investigate the influence of the systematic extension of the ligated phenazine ligand in the G. mellonella model as a first step towards assessing the in-vivo tolerance and mode of action of the complex series with respect to the well-studied oxidative chemical nuclease, Cu-Phen. The Lethal Dose₅₀ (LD₅₀) values were established over dose ranges of 2 - 30 μg at 4-, 24-, 48- and 72 h by mortality assessment, with Cu-Phen eliciting the highest mortality at 4 h (Cu-Phen, 12.62 μg < Cu-DPQ-Phen, 21.53 μg < Cu-DPPZ-Phen, 26.07 μg). At other timepoints, a similar profile was observed as the phenazine π-backbone within the complex scaffold was extended. Assessment of both cellular response and related gene expression demonstrated that the complexes did not initiate an immune response. However, Label-Free Quantification proteomic data indicated the larval response was associated with upregulation of key proteins such as Glutathione S-transferase, purine synthesis and glycolysis/gluconeogenesis (e.g. fructose-bisphosphate aldolase and glyceraldehyde-3-phosphate). Both Cu-Phen and Cu-DPQ-Phen elicited a similar in-vivo response in contrast to Cu-DPPZ-Phen, which displayed a substantial increase in nitrogen detoxification proteins and proteins with calcium binding sites. Overall, the response of G. mellonella larvae exposure to the complex series is dominated by detoxification and metabolic proteome response mechanisms.

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.

The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications

Ruthenium(ii) [Ru(ii)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.

Competitive DNA binding of Ru(bpy)2dppz2+ enantiomers studied with isothermal titration calorimetry (ITC) using a direct and general binding isotherm algorithm

While isothermal titration calorimetry (ITC) is widely used and sometimes referred to as the "gold standard" for quantitative measurements of biomolecular interactions, its usage has so far been limited to the analysis of the binding to isolated, non-cooperative binding sites. Studies on more complicated systems, where the binding sites interact, causing either cooperativity or anti-cooperativity between neighboring bound ligands, are rare, probably due to the complexity of the methods currently available. Here we have developed a simple algorithm not limited by the complexity of a binding system, meaning that it can be implemented by anyone, from analyzing systems of simple, isolated binding sites to complicated interactive multiple-site systems. We demonstrate here that even complicated competitive binding calorimetric isotherms can be properly analyzed, provided that ligand-ligand interactions are taken into account. As a practical example, the competitive binding interactions between the two enantiomers of Ru(bpy)₂dppz²⁺ (Ru-bpy) and poly(dAdT)₂ (AT-DNA) are analyzed using our new algorithm, which provided an excellent global fit for the ITC experimental data.

Photochemically active DNA-intercalating ruthenium and related complexes - insights by combining crystallography and transient spectroscopy

Recent research on the study of the interaction of ruthenium polypyridyl compounds and defined sequence nucleic acids is reviewed. Particular emphasis is paid to complexes [Ru(LL)2(Int)]2+ containing potentially intercalating ligands (Int) such as dipyridophenazine (dppz), which are known to display light-switching or photo-oxidising behaviour, depending on the nature of the ancillary ligands. X-ray crystallography has made a key contribution to our understanding, and the first complete survey of structural results is presented. These include sequence, enantiomeric, substituent and structural specificities. The use of ultrafast transient spectroscopic methods to probe the ultrafast processes for complexes such as [Ru(TAP)2(dppz)]2+ and [Ru(phen)2(dppz)]2+ when bound to mixed sequence oligonucleotides are reviewed with particular attention being paid to the complementary advantages of transient (visible) absorption and time-resolved (mid) infra-red techniques to probe spectral changes in the metal complex and in the nucleic acid. The observed photophysical properties are considered in light of the structural information obtained from X-ray crystallography. In solution, metal complexes can be expected to bind at more than one DNA step, so that a perfect correlation of the photophysical properties and factors such as the orientation or penetration of the ligand into the intercalation pocket should not be expected. This difficulty can be obviated by carrying out TRIR studies in the crystals. Dppz complexes also undergo insertion, especially with mismatched sequences. Future areas for study such as those involving non-canonical forms of DNA, such as G-quadruplexes or i-motifs are also briefly considered.

Binding Differences of Two Homochiral [Ru(bpy)2dppz]2+ Complexes with poly(U)·poly(A)*poly(U) Triplex RNA

The first investigation of chiral ruthenium(II) complexes Δ- and Λ-[Ru(bpy)₂dppz]²⁺ and triplex RNA poly(U)·poly(A)*poly(U) was carried out, which showed that Δ enantiomer displayed significant ability in stabilizing model triplex RNA.

Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects

X-ray crystal structures of three Λ-[Ru(L)2 dppz]2+ complexes (dppz=dipyridophenazine; L=1,10-phenanthroline (phen), 2,2'-bipyridine (bpy)) bound to d((5BrC)GGC/GCCG) showed the compounds intercalated at a 5'-CG-3' step. The compounds bind through canted intercalation, with the binding angle determined by the guanine NH2 group, in contrast to symmetrical intercalation previously observed at 5'-TA-3' sites. This result suggests that canted intercalation is preferred at 5'-CG-3' sites even though the site itself is symmetrical, and we hypothesise that symmetrical intercalation in a 5'-CG-3' step could give rise to a longer luminescence lifetime than canted intercalation.

The Structure of Linkers Affects the DNA Binding Properties of Tethered Dinuclear Ruthenium(II) Metallo-Intercalators

With the long-term aim of enhancing the binding properties of dinuclear Ru^II -based DNA light-switch complexes, a series of eight structurally related mono- and dinuclear systems are reported in which the linker of the bridging ligand has been modulated. These tethered systems have been designed to explore issues of steric demand at the binding site and the thermodynamic cost of entropy loss upon binding. Detailed spectroscopic and isothermal titration calorimetry (ITC) studies on the new complexes reveal that one of the linkers produces a dinuclear system that binds to duplex DNA with an affinity (K_b >10⁷  m^-1 ) that is higher than its corresponding monometallic complex and is the highest affinity for a non-threading bis-intercalating metal complex. These studies confirm that the tether has a major effect on the binding properties of dinuclear complexes containing intercalating units and establishes key design rules for the construction of dinuclear complexes with enhanced DNA binding characteristics.

Two ruthenium complexes capable of storing multiple electrons on a single ligand – photophysical, photochemical and electrochemical properties of [Ru(phen)2(TAPHAT)]2+ and [Ru(phen)2(TAPHAT)Ru(phen)2]4+

The photophysical, photochemical and electrochemical properties of two newly synthesized ruthenium(ii) complexes are reported.

Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation

DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [μ-dppzip(phen)4Ru2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)2dppz) and the distal subunit (Ru(phen)2ip), respectively, each of which can be either right-handed (Δ) or left-handed (Λ). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Δxeq, and the dynamic DNA structural deformations during ligand association xon and dissociation xoff. We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a Kd of 27 ± 3 nM for (Δ,Λ)-Piz to a Kd of 622 ± 55 nM for (Λ,Δ)-Piz. The striking affinity decrease is correlated with increasing Δxeq from 0.30 ± 0.02 to 0.48 ± 0.02 nm and xon from 0.25 ± 0.01 to 0.46 ± 0.02 nm, but limited xoff changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.

Transition Metal Intercalators as Anticancer Agents-Recent Advances

The diverse anticancer utility of cisplatin has stimulated significant interest in the development of additional platinum-based therapies, resulting in several analogues receiving clinical approval worldwide. However, due to structural and mechanistic similarities, the effectiveness of platinum-based therapies is countered by severe side-effects, narrow spectrum of activity and the development of resistance. Nonetheless, metal complexes offer unique characteristics and exceptional versatility, with the ability to alter their pharmacology through facile modifications of geometry and coordination number. This has prompted the search for metal-based complexes with distinctly different structural motifs and non-covalent modes of binding with a primary aim of circumventing current clinical limitations. This review discusses recent advances in platinum and other transition metal-based complexes with mechanisms of action involving intercalation. This mode of DNA binding is distinct from cisplatin and its derivatives. The metals focused on in this review include Pt, Ru and Cu along with examples of Au, Ni, Zn and Fe complexes; these complexes are capable of DNA intercalation and are highly biologically active.

Delta chirality ruthenium 'light-switch' complexes can bind in the minor groove of DNA with five different binding modes

[Ru(phen)₂(dppz)]²⁺ has been studied since the 1990s due to its 'light-switch' properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding. The luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, and therefore is sensitive to changes in both binding site of the cation and chromophore orientation. The compound is also chiral, and there are distinct differences between the enantiomers in terms of the emission behaviour when bound to a variety of DNA sequences. Whilst a number of binary DNA-complex X-ray crystal structures are available, most include the Λ enantiomer and there is very little structural information about binding of the Δ enantiomer. Here, we present the first X-ray crystal structure of a Δ enantiomer bound to well-matched DNA, in the absence of the other, Λ enantiomer. We show how the binding site observed here can be related to a more general pattern of motifs in the crystallographic literature and propose that the Δ enantiomer can bind with five different binding modes, offering a new hypothesis for the interpretation of solution data.

Monitoring guanine photo-oxidation by enantiomerically resolved Ru(II) dipyridophenazine complexes using inosine-substituted oligonucleotides

The intercalating [Ru(TAP)2(dppz)](2+) complex can photo-oxidise guanine in DNA, although in mixed-sequence DNA it can be difficult to understand the precise mechanism due to uncertainties in where and how the complex is bound. Replacement of guanine with the less oxidisable inosine (I) base can be used to understand the mechanism of electron transfer (ET). Here the ET has been compared for both Λ- and Δ-enantiomers of [Ru(TAP)2(dppz)](2+) in a set of sequences where guanines in the readily oxidisable GG step in {TCGGCGCCGA}2 have been replaced with I. The ET has been monitored using picosecond and nanosecond transient absorption and picosecond time-resolved IR spectroscopy. In both cases inosine replacement leads to a diminished yield, but the trends are strikingly different for Λ- and Δ-complexes.

Direct observation by time-resolved infrared spectroscopy of the bright and the dark excited states of the [Ru(phen)2(dppz)]2+ light-switch compound in solution and when bound to DNA

The [Ru(phen)2(dppz)]2+ complex (1) is non-emissive in water but is highly luminescent in organic solvents or when bound to DNA, making it a useful probe for DNA binding. To date, a complete mechanistic explanation for this "light-switch" effect is still lacking. With this in mind we have undertaken an ultrafast time resolved infrared (TRIR) study of 1 and directly observe marker bands between 1280-1450 cm-1, which characterise both the emissive "bright" and the non-emissive "dark" excited states of the complex, in CD3CN and D2O respectively. These characteristic spectral features are present in the [Ru(dppz)3]2+ solvent light-switch complex but absent in [Ru(phen)3]2+, which is luminescent in both solvents. DFT calculations show that the vibrational modes responsible for these characteristic bands are predominantly localised on the dppz ligand. Moreover, they reveal that certain vibrational modes of the "dark" excited state couple with vibrational modes of two coordinating water molecules, and through these to the bulk solvent, thus providing a new insight into the mechanism of the light-switch effect. We also demonstrate that the marker bands for the "bright" state are observed for both Λ- and Δ-enantiomers of 1 when bound to DNA and that photo-excitation of the complex induces perturbation of the guanine and cytosine carbonyl bands. This perturbation is shown to be stronger for the Λ-enantiomer, demonstrating the different binding site properties of the two enantiomers and the ability of this technique to determine the identity and nature of the binding site of such intercalators.

Synthesis of cis-[Cr(diimine)2(1-methylimidazole)2](3+) Complexes and an Investigation of Their Interaction with Mononucleotides and Polynucleotides

A protocol is presented for the synthesis of chromium(III) complexes of the type cis-[Cr(diimine)2(1-methylimidazole)2](3+). These compounds exhibit large excited-state oxidizing powers and strong luminescence in solution. Emission is quenched by added guanine, yielding rate constants that track the driving force for guanine oxidation. The cis-[Cr(TMP)(DPPZ)(1-MeImid)2](3+) species binds strongly to duplex DNA with a preference for AT base sites in the minor groove and may serve as a precursor for photoactivated DNA covalent adduct formation.