A theoretical study of Ru(II) polypyridyl DNA intercalators

Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone

The influence of hydrogen bonds in model intercalated systems between guanine-cytosine and adenine-thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10-phenanthroline (phen) and derivatives obtained by substitution with OH and NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6-DH2, M06-2X and B3LYP-D3 along with the recently developed near linear-scaling coupled cluster method DLPNO-CCSD(T) for benchmark calculations. Our results given by QTAIM and non-covalent interaction analysis confirmed the existence of hydrogen bonds created by OH and NH2 . The trends in the energy decomposition analysis for the interaction energy, ΔEint , showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp . Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by OH and NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint . The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.

Theoretical Investigation of the 4,5-Dibromorodamine Methyl Ester (TH9402) Photosensitizer Used in Photodynamic Therapy: Photophysics, Reactions in the Excited State, and Interactions with DNA

Photosensitizer (PS) molecules play a critical role in photodynamic therapy of cancer and the understanding of the molecular mechanism involved in the photophysics of these compounds, and their reactions in the excited state are, therefore, of great interest for the development of this technique. In this article, the photophysics of the cationic PS 4,5-dibromorodamine methyl ester (TH9402), its electron- and energy-transfer reactions in the excited triplet state, with molecular oxygen, nitric oxide, guanosine-5'-monophosphate (GMP), and guanine, and the interaction with DNA were evaluated. Time-dependent density functional theory calculations at the TPSSh/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water solution reveals that the PS has a bright S₁ state 2.33 eV above the ground state that produces a fluorescent rate constant of 5.40 × 10⁷ s^-1, calculated using Fermi's golden rule within a path integral formalism. Once excited to the bright state, the main intersystem crossing (ISC) channel involves the coupling with the T₂ state just below S₁ (S₁ → T₂ → T₁) with an overall ISC rate constant of 10.1 × 10⁷ s^-1, in good agreement with the experimental data. Excited-state reaction thermodynamics, computed at the M06-2X/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water, showed that from all the excited-state electron-transfer reactions studied, only the transfer from GMP to the PS is thermodynamically favorable, independent of the protonation state of guanosine, which indicates a possible DNA photo-oxidation mechanism for the PS. Triplet-triplet energy-transfer reactions from TH9402 to molecular oxygen, producing reactive singlet oxygen, and to the deprotonated guanosine, producing ³GMP^2-, are also thermodynamically favorable, with ΔG = -2.0 and -24.0 kcal//mol, respectively. However, the energy transfer to the monoprotonated guanosine is not favorable, (ΔG = 36.1), suggesting that in the DNA double-strand environment, this energy-transfer process may not be observed. The results show that the PS can act through electron transfer and triplet-triplet energy-transfer reactions involved in mechanism types I and II in photodynamic therapy. Interactions of TH9402 with the d(AGACGTCT)₂ octanucleotide revealed that the PS can intercalate between the d(GpC)-d(CpG) base pairs in three different orientations and, upon intercalation, the π → π* transition of the PS shows a bathochromic shift up to 90 nm and up to 60% decrease in intensity. Interactions through groove binding showed a smaller bathochromic shift of 52.2 nm and a 56% decrease in intensity of the main transition band.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

Influence of the Protonation State on the Excited-State Dynamics of Ruthenium(II) Complexes with Imidazole π-Extended Dipyridophenazine Ligands

Ruthenium(II) complexes, like [(tbbpy)₂Ru(dppz)]²⁺ (Ru-dppz; tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine, dppz = dipyrido-[3,2-a:2',3'-c]phenazine), have emerged as suitable photosensitizers in photoredox catalysis. Since then, there has been ongoing interest in the design of π-extended Ru-dppz systems with red-shifted visible absorption maxima and sufficiently long-lived excited states independent of the solvent or pH value. Herein, we explore the photophysical properties of protonation isomers of the linearly π-extended [(tbbpy)₂Ru(L)]²⁺-type complexes bearing a dppz ligand with directly fused imidazole (im) and methyl-imidazole units (mim) as L. Steady-state UV-vis absorption, resonance Raman, as well as time-resolved emission and transient absorption spectroscopy reveal that Ru-im and Ru-mim show desirable properties for the application in photocatalytic processes, i.e., strong visible absorbance and two long-lived excited states in the ³ILCT and ³MLCT manifold, at pH values between 3 and 12. However, protonation of the (methyl-)imidazole unit at pH ≤ 2 unit causes decreased excited-state lifetimes and an emission switch-off.

Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action

Phenanthriplatin (PtPPH) is a monovalent platinum(II)-based complex with a large cytotoxicity against cancer cells. Although the aqua-activated drug has been assumed to be the precursor for DNA damage, it is still under debate whether the way in which that metallodrug attacks to DNA is dominated by a direct binding to a guanine base or rather by an intercalated intermediate product. Aiming to capture the mechanism of action of PtPPH, the present contribution used theoretical tools to systematically assess the sequence of all possible mechanisms on drug activation and reactivity, for example, hydrolysis, intercalation, and covalent damage to DNA. Ab initio quantum mechanical (QM) methods, hybrid QM/QM′ schemes, and independent gradient model approaches are implemented in an unbiased protocol. The performed simulations show that the cascade of reactions is articulated in three well-defined stages: (i) an early and fast intercalation of the complex between the DNA bases, (ii) a subsequent hydrolysis reaction that leads to the aqua-activated form, and (iii) a final formation of the covalent bond between PtPPH and DNA at a guanine site. The permanent damage to DNA is consequently driven by that latter bond to DNA but with a simultaneous π–π intercalation of the phenanthridine into nucleobases. The impact of the DNA sequence and the lateral backbone was also discussed to provide a more complete picture of the forces that anchor the drug into the double helix.

Cu(II) complex with auxin (3-indoleacetic acid) and an aromatic planar ligand: synthesis, crystal structure, biomolecular interactions and radical scavenging activity

A novel water soluble ternary copper(II) complex,-[Cu₂(phen)₂(3-IAA)₂(H₂O)](ClO₄)₂·H₂O-(phen: 1,10-phenanthroline, 3-IAA: 3-indoleacetic acid), has been synthesized and characterized by elemental CHN analysis, ESI-TOF, FTIR and single-crystal X-ray diffraction techniques. Interaction of the complex with calf thymus DNA (CT-DNA) has been investigated by absorption spectral titration, ethidium bromide (EB) and Hoechst 33258 displacement assay. The interactions between the complex and bovine serum albumin (BSA) were investigated by electronic absorption and fluorescence spectroscopy methods. The experimental results indicate that the fluorescence quenching mechanism between the complex and BSA is a static quenching process. The Stern-Volmer constants, binding constants, binding sites and the corresponding thermodynamic parameters (ΔG, ΔH, ΔS) of BSA + complex systems were determined at different temperatures. The binding distance between the complex and BSA was calculated according to Förster non-radiation energy transfer theory (FRET). The effect of the complex on the conformation of BSA was also examined using synchronous, two dimensional (2D) and three dimensional (3D) fluorescence spectroscopy. Furthermore, the oxygen radical scavenging activity of the complex was determined in terms of IC₅₀, using the DPPH and H₂O₂ method, to show that it particularly enables electron loss from radical species. This study highlights the importance of indole and moieties in the development of antioxidant agents. A potent drug candidate novel water soluble ternary copper(II) complex,-[Cu₂(phen)₂(3-IAA)₂(H₂O)] (ClO₄)₂·H₂O-(phen: 1,10-phenanthroline, 3-IAA: 3-indoleacetic acid), has been synthesized and characterized by elemental CHN analysis, FTIR, ESI-MS and single-crystal X-ray diffraction techniques. The complex has been tested for in vitro biomacromolecular interactions by spectroscopic methods. Furthermore, radical scavenging activities of the complex were also investigated.

Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions

Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.

Photophysics of Ruthenium(II) Complexes with Thiazole π-Extended Dipyridophenazine Ligands

Transition-metal-based donor-acceptor systems can produce long-lived excited charge-transfer states by visible-light irradiation. The novel ruthenium(II) polypyridyl type complexes Ru1 and Ru2 based on the dipyridophenazine ligand (L0) directly linked to 4-hydroxythiazoles of different donor strengths were synthesized and photophysically characterized. The excited-state dynamics were investigated by femtosecond-to-nanosecond transient absorption and nanosecond emission spectroscopy complemented by time-dependent density functional theory calculations. These results indicate that photoexcitation in the visible region leads to the population of both metal-to-ligand charge-transfer (¹MLCT) and thiazole (tz)-induced intraligand charge-transfer (¹ILCT) states. Thus, the excited-state dynamics is described by two excited-state branches, namely, the population of (i) a comparably short-lived phenazine-centered ³MLCT state (τ ≈ 150-400 ps) and (ii) a long-lived ³ILCT state (τ ≈ 40-300 ns) with excess charge density localized on the phenazine and tz moieties. Notably, the ruthenium(II) complexes feature long-lived dual emission with lifetimes in the ranges τ_Em,1 ≈ 40-300 ns and τ_Em,2 ≈ 100-200 ns, which are attributed to emission from the ³ILCT and ³MLCT manifolds, respectively.

Zinc Complexes with Nitrogen Donor Ligands as Anticancer Agents

The search for anticancer metal-based drugs alternative to platinum derivatives could not exclude zinc derivatives due to the importance of this metal for the correct functioning of the human body. Zinc, the second most abundant trace element in the human body, is one of the most important micro-elements essential for human physiology. Its ubiquity in thousands of proteins and enzymes is related to its chemical features, in particular its lack of redox activity and its ability to support different coordination geometries and to promote fast ligands exchange. Analogously to other trace elements, the impairment of its homeostasis can lead to various diseases and in some cases can be also related to cancer development. However, in addition to its physiological role, zinc can have beneficial therapeutic and preventive effects on infectious diseases and, compared to other metal-based drugs, Zn(II) complexes generally exert lower toxicity and offer few side effects. Zinc derivatives have been proposed as antitumor agents and, among the great number of zinc coordination complexes which have been described so far, this review focuses on the design, synthesis and biological studies of zinc complexes comprising N-donor ligands and that have been reported within the last five years.

Exploring the cytotoxic activity of new phenanthroline salicylaldimine Zn(II) complexes

Zinc(II) complexes bearing N-salicylideneglycinate (Sal-Gly) and 1,10-phenanthroline (phen) or phenanthroline derivatives [NN = 5-chloro-1,10-phenanthroline, 5-amine-1,10-phenanthroline (amphen), 4,7-diphenyl-1,10-phenanthroline (Bphen) and 5,6-epoxy-5,6-dihydro-1,10-phenanthroline] are synthesized. Complexes formulated as [Zn(NN)₂(H₂O)₂]²⁺(NN = phen and amphen), are also prepared. The cytotoxicity of the compounds is evaluated towards a panel of human cancer cells: ovarian (A2780), breast (MCF7) and cervical (HeLa), as well as non-tumoral V79 fibroblasts. All compounds display higher cytotoxicity than cisplatin (IC₅₀ = 22.5 ± 5.0 μM) towards ovarian cells, showing IC₅₀values in the low micromolar range. Overall, all compounds show higher selectivity for the A2780 cells than for the non-tumoral cells and higher selectivity indexes (IC₅₀(V79)/IC₅₀(A2780) than cisplatin. [Zn(Sal-Gly)(NN)(H₂O)] complexes induce caspase-dependent apoptosis in A2780 cells, except [Zn(Sal-Gly)(Bphen)(H₂O)], one of the most cytotoxic of the series. The cellular uptake in the ovarian cells analyzed by Inductively Coupled Plasma mass spectrometry indicates different Zn distribution profiles. Transmission electronic microscopy shows mitochondria alterations and apoptotic features consistent with caspase activation; cells incubated with [Zn(Sal-Gly)(amphen)(H₂O)] present additional nuclear membrane alterations in agreement with significant association with the nucleus. The increase of reactive oxygen species and lipid peroxidation forms could be related to apoptosis induction. [Zn(NN)₂(H₂O)₂]²⁺complexes have high ability to bind DNA through intercalation/groove binding, and circular dichroism data suggests that the main type of species that interact with DNA is [Zn(NN)]²⁺. Studies varying the % of fetal bovine serum (1-15%) in cell media show that albumin binding decreases the complex activity, indicating that distinct speciation of Zn- and phen-containing species in cell media may affect the cytotoxicity.

Charge-Transfer versus Charge-Separated Triplet Excited States of [ReI (dmp)(CO)3 (His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.

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).

Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment

Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.

Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study

The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.

Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors

We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.

A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs

This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.

Ruthenium(ii) complexes with dppz: from molecular photoswitch to biological applications

The present article describes the recent advances in biological applications of the Ru-dppz systems in DNA binding, cellular imaging, anticancer drugs, phototherapy, protein aggregation detecting and chemosensors.

Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

We investigate the attack of the nitrogen dioxide radical (NO^•₂) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO^•₂ radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO₂-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO^•₂ radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

Photophysical properties of ruthenium(II) polypyridyl DNA intercalators: effects of the molecular surroundings investigated by theory

The environmental effects on the structural and photophysical properties of [Ru(L)2 (dppz)](2+) complexes (L=bpy=2,2'-bipyridine, phen=1,10-phenanthroline, tap=1,4,5,8-tetraazaphenanthrene; dppz=dipyrido[3,3-a:2',3'-c]phenazine), used as DNA intercalators, have been studied by means of DFT, time-dependent DFT, and quantum mechanics/molecular mechanics calculations. The electronic characteristics of the low-lying triplet excited states in water, acetonitrile, and DNA have been investigated to decipher the influence of the environment on the luminescent behavior of this class of molecules. The lowest triplet intra-ligand (IL) excited state calculated at λ≈800 nm for the three complexes and localized on the dppz ligand is not very sensitive to the environment and is available for electron transfer from a guanine nucleobase. Whereas the lowest triplet metal-to-ligand charge-transfer ((3)MLCT) states remain localized on the ancillary ligand (tap) in [Ru(tap)2 (dppz)](2+), regardless of the environment, their character is drastically modified in the other complexes [Ru(phen)2 (dppz)](2+) and [Ru(bpy)2 (dppz)](2+) upon going from acetonitrile (MLCTdppz/phen or MLCTdppz/bpy) to water (MLCTdppz) and DNA (MLCTphen and MLCTbpy). The change in the character of the low-lying (3) MLCT states accompanying nuclear relaxation in the excited state controls the emissive properties of the complexes in water, acetonitrile, and DNA. The light-switching effect has been rationalized on the basis of environment-induced control of the electronic density distributed in the lowest triplet excited states.

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)₂ <d(CpA)₂ <d(ApT)₂ <d(ApA)₂ <d(GpT)₂ <d(GpA)₂ <d(ApG)₂ <d(CpG)₂ <d(GpG)₂ <d(GpC)₂, where the energy differences between the last four dimers, d(ApG)₂, d(CpG)₂, d(GpG)₂ and d(GpC)₂, is within 4.0 kcal mol⁻¹, and the energy between the most and the least stable isomers is 13.4 kcal mol⁻¹. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.

Preparation of a DNA-bound [Ru(bpy)₂(mbpibH2)]²+ film and its two-mode luminescence tuning by copper(II) ions and EDTA

An imidazophenanthroline-containing ruthenium(II) complex [Ru(bpy)(2)(mbpibH2)](2+) (bpy=2,2'-bipyridine, mbpibH2=1,3-bis([1,10]phenanthroline[5,6-d]imidazol-2-yl)benzene) can bind DNA through groove-binding and/or non-classical intercalation modes, revealed by spectrophotometric methods, viscosity measurements and variable ionic strength experiments. On the basis of binding interactions between cationic [Ru(bpy)(2)(mbpibH2)](2+) and anionic DNA at a molar ratio of 1:1, a yellow transparent cast film has been assembled on an indium-tin oxide (ITO) surface using a solution-based self-standing method. The prepared DNA-[Ru(bpy)(2)(mbpibH2)](2+) film shows a bi-exponential luminescence decay with τ(1)=62.1 ns (8.0%) and τ(2)=594.5 ns (92.0%), whose lifetimes become much shorter than those of DNA-bound [Ru(bpy)(2)(mbpibH2)](2+) in buffer solutions. The Ru(II) complex with a free bi-dentate coordination site in the DNA cast film shows tunable luminescence, quenched dynamically by Cu(2+) and restored by using EDTA to eliminate two modes of Cu(2+)-binding. The results from this study provide a significant foundation for better understanding the fabrication and modulation of a DNA-based solid luminescence device using the Ru(II) complexes as DNA-concentrating and signal-sensing agents.

Crystal structure of Δ-[Ru(bpy)₂dppz]²⁺ bound to mismatched DNA reveals side-by-side metalloinsertion and intercalation

DNA mismatches represent a novel target in the development of diagnostics and therapeutics for cancer, because deficiencies in DNA mismatch repair are implicated in cancers, and cells that are repair-deficient show a high frequency of mismatches. Metal complexes with bulky intercalating ligands serve as probes for DNA mismatches. Here, we report the high-resolution (0.92 Å) crystal structure of the ruthenium 'light switch' complex Δ-[Ru(bpy)(2)dppz](2+) (bpy = 2,2'-bipyridine and dppz = dipyridophenazine), which is known to show luminescence on binding to duplex DNA, bound to both mismatched and well-matched sites in the oligonucleotide 5'-(dCGGAAATTACCG)(2)-3' (underline denotes AA mismatches). Two crystallographically independent views reveal that the complex binds mismatches through metalloinsertion, ejecting both mispaired adenosines. Additional ruthenium complexes are intercalated at well-matched sites, creating an array of complexes in the minor groove stabilized by stacking interactions between bpy ligands and extruded adenosines. This structure attests to the generality of metalloinsertion and metallointercalation as DNA binding modes.