AT‐Specific DNA Binding of Binuclear Ruthenium Complexes at the Border of Threading Intercalation

The binuclear ruthenium complex [μ‐bidppz(phen)₄Ru₂]⁴⁺ has been extensively studied since the discovery of its unusual threading intercalation interaction with DNA, a binding mode with extremely slow binding and dissociation kinetics. The complex has been shown to be selective towards long stretches of alternating AT base pairs, which makes it interesting, for example, as a model compound for anti‐malaria drugs due to the high AT content of the genome of the malaria parasite P. falciparum. We have investigated the effect of bridging ligand structure on threading intercalation ability and found that length and rigidity as well as the size of the intercalated ring system are all factors that affect the rate and selectivity of the threading intercalation. In particular, we discovered a new DNA‐threading compound, [μ‐dppzip(phen)₄Ru₂]⁴⁺, which appears to be just at the border of being capable of threading intercalation and displays even greater selectivity for AT‐DNA than the parent compound, [μ‐bidppz(phen)₄Ru₂]⁴⁺.     

DNA-binding of semirigid binuclear ruthenium complex delta,delta-[mu-(11,11'-bidppz)(phen)(4)ru(2)](4+): extremely slow intercalation kinetics

We here report a remarkably slow rearrangement of binding modes for a binuclear ruthenium(II) complex upon interaction with DNA. It has been previously shown that Delta,Delta-[mu-(11,11'-bidppz)(phen)4Ru2]4+ binds to DNA in one of the grooves. However, we find that this is only an initial, metastable, binding mode, which is extremely slowly reorganized into an intercalative binding geometry. The slow rearrangement and dissociation, revealed by flow linear dichroism and fluorescence spectroscopy, are concluded to be a result from the complex being threaded through the DNA, with one of the bridging aromatic dppz ligands intercalated between the base pairs of the DNA, placing one metal center in the minor groove and one in the major groove. A negative LD, a high luminescence quantum yield, and long luminescence lifetimes, similar to the intercalating complex Delta-[Ru(phen)2dppz]2+, indicate intercalation of the bidppz moiety. The unique slow dissociation of the complex in its final DNA-binding mode suggests that this class of threading, partially intercalated binuclear complexes may be interesting in the context of cancer therapy. Also, their unique optical and photophysical properties could make such complexes, either alone or scaffolded by DNA structures, of interest for the development of nanometer-sized molecular optoelectronic devices.     

Kinetic characterization of an extremely slow DNA binding equilibrium

We here exploit the recently reported thermodynamic preference for poly(dAdT)(2) over mixed-sequence calf thymus (ct) DNA of two binuclear ruthenium complexes, DeltaDelta-[mu-bidppz(bipy)4Ru2](4+) (B) and DeltaDelta-[mu-bidppz(phen)(4)Ru(2)](4+) (P), that bind to DNA by threading intercalation, to determine their intrinsic dissociation rates. After adding poly(dAdT)(2) as a sequestering agent to B or P bound to ct-DNA, the observed rate of change in luminescence upon binding to the polynucleotide reflects the rate of dissociation from the mixed sequence. The activation parameters for the threading and dissociation rate constants allow us for the first time to characterize the thermodynamics of the exceedingly slow threading intercalation equilibrium of B and P with ct-DNA. The equilibrium is found to be endothermic by 33 and 76 kJ/mol, respectively, and the largest part of the enthalpy difference between the complexes originates from the forward threading step. At physiological temperature (37 degrees C) B and P have dissociation half-lives of 18 and 38 h, respectively. This is to our knowledge the slowest dissociating noncovalently bound DNA-drug reported. SDS sequestration is the traditional method for determination of rate constants for cationic drugs dissociating from DNA. However, the rates may be severely overestimated for slowly dissociating molecules due to unwanted catalysis by the SDS monomers and micelles. Having determined the intrinsic dissociation rates with poly(dAdT)(2) as sequestering agent, we find that the catalytic effect of SDS on the dissociation rate may be up to a factor of 60, and that the catalysis is entropy driven. A simple kinetic model for the SDS concentration dependence of the apparent dissociation rate suggests an intermediate that involves both micelles and DNA-threaded complex.     

Mechanically manipulating the DNA threading intercalation rate

The dumbbell shaped binuclear ruthenium complex DeltaDelta-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur.     

Complex DNA binding kinetics resolved by combined circular dichroism and luminescence analysis

We recently reported that ruthenium complexes, with general structure [mu-bidppz(bipy)4Ru2](4+) (B) or [mu-bidppz(phen)4Ru2](4+) (P) (bidppz=11,11'-bi(dipyrido[3,2- a:2',3'-c]phenazinyl)), show extreme kinetic selectivity for long AT tracts over mixed-sequence calf thymus DNA (ct-DNA), a selectivity that also varies markedly with the size (between B and P) and sense of chirality of the complex. Earlier studies, exploiting the great increase in luminescence intensity when the compound intercalates, have yielded complex kinetics indicating the presence of both first- and second-order processes. Even with a homogeneous DNA sequence, such as poly(dAdT)2, the luminescence kinetics generally requires more than a single exponential for a satisfactory fit. We here reveal that at least part of the complexity is a result of the extreme sensitivity of the effective quantum yield of the complexes, so that the luminescence trajectories also reflect subtle variations in the environment and binding geometry that the complex is sampling on its path to its final binding site. By monitoring the rearrangement process using circular dichroism (CD), we show that threading of both enantiomers of B and P into poly(dAdT)2 is effectively a monoexponential process, as expected if the compounds are not affecting each other during the intercalation process. Thus, the complex luminescence trajectories may be explained by slow relaxations in the binding geometry (DNA conformation) and associated changes in the environment of the entering complexes. To further disentangle the intriguing features of the threading intercalation kinetics, and how they may depend on the flexibility and size of the ruthenium complexes, we have also designed and studied two new ruthenium complexes, [mu-dtpf(phen)4Ru2](4+) (F) (dtpf=4,5,9,12,16,17,21,25-octaaza-23 H-ditriphenyleno[2,3-b:2,3-h]fluorene), in which the bridging ligand is made totally rigid, and [mu-bidppz([12]aneS4) 2Ru2](4+) (S), which has less bulky, nonaromatic ancillary ligands. The threading of F into poly(dAdT)2, also found to be a monoexponential process, is about 3 times slower than for P, indicating that the flexibility of the bridging ligand is an important factor for the intercalation rate. Surprisingly, in contrast to all other compounds, S requires two exponentials to fit its binding kinetics as monitored by CD. Also surprisingly, in view of the smaller steric bulk, even the fastest phase is roughly 2 times slower for S than for B and P. Thus, not only the size of the ancillary ligand but also other properties that can influence the energy landscape of the threading path are rate-determining factors. With mixed-sequence ct-DNA, threading of B and that of P are both multiphasic processes when monitored with CD as well as with luminescence. The rate constants for threading into ct-DNA show much larger variations between complexes than for poly(dAdT)2, confirming earlier results based on luminescence data.     

Mechanism of DNA threading intercalation of binuclear Ru complexes: uni- or bimolecular pathways depending on ligand structure and binding density

In the long succession of small transition-metal compounds interacting reversibly with DNA, semirigid binuclear ruthenium complexes stand out by displaying exceptionally slow binding kinetics. To reach the final intercalated state, one of the bulky metal centers has to be threaded through the base stack, leading to a high level of structural discrimination. This makes the idea of utilizing binuclear complexes interesting in applications involving DNA sequence or conformation recognition. The finding that threading intercalation of the two structural analogues, Lambda,Lambda-[mu-(11,11'-bidppz)X4Ru2]4+, X = 2,2'-bipyridine (Lambda,Lambda-B4) and X = 1,10'-phenanthroline (Lambda,Lambda-P4), into poly(dA-dT)2 can be described by surprisingly simple rate laws encouraged more extensive studies and analysis of these two systems. Kinetic measurements at different [basepair]/[complex] ratios show that Lambda,Lambda-B4 intercalates via a pseudo-first-order mechanism independent of binding density, whereas Lambda,Lambda-P4 displays a gradual transition from apparent first- to second-order kinetics when decreasing the [basepair]/[complex] mixing ratio. By employing the probabilistic method of McGhee and von Hippel, a rate law based on a supposed mechanism has been globally fitted and numerically integrated to describe threading of Lambda,Lambda-P4. In contrast to Lambda,Lambda-B4, the first-order mechanism of this analogue appears to require a long stretch of nonthreaded DNA. The results show that ancillary ligand structures indeed affect the mechanism of DNA threading, demonstrating the potential use of semirigid binuclear ruthenium complexes to target DNA.     

Monitoring the DNA binding kinetics of a binuclear ruthenium complex by energy transfer: evidence for slow shuffling

The semirigid binuclear ruthenium complex Delta,Delta-[mu-(11,11'-bidppz)(phen)(4)Ru(2)](4+) has been shown to rearrange slowly from an initial groove-bound nonluminescent state to a final intercalated emissive state by threading one of its bulky Ru(phen)(2) moieties through the DNA base stack. When this complex binds to poly[d(A-T)(2)], a further increase in emission from the complex is observed after completion of the intercalation, assigned to reorganization of the intercalated complex. We here report a study of the threading process in poly[d(A-T)(2)], in which the minor groove binding dye DAPI is used as an energy transfer probe molecule to assess the distribution of ruthenium complex during and also after the actual threading phase. The emission from DAPI is found to change with the same rate as the emission from the ruthenium complex, and furthermore, DAPI does not disturb the binding kinetics of the latter, justifying it as a good probe of both the threading and the reorganization processes. We conclude from the change in the emission from both DAPI and the ruthenium complex with time that DAPI-ruthenium interactions are most pronounced during the process of threading of the complex, suggesting that the complexes are initially threaded slightly anticooperatively and thereafter redistribute along the DNA to reach their thermodynamically most favorable distribution. The final distribution is characterized by a small but significant binding cooperativity, probably as a result of hydrophobic interactions between the complex ions despite their tetravalent positive charges. The mechanism of "shuffling" the complex along the DNA chain is discussed, i.e., whether the ruthenium complex remains threaded (requiring sequential base-pair openings) or if unthreading followed by lateral diffusion within the ionic atmosphere of the DNA and rethreading occurs.     

Poly-intercalators Carrying Threading Intercalator Moieties as Novel DNA Targeting Ligands

Threading intercalators are a novel class of intercalators that carry two substituents along the diagonal positions of an aromatic ring. These substituents are projecting out in DNA grooves when bound to DNA. Poly-intercalators carrying threading intercalating parts are quite novel and were recently found to show a unique DNA binding behavior. We review herein two types of poly-intercalators. First, tris-intercalators carrying a threading intercalator part in the middle of the molecule are described. These intercalators appear to intercalate into double stranded DNA in a special binding manner, which we call the penetrating mode, in which all the three intercalating units are arranged linearly with one of them penetrating into the DNA ladder. We synthesized two tris-intercalators ( 3 and 4) of this type and studied their binding behavior for double stranded DNA. All the experimental results were consistent with the proposed penetrating mode. Another type of threading poly-intercalators is a macrocyclic bis-threading intercalator ( 5). We found that this compound can bis-intercalate to double stranded DNA when the base pairing is disrupted temporarily to form a complex with a unique structure like a catenane. On the basis of a study of the interaction of such intercalators we envisage that DNA is a flexible and dynamic entity. These novel families of poly-intercalators will expand the scope of DNA poly-intercalation chemistry with possible medicinal applications.     

Photoinduced Electron Transfer in Pentaammineruthenium(II) Complexes of 1-(4-Cyanophenyl)imidazole

A new bridging ligand, 1-(4-cyanophenyl)imidazole (CPI) has been prepared, as well as its N-methylated derivative 1-methyl-3-(4-cyanophenyl)imidazolium iodide (CPI-Me(+)I(-)). The mononuclear and binuclear complexes [(NH(3))(5)Ru-CPI-Me](3+) and [(NH(3))(5)Ru-CPI-Ru(NH(3))(5)](4+) have been obtained. Free CPI is planar, according to theoretical calculations (MMX and MNDO), and its luminescence properties suggest the occurence of a twisted internal charge transfer (TICT) state. The comparison of the two ruthenium complexes reveals the spectral and electrochemical features of coordination by the cyanophenyl or by the imidazole groups. Controlled oxidation of the binuclear complex [(NH(3))(5)Ru-CPI-Ru(NH(3))(5)](4+) yields the mixed valence species [(NH(3))(5)Ru-CPI-Ru(NH(3))(5)](5+) in which the ruthenium coordinated to the cyanophenyl group is ruthenium(II) while the ruthenium linked to imidazole is ruthenium(III). An intervalence band is observed at 640 nm (epsilon = 188), from which the effective metal-metal coupling through the bridging ligand is determined as 0.032 eV. This value is satisfactorily reproduced by a theoretical calculation using the effective Hamiltonian theory. Finally the binuclear complex exhibits a weak luminescence when excited either on the ligand band near 260 nm or on the metal-to-ligand charge transfer band near 410 nm. The CPI ligand is the first example of a TICT-forming species with appreciable coupling between metallic sites and can be considered as a first step toward a molecular switch.     

p-Carborane: a new cage spacer for photoactive metal polypyridine dyads

The first example of a binuclear ruthenium complex involving the p-carborane framework in the bridging ligand is reported. The bridging ligand is a symmetric linear array comprising a central p-carborane unit, two p-phenylene spacers, and two 5-yl-2,2'-bipyridine coordinating units. A homobinuclear Ru(II) complex, with 2,2'-bipyridine as peripheral ligands, was synthesized and characterized. The Ru(II)-Ru(III) mixed-valence species, obtained by partial oxidation, has been investigated with steady-state and time-resolved techniques in CH3CN. The rate of photoinduced electron transfer is 2.3 x 10(8) s(-1).     

Switching of the electronic communication between two {Ru(trpy)(bpy)} (trpy = 2,2':6',2' '-terpyridine and bpy = 2,2'-bipyridine) centers by protonation on the bridging dimercaptothiadiazolato ligand

A stable Ru(II)/Ru(III) mixed-valence state was observed in acetonitrile for the ruthenium binuclear complex bridged by dimercaptothiadiazolate (DeltaE(1/2) = 220 mV for Ru(2)(II,II)/Ru(2)(II,III) and Ru(2)(II,III)/Ru(2)(III,III) processes; K(com) = 5.3 x 10(3)). Upon protonation of the bridging ligand by the addition of equimolar p-toluenesulfonic acid, however, the mixed-valence state diminished (DeltaE(1/2) = 0 mV). The bridging ligand operates as a proton-induced switch of the electronic communication in the dimeric complex.     

Photoinduced DNA Cleavage and Photocytotoxic of Phenanthroline-Based Ligand Ruthenium Compounds

The photophysical and biological properties of two new phenanthroline-based ligand ruthenium complexes were investigated in detail. Their DNA interaction modes were determined to be the intercalation mode using spectra titration and viscosity measurements. Under irradiation, obvious photo-reduced DNA cleavages were observed in the two complexes via singlet oxygen generation. Furthermore, complex 2 showed higher DNA affinity, photocleavage activity, and singlet oxygen quantum yields than complex 1. The two complexes showed no toxicity towards tumor cells (HeLa, A549, and A375) in the dark. However, obvious photocytotoxicities were observed in the two complexes. Complex 2 exhibited large PIs (phototherapeutic indices) (ca. 400) towards HeLa cells. The study suggests that these complexes may act as DNA intercalators, DNA photocleavers, and photocytotoxic agents.     

Binding geometry and photophysical properties of DNA-threading binuclear ruthenium complexes

The DNA binding conformation and the photophysical properties of the semiflexible binuclear ruthenium complex [micro-bidppz(phen)4Ru2]4+ (2) were studied with optical spectroscopy and compared to the rigid, planar homologue in syn conformation [micro-dtpf(phen)4Ru2]4+ (3) and the parent "light-switch" complex [Ru(phen)2dppz]2+ (1). Comparison of calculated and observed absorption bands of the bridging ligand, bidppz, confirm earlier suggestions that 2 is significantly nonplanar, both free in solution and when intercalated into poly(dAdT)2, but the conclusion that the intercalated conformation is an anti rotamer is not substantiated by comparison of linear and circular dichroism spectra of 2 and 3. The behavior of the emission quantum yield as a function of temperature is similar for the two binuclear complexes 2 and 3 in different protic solvents, and a quantitative analysis suggests that, in solution, the solvent is more strongly hydrogen bonded to the excited state of 2 than to 1. However, the observation that for 2 the radiative rate constant increases to a value similar to 1 upon intercalation into DNA suggests that the difference between 1 and 2 in accepting hydrogen bonds is less pronounced when intercalated.     

Micelle-sequestered dissociation of cationic DNA-intercalated drugs: unexpected surfactant-induced rate enhancement

Detergent sequestration using micelles as a hydrophobic sink for dissociated drug molecules is an established technique for determination of dissociation rates. The anionic surfactant molecules are generally assumed not to interact with the anionic DNA and thereby not to affect the rate of dissociation. By contrast, we here demonstrate that the surfactant molecules sodium dodecyl sulfate (SDS), sodium decyl sulfate, and sodium octyl sulfate all induce substantial rate enhancements of the dissociation of intercalators from DNA. Four different cationic DNA intercalators are studied with respect to surfactant-induced dissociation. Except for the smallest intercalator, ethidium, the dissociation rate constants increase monotonically with surfactant concentration both below cmc and (more strongly) above cmc, much more than expected from electrostatic effects of increased counterion concentration. The rate enhancement, most pronounced for the bulky, multicationic, hydrophobic DNA ligands in this study, indicates a reduction of the activation energy for the ligand to pass out from a deeply penetrating intercalation site of DNA. The discovery that surfactants enhance the rate of dissociation of cationic DNA-intercalators implies that rate constants previously determined by micelle-sequestered dissociation may have been overestimated. As an alternative, more reliable method, we suggest instead the addition of excess of dummy DNA as an absorbent for dissociated ligand.     

DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate

Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine-thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6-44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism. We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed "click" reaction. Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.     

Novel platinum(II)-based anticancer complexes and molecular hosts as their drug delivery vehicles

Platinum(II)-based DNA intercalators where the intercalating ligand is 1,10-phenanthroline or a phenanthroline derivative and where the ancillary ligand is either achiral (e.g. ethylenediamine) or chiral (e.g. diaminocyclohexane) show a range of cytotoxicities with a defined structure-activity relationship. The most cytotoxic are those that contain methylated-phenanthroline ligands and 1S,2S-diaminocyclohexane (S,S-dach) as the ancillary ligand. We have developed a new purification method using Sep-Pak C-18 reverse phase columns, which means these metal complexes can be made faster and cheaper compared to published methods. Platinum(II)-based complexes containing imidazole, pyrrole and beta-alanine subunits, that are capable of recognising specific DNA base-pair sequences have also been synthesised. These include linear or hairpin polyamide ligands that can recognise DNA sequences up to seven base-pairs in length and contain single platinum centres capable of forming monofunctional adducts with DNA. We have now synthesised and characterised, by (1)H and (195)Pt NMR, ESI-MS and elemental analysis, the first dinuclear platinum(II) DNA sequence selective agent. Finally, using (1)H NMR we have examined the encapsulation of our platinum(II)-based DNA intercalators by cucurbit[6]uril (CB[6]). Encapsulation by CB[6] was found to not significantly change the cytotoxicity of five platinum(II)-based DNA intercalators, indicating it may have utility as a molecular carrier for improved drug delivery.     

Controlling the torsion angle via adventitious cation binding

We report herein the synthesis of a linear binuclear ruthenium(II) complex, and the corresponding free ligand, for which the organic connector is a geometrically-constrained crown ether that binds added cations.     

单核、对称双核钌配合物在铂电极上的电化学行为

利用循环伏安、循环交流伏安和微分电容测定等电化学方法研究了由2,2'-联吡啶(bpy)和桥联配体1,4-二(2-咪唑并[4,5-f][1,10]邻菲咯啉)苯(DIPB)配位而成的单核钌配合物[Rul:Ru(bpy)~2(DIPB)(ClO~4)~2]和对称双核钌配合物[Ru2:(bpy)~2Ru(DIPB)Ru(bpy)~2(ClO~4)~4]在铂电极上的电化学行为。研究结果表明,在0.1mol/L高氯酸四丁基铵(TBAP)的乙腈溶液中,这两种配合物的中心钌离子在铂电极上均呈现一对氧化还原峰,而配体2,2'-联吡啶则呈现两对氧化还原峰。单核Ru1和双核Ru2所对应的各组氧化还原峰分别符合可逆的单电子和二电子传递反应过程的特征,所对应的条件电位(FormalPotential)Ru2较ru1有轻微正移。Ru1和Ru2所对应的配位阳孩子的扩散系数分别为9.93×10^-^6cm^2/s和3.50×10^-^6cm^2/s。在循环交流法和微分电容法确定的时间量程内,两中心钌离子在桥联配体间的电子传递过程较它与电极间的慢。     

Building molecular-scale bridges having restricted rotation

The synthesis is reported of a binuclear ruthenium(II) bis(2,2′:6′,2″-terpyridine) complex for which the polytopic ligand incorporates a central, torsionally-constrained biphenylene group. In principle, the dihedral angle between the two phenylene rings can be controlled by the length of the constraining strap.     

Architecture of supramolecular metal complexes for photocatalytic CO2 reduction: ruthenium-rhenium bi- and tetranuclear complexes

We study the electrochemical, spectroscopic, and photocatalytic properties of a series of Ru(II)-Re(I) binuclear complexes linked by bridging ligands 1,3-bis(4'-methyl-[2,2']bipyridinyl-4-yl)propan-2-ol (bpyC3bpy) and 4-methyl-4'-[1,10]phenanthroline-[5,6-d]imidazol-2-yl)bipyridine (mfibpy) and a tetranuclear complex in which three [Re(CO)3Cl] moieties are coordinated to the central Ru using the bpyC3bpy ligands. In the bpyC3bpy binuclear complexes, 4,4'-dimethyl-2,2'-bipyridine (dmb) and 4,4'-bis(trifluoromethyl)-2,2'-bipyridine ({CF3}2bpy), as well as 2,2'-bipyridine (bpy), were used as peripheral ligands on the Ru moiety. Greatly improved photocatalytic activities were obtained only in the cases of [Ru{bpyC3bpyRe(CO)3Cl}3]2+ (RuRe3) and the binuclear complex [(dmb)2Ru(bpyC3bpy)Re(CO)3Cl]2+ (d2Ru-Re), while photocatalytic responses were extended further into the visible region. The excited state of ruthenium in all Ru-Re complexes was efficiently quenched by 1-benzyl-1,4-dihydronicotinamide (BNAH). Following reductive quenching in the case of d2Ru-Re, generation of the one-electron-reduced (OER) species, for which the added electron resides on the Ru-bound bpy end of the bridging ligand bpyC3bpy, was confirmed by transient absorption spectroscopy. The reduced Re moiety was produced via a relatively slow intramolecular electron transfer, from the reduced Ru-bound bpy to the Re site, occurring at an exchange rate (DeltaG approximately 0). Electron transfer need not be rapid, since the rate-determining process is reduction of CO2 with the OER species of the Re site. Comparison of these results with those for other bimetallic systems gives us more general architectural pointers for constructing supramolecular photocatalysts for CO2 reduction.