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.     

Enantioselective DNA threading dynamics by phenazine-linked.

The interactions between the stereoisomers of the chiral bis-intercalator [mu-C4(cpdppz)(2)-(phen)(4)Ru(2)](4+) and DNA reveal interesting dynamic discrimination properties. The two enantiomers Delta-Delta and Lambda-Lambda both form very strong complexes with calf thymus DNA with similar thermodynamic affinities. By contrast, they display considerable variations in their binding kinetics. The Delta-Delta enantiomer has higher affinity for calf thymus DNA than for [poly(dA-dT)](2), and the association kinetics of the dimer to DNA, as well as to polynucleotides, requires a multiexponential fitting function. The dissociation reaction, on the other hand, could be described by a single exponential for [poly(dA-dT)](2), whereas two exponentials were required for mixed-sequence DNA. To understand the key mechanistic steps of the reaction, the kinetics was studied at varied salt concentration for different choices of DNA and chirality of the threading complex. The enantiomers were found to have markedly different dissociation rates, the Lambda-Lambda enantiomer dissociating about an order of magnitude faster than the Delta-Delta enantiomer. Also, the salt dependence of the dissociation rate constants differed between the enantiomers, being stronger for the Lambda-Lambda enantiomer than for the Delta-Delta enantiomer. Since the dissociation reaction requires unthreading of bulky parts of the bis-intercalator through the DNA helix, a considerable conformational change of the DNA must be involved, possibly defining the rate-limiting step.     

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.     

Carbon monoxide-releasing micelles for immunotherapy

With the discovery of important biological roles of carbon monoxide (CO), the use of this gas as a therapeutic agent has attracted attention. However, the medical application of this gas has been hampered by the complexity of the administration method. To overcome this problem, several transition-metal carbonyl complexes, such as Ru(CO)(3)Cl(glycinate), [Ru(CO)(3)Cl(2)](2), and Fe(η(4)-2-pyrone)(CO)(3), have been used as CO-releasing molecules both in vitro and in vivo. We sought to develop micellar forms of metal carbonyl complexes that would display slowed diffusion in tissues and thus better ability to target distal tissue drainage sites. Specifically, we aimed to develop a new CO-delivery system using a polymeric micelle having a Ru(CO)(3)Cl(amino acidate) structure as a CO-releasing segment. The CO-releasing micelles were prepared from triblock copolymers composed of a hydrophilic poly(ethylene glycol) block, a poly(ornithine acrylamide) block bearing Ru(CO)(3)Cl(ornithinate) moieties, and a hydrophobic poly(n-butylacrylamide) block. The polymers formed spherical micelles in the range of 30-40 nm in hydrodynamic diameter. Further characterization revealed the high CO-loading capacity of the micelles. CO-release studies showed that the micelles were stable in physiological buffer and serum and released CO in response to thiol-containing compounds such as cysteine. The CO release of the micelles was slower than that of Ru(CO)(3)Cl(glycinate). In addition, the CO-releasing micelles efficiently attenuated the lipopolysaccharide-induced NF-κB activation of human monocytes, while Ru(CO)(3)Cl(glycinate) did not show any beneficial effects. Moreover, cell viability assays revealed that the micelles significantly reduced the cytotoxicity of the Ru(CO)(3)Cl(amino acidate) moiety. This novel CO-delivery system based on CO-releasing micelles may be useful for therapeutic applications of CO.     

Intercalation is not required for DNA light-switch behavior

The DNA light-switch complex [Ru(bpy)2(tpphz)]2+ (1, bpy = 2,2'-bipyridine, tpphz = tetrapyrido[3,2-a:2',3'-c:3',2'-h:2',3'-j]phenazine) is luminescent when bound to DNA and in organic solvents and weakly emissive in water. To date, light-switch behavior by transition metal complexes has generally been regarded as confirmation of DNA intercalation. In contrast, the present work demonstrates that the nonintercalating bimetallic complex [(bpy)2Ru(tpphz)Ru(bpy)2]4+ (2) behaves as a DNA light-switch. Weak emission from the 3MLCT excited state of 2 is observed in water with lambda(em) = 623 nm (phi(em) = 1.4 x 10(-4)), and a red shift (lambda(em) = 702 nm) and 40-fold increase in intensity are observed upon addition of 100 microM calf thymus DNA (ct-DNA). Addition of increasing concentrations of 2 to 1 mM herring sperm DNA does not result in an increase in the viscosity of the solution, indicating that the complex is not an intercalator. Additionally, experiments were conducted to ensure that the emission enhancement did not arise from threading intercalation of the complex. The in situ generation of 2 intercalated between the base pairs of ct-DNA in a threading fashion, however, exhibits emission maximum at 685 nm, which is blue-shifted from that of surface-bound 2. DFT calculations show low-lying orbitals in 2 that are expected to exhibit nonemissive character when contributing to the MLCT state, in accord with the lower emission intensity observed for 2 relative to that for 1. To our knowledge, the present work is the first example of a nonintercalating light-switch metal complex, thus showing that light-switch behavior cannot be used exclusively as confirmation of intercalation.     

Intercalation of fac-[(4,4'-bpy)ReI(CO)3(dppz)]+, dppz = dipyridyl[3,2-a:2'3'-c]phenazine, in polynucleotides. On the UV-vis photophysics of the Re(I) intercalator and the redox reactions with pulse radiolysis-generated radicals

The intercalation of fac-[(4,4'-bpy)Re(I)(CO)3(dppz)]+ (dppz = dipyridyl[3,2-a:2'3'-c]phenazine) in polynucleotides, poly[dAdT]2 and poly[dGdC]2, where A = adenine, G = guanine, C = cytosine and T = thymine, is a major cause of changes in the absorption and emission spectra of the complex. A strong complex-poly[dAdT]2 interaction drives the intercalation process, which has a binding constant, Kb approximately 1.8 x 10(5) M(-1). Pulse radiolysis was used for a study of the redox reactions of e(-)(aq), C*H(2)OH and N3* radicals with the intercalated complex. These radicals exhibited more affinity for the intercalated complex than for the bases. Ligand-radical complexes, fac-[(4,4'-bpy*)Re(I)(CO)3(dppz)] and fac-[(4,4'-bpy)Re(I)(CO)3(dppz *)], were produced by e(-)(aq) and C*H(2)OH, respectively. A Re(II) species, fac-[(4,4'-bpy)Re(II)(CO)3(dppz)](2+), was produced by N3* radicals. The rate of annihilation of the ligand-radical species was second order on the concentration of ligand-radical while the disappearance of the Re(II) complex induced the oxidative cleavage of the polynucleotide strand.     

Fluorescence of the DNA double helices (dAdT)n.(dAdT)n studied by femtosecond spectroscopy

Polymeric and oligomeric DNA helices, poly(dAdT).poly(dAdT) and (dAdT)(10).(dAdT)(10), composed of 200-400 and 20 adenine-thymine base pairs, respectively, are studied by fluorescence upconversion. Fluorescence decays, anisotropy decays and time-resolved spectra, obtained for this alternating base sequence, are compared with those determined previously for the homopolymeric sequence (dA)(n).(dT)(n). It is shown that identical fluorescence decays may correspond to quite different anisotropy decays and vice versa, both varying with the emission wavelength, the base sequence and the duplex size. Our observations cannot be explained in terms of monomer and excimer emission exclusively, as concluded in the past on the basis of steady-state measurements. Excitons also contribute to the fluorescence. These are rapidly trapped by excimers, characterized by long-lived weak emission.     

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly?A, poly?G, poly?C, poly?U), double-stranded DNA polynucleotides (poly?dAdT-poly?dAdT, poly?dGdC-poly?dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly?dAdT-poly?dAdT, at variance to preferred binding of Im and Py to only major groove of poly?dGdC-poly?dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.     

Dual molecular light switches for pH and DNA based on a novel Ru(II) complex. A non-intercalating Ru(II) complex for DNA molecular light switch

A new Ru(II) complex of [Ru(phen)(2)(Hcdpq)](ClO(4))(2) {phen = 1,10-phenanthroline, Hcdpq = 2-carboxyldipyrido[3,2-f:2',3'-h]quinoxaline} was synthesized and characterized. The spectrophotometric pH and calf thymus DNA (ct-DNA) titrations showed that the complex acted as a dual molecular light switch for pH and ct-DNA with emission enhancement factors of 17 and 26, respectively. It was shown to be capable of distinguishing ct-DNA from yeast RNA with this binding selectivity being superior to two well-known DNA molecular light switches of [Ru(bpy)(2)(dppz)](2+) {bpy =2,2'-bipyridine, and dppz = dipyrido-[3,2-a:2',3'-c]phenazine}and ethidium bromide. The complex bond to ct-DNA probably in groove mode with a binding constant of (4.67 ± 0.06) × 10(3) M(-1) in 5 mM Tris-HCl, 50 mM NaCl (pH = 7.10) buffer solution, as evidenced by UV-visible absorption and luminescence titrations, the dependence of DNA binding constants on NaCl concentrations, DNA competitive binding with ethidium bromide, and emission lifetime and viscosity measurements. To get insight into the light-switch mechanism, theoretical calculations were also performed by applying density functional theory (DFT) and time-dependent DFT.     

Effect of ionic surfactants on the hydration behavior of triblock copolymer micelles: a solvation dynamics study of coumarin 153

Dynamic fluorescence Stokes shift measurements of coumarin 153 (C153) have been carried out to study the influence of ionic surfactants (sodium dodecyl sulfate, SDS and hexadecyltrimethylammonium chloride, CTAC) on the hydration behavior of aqueous poly(ethylene oxide)(20)-poly(propylene oxide)(70)-poly(ethylene oxide)20 (P123) block copolymer micelles. Increase in SDS or CTAC concentration at a fixed P123 concentration induces the steady-state emission spectra of C153 to shift gradually toward lower energy. This is attributed to an increase in polarity (due to enhanced hydration) experienced by the probe as a consequence of incorporation of ionic head groups in the Corona region. The observed dynamic fluorescence Stokes shift value decreases more in mixed micellar systems than in pure copolymer micelles and the trends are quite similar in the presence of SDS and CTAC. The spectral shift correlation functions were observed to be nonexponential in nature. Critical analysis of the spectral shift correlation function indicates a fast solvation component (<0.2 ns) in P123 micelles, which was absent in the presence of ionic surfactants. Due to increased hydration in the presence of ionic surfactants, the initial fast solvation event was elusive in mixed copolymer-surfactant systems, reflecting the absence of faster solvation component and reduced observed Stokes shift in mixed systems. It has been argued that in the low surfactant concentration region, increase in hydration with the incorporation of ionic head groups in the Corona region is mainly due to increase in mechanically trapped water content. However, at higher surfactant concentrations, bound water content dominates and leads to slower solvation dynamics. The present results also indicate that though CTAC alters the Corona hydration more efficiently than SDS, the overall influence of ionic surfactants on the Corona hydration is grossly similar irrespective of the cationic or anionic nature of the surfactants. Interaction of SDS and CTAC with poly(ethylene oxide)(100)-poly(propylene oxide)(70)-poly(ethylene oxide)(100) (F127) block copolymer micelles has also been studied to comprehend the effect of copolymer composition. The overall trends in dynamic fluorescence Stokes shift and solvation times are similar in both the copolymer micelles.     

NMR investigations of self-aggregation characteristics of SDS in a model assembled tri-block copolymer solution

The present work was undertaken with a view to understand the influence of a model non-ionic tri-block copolymer PEO-PPO-PEO (poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)) with molecular weight 5800 i.e., P123 [(EO)(20)-(PO)(70)-(EO)(20)] on the self-aggregation characteristics of the anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D(2)O) using NMR chemical shift, self-diffusion and nuclear spin-relaxation as suitable experimental probes. In addition, polymer diffusion has been monitored as a function of SDS concentration. The concentration-dependent chemical shift, diffusion data and relaxation data indicated the significant interaction of polymeric micelles with SDS monomers and micelles at lower and intermediate concentrations of SDS, whereas the weak interaction of the polymer with SDS micelles at higher concentrations of SDS. It has been observed that SDS starts aggregating on the polymer at a lower concentration i.e., critical aggregation concentration (cac=1.94 mM) compared to polymer-free situation, and the onset of secondary micelle concentration (C(2)=27.16 mM) points out the saturation of the 0.2 wt% polymer or free SDS monomers/micelles at higher concentrations of SDS. It has also been observed that the parameter cac is almost independent in the polymer concentrations of study. The TMS (tetramethylsilane) has been used as a solubilizate to measure the bound diffusion coefficient of SDS-polymer mixed system. The self-diffusion data were analyzed using two-site exchange model and the obtained information on aggregation dynamics was commensurate with that inferred from chemical shift and relaxation data. The information on slow motions of polymer-SDS system was also extracted using spin-spin and spin-lattice relaxation rate measurements. The relaxation data points out the disintegration of polymer network at higher concentrations of SDS. The present NMR investigations have been well corroborated by surface tension and conductivity measurements.     

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.     

Linkage effects of chromium(III) acetylacetonato units on chiral induction of liquid crystal phases

The linkage effects of polynuclear metal complexes on chiral induction have been studied by application of the chiral oligomers of acetylacetonato chromium(III) units as a dopant, inducing chiral nematic phases. The compounds were prepared by reacting [Cr(acac)(3)] (acac = acetylacetonato) and 1,1,2,2-tetraacetylethane (taetH(2)) in solid phase at 160 degrees C. Binuclear diastereomers were separated on a silica gel column, followed by chromatographic resolution on a chiral column packed with an ion-exchange adduct of Delta-[Ru(phen)(3)](2+) (phen = 1,10-phenanthroline) and synthetic hectorite. An enantiomeric pair (DeltaDelta- and LambdaLambda-[Cr(acac)(2)(taet)Cr-(acac)(2)]) and a meso species (DeltaLambda-[Cr(acac)(2)(taet)Cr(acac)(2)]) were identified. The binuclear enantiomers were doped into a room-temperature nematic liquid crystal, N-methoxybenzylidene-4-n-butylaniline. Helical twisting power (beta(M)) was found to be +97.9 and -88.9 microm(-1) for LambdaLambda- and DeltaDelta-[Cr(acac)(2)(taet)Cr(acac)(2)], respectively. The values were compared with beta(M) for the monomeric enantiomers (+99.5 and -91.0 microm(-1) for Lambda- and Delta-[Cr(acac)(3)], respectively). The results are interpreted on the basis of the surface chirality model. DeltaDelta-[Cr(acac)(2)(taet)Cr(acac)(2)] was found to photoisomerize both in a hexane solution and in a liquid crystal phase of ZLI-1132. The quantum yield of photoisomerization in a liquid crystal phase was lowered to ca. 30% of that in a hexane solution.     

Effect of SDS on the self-assembly behavior of the PEO-PPO-PEO triblock copolymer (EO)20(PO)70(EO)20

The mixed micellar system comprising the poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)-based triblock copolymer (EO)(20)(PO)(70)(EO)(20) (P123) and the anionic surfactant sodium dodecyl sulfate (SDS) has been investigated in aqueous media by small-angle neutron scattering (SANS) and viscosity measurements. The aggregation number of the copolymer in the micelles decreases upon addition of SDS, but a simultaneous enhancement in the degree of micellar hydration leads to a significant increase in the micellar volume fraction at a fixed copolymer concentration. This enhancement in the micellar hydration leads to a marked increase in the stability of the micellar gel phase until it is destroyed at very high SDS concentration. Mixed micellar systems with low and intermediate SDS concentrations form the micellar gel phase in much wider temperature and copolymer concentration ranges than the pure copolymer micellar solution. A comparison of the observed results with those for the copolymers (EO)(26)(PO)(40)(EO)(26) (P85) and (EO)(99)(PO)(70)(EO)(99) (F127) suggests that the composition of the copolymers plays a significant role in determining the influence of SDS on the gelation characteristics of the aqueous copolymer solutions. Copolymers with high PO/EO ratios show an enhancement in the stability of the gel phase, whereas copolymers with low PO/EO ratios show a deterioration of the same in the presence of SDS.     

Synthesis of [Ru(phen)(2)dppz](2+)-tethered oligo-DNA and studies on the metallointercalation mode into the DNA duplex

To explore the binding properties of [Ru(phen)(2)dppz](2+) complex (phen = 1,10-phenanthroline, dppz = dipyrido[3,2-a:2',3'-c]phenazine) in a sequence-specific manner in DNA duplex, it was tethered through the dppz ligand to a central position as well as both at the 3'- and 5'-ends of oligodeoxyribonucleotide (ODN). The middle [Ru(phen)(2)dppz](2+)-ODN tethered was resolved and isolated as four pure diastereomers, while the 3'- or 5'-[Ru(phen)(2)dppz](2+)-ODNs were inseparable on RP-HPLC. Thermal stability of the (Ru(2+)-ODN).DNA duplexes is found to increase considerably (DeltaT(m) = 12.8-23.4 degrees C), depending upon the site of the covalent attachment of the tethered [Ru(phen)(2)dppz](2+) complex, or the chirality of the [Ru(phen)(2)dppz](2+)-linker tethered at the middle of the ODN, compared to the unlabeled counterpart. Gross differences in CD between the [Ru(phen)(2)dppz](2+)-tethered and the native DNA duplexes showed that the global duplex conformation of the former has considerably altered from the B-type, but is still recognized by DNase I. The thermal melting studies, CD measurements, as well as DNase I digestion data, are interpreted as a result of intercalation of the dppz moiety, which is realized by threading of the Ru(phen)(2) complex part through the DNA duplex core. DNase I footprinting with four diastereomerically pure middle ([Ru(phen)(2)dppz](2+)-ODN).DNA duplexes furthermore showed that the tethered [Ru(phen)(2)dppz](2+)-linker chirality dictates the stereochemical accessibility of various phosphodiester moieties (around the intercalation site) toward the cleavage reaction by the enzyme. The diastereomerically pure ruthenium-modified duplexes, with the well-defined pi-stack, will be useful to explore stereochemistry-dependent energy- and electron-transfer chemistry to understand oxidative damage to the DNA double helix as well as the long-range energy- and electron-transfer processes with DNA as a reactant.     

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⁺.     

Photophysical Behavior of a New Gemini Surfactant in Neat Solvents and in Micellar Environments

A novel fluorescent gemini surfactant, 1,4-bis-(2'-(N-dodecyl pyridinio-4"-yl)ethenyl)benzene dibromide, abbreviated BDPEBB, has been synthesized and its photophysical properties have been studied in different environments. BDPEBB has a limited solubility in alcohols where it is found in aggregate form at concentrations>/=1 mM. In other solvents, e.g., water, it is only found in aggregate form, even at much lower concentrations. Solvent polarity has a small and insignificant solvatochromic effect but alcohols give a specific interaction with BDPEBB, causing a significant hypsochromic shift in absorption maxima and a large increase in relative fluorescence efficiency. Pyrene fluorescence is effectively quenched by BDPEBB. Pyrene also forms associative complexes with BDPEBB in water. These complexes are partly dissociated in the presence of surfactant micelles. Triton X-100 micelles provide a favorable environment for BDPEBB solubilization well distinguished from the behavior of ionic surfactants. Small quantities of BDPEBB have a large influence on the behavior of aqueous sodium dodecylsulfate (SDS) and sodium decylsulfate (SDeS) micelles, inducing the formation of large aggregates, visible by the naked eye. These large aggregates are most probably microcrystals of BDPEBB(2+)/2DS(-) or BDPEBB(2+)/2DeS(-). The aggregation number of SDS and SDeS micelles in the absence and in the presence of BDPEBB has been calculated by exploitation of the static luminescence quenching kinetics of Ru(bpy)(3)(2+) by 9-methylanthracene, both solubilized in the micellar phase. It has been observed that Ru(bpy)(3)(2+) inhibits the precipitation of SDeS micelles in the presence of BDPEBB. Our results suggest that double-chain surfactant chromophores should be employed with particular care if they are to be used as probes of the micellar phase. Copyright 2000 Academic Press.     

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.     

A combined parahydrogen and theoretical study of H2 activation by 16-electron d8 ruthenium(0) complexes and their subsequent catalytic behaviour

The photochemical reaction of Ru(CO)(3)(L)(2), where L = PPh(3), PMe(3), PCy(3) and P(p-tolyl)(3) with parahydrogen (p-H(2)) has been studied by in-situ NMR spectroscopy and shown to result in two competing processes. The first of these involves loss of CO and results in the formation of the cis-cis-trans-L isomer of Ru(CO)(2)(L)(2)(H)(2), while in the second, a single photon induces loss of both CO and L and leads to the formation of cis-cis-cis Ru(CO)(2)(L)(2)(H)(2) and Ru(CO)(2)(L)(solvent)(H)(2) where solvent = toluene, THF and pyridine (py). In the case of L = PPh(3), cis-cis-trans-L Ru(CO)(2)(L)(2)(H)(2) is shown to be an effective hydrogenation catalyst with rate limiting phosphine dissociation proceeding at a rate of 2.2 s(-1) in pyridine at 355 K. Theoretical calculations and experimental observations show that H(2) addition to the Ru(CO)(2)(L)(2) proceeds to form cis-cis-trans-L Ru(CO)(2)(L)(2)(H)(2) as the major product via addition over the pi-accepting OC-Ru-CO axis.     

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.