Os(phen)2dppz2+ in Photoinduced DNA-Mediated Electron Transfer Reactions

From Chemotherapy to Phototherapy - Changing the Therapeutic Action of a Metallo-Intercalating RuII -ReI Luminescent System by Switching its Sub-Cellular Location

The synthesis of a new heterodinuclear ReI RuII metallointercalator containing RuII (dppz) and ReI (dppn) moieties is reported. Cell-free studies reveal that the complex has similar photophysical properties to its homoleptic M(dppz) analogue and it also binds to DNA with a similar affinity. However, the newly reported complex has very different in-cell properties to its parent. In complete contrast to the homoleptic system, the RuII (dppz)/ReI (dppn) complex is not intrinsically cytotoxic but displays appreciable phototoxic, despite both complexes displaying very similar quantum yields for singlet oxygen sensitization. Optical microscopy suggests that the reason for these contrasting biological effects is that whereas the homoleptic complex localises in the nuclei of cells, the RuII (dppz)/ReI (dppn) complex preferentially accumulates in mitochondria. These observations illustrate how even small structural changes in metal based therapeutic leads can modulate their mechanism of action.

Photophysical Properties and DNA Binding of Two Intercalating Osmium Polypyridyl Complexes Showing Light-Switch Effects

The synthesis and photophysical characterization of two osmium(II) polypyridyl complexes, [Os(TAP)₂dppz]²⁺ (1) and [Os(TAP)₂dppp2]²⁺ (2) containing dppz (dipyrido[3,2-a:2′,3′-c]phenazine) and dppp2 (pyrido[2′,3′:5,6]pyrazino[2,3-f][1,10]phenanthroline) intercalating ligands and TAP (1,4,5,8-tetraazaphenanthrene) ancillary ligands, are reported. The complexes exhibit complex electrochemistry with five distinct reductive redox couples, the first of which is assigned to a TAP-based process. The complexes emit in the near-IR (1 at 761 nm and 2 at 740 nm) with lifetimes of >35 ns with a low quantum yield of luminescence in aqueous solution (∼0.25%). The Δ and Λ enantiomers of 1 and 2 are found to bind to natural DNA and with AT and GC oligodeoxynucleotides with high affinities. In the presence of natural DNA, the visible absorption spectra are found to display significant hypochromic shifts, which is strongly evident for the ligand-centered π–π* dppp2 transition at 355 nm, which undergoes 46% hypochromism. The emission of both complexes increases upon DNA binding, which is observed to be sensitive to the Δ or Λ enantiomer and the DNA composition. A striking result is the sensitivity of Λ-2 to the presence of AT DNA, where a 6-fold enhancement of luminescence is observed and reflects the nature of the binding for the enantiomer and the protection from solution. Thermal denaturation studies show that both complexes are found to stabilize natural DNA. Finally, cellular studies show that the complexes are internalized by cultured mammalian cells and localize in the nucleus.

Osmium(II) polypyridyl complexes comprising extended dipyrido[3,2-a:2′,3′-c]phenazine (1) and pyrido[2′,3′:5,6]pyrazino[2,3-f][1,10]phenanthroline (2) intercalating ligands are shown to be effective DNA binders accompanied by enhanced near-IR emission. The emission response to B-DNA is found to be sensitive to the enantiomer and the composition of DNA, with greater emission observed for AT-rich sequences. Thermal denaturation studies show that both complexes stabilize natural DNA. Cellular studies show that the complexes are internalized by cultured mammalian cells and localize in the nucleus.

Chiral Os(II) Polypyridyl Complexes as Enantioselective Nuclear DNA Imaging Agents Especially Suitable for Correlative High-Resolution Light and Electron Microscopy Studies

The high-resolution technique transmission electron microscopy (TEM), with OsO₄ as the traditional fixative, is an essential tool for cell biology and medicine. Although OsO₄ has been extensively used, it is far from perfect because of its high volatility and toxicity. Os(II) polypyridyl complexes like [Os(phen)₂(dppz)]²⁺ (phen = 1,10-phenanthroline; dppz = dipyridophenazine) are not only the well-known molecular DNA "light-switches" but also the potential ideal candidates for TEM studies. Here, we report that the cell-impermeable cationic [Os(phen)₂(dppz)]²⁺ can be preferentially delivered into the live-cell nucleus through ion-pairing with chlorophenolate counter-anions, where it functions as an unparalleled enantioselective nuclear DNA imaging reagent especially suitable for correlative light and electron microscopy (CLEM) studies in both living and fixed cells, which can clearly visualize chromosome aggregation and decondensation during mitosis simultaneously. We propose that the chiral Os(II) polypyridyl complexes can be used as a distinctive group of enantioselective high-resolution CLEM imaging probes for live-cell nuclear DNA studies.

Enantioselective and Differential Fluorescence Lifetime Imaging of Nucleus and Nucleolus by the Two Enantiomers of Chiral Os(II) Polypyridyl Complex

The nucleolus is an important subnuclear structure, but very few dyes are available for nucleolar imaging. Here we show that the Λ-enantiomer of [Os(phen)₂(dppz)]Cl₂ can differentially distinguish the nucleolus from nucleus in living cells with tetrachlorophenolate as counteranion, while the Δ-enantiomer can do so in fixed cells by FLIM imaging. Further studies with three specific metabolic inhibitors for nucleolar protein synthesis found that the lifetime changes of the two enantiomers in the nucleolus can reflect the alteration of the cellular microenvironment, which is related to the general pathological status of the nucleolus. We then observed dynamical architecture changes of the nucleolus, chromosome and spindle apparatus during cell differentiation by these two enantiomers. The chiral Os(II) complex shows many advantages as compared to the commercially available nucleolus dye Syto 9: it displays a much larger Stokes shift value with a near-red emission and a longer lifetime, it can image spindle apparatus during mitosis, and more importantly, it is enantioselective.

Photophysical and Cellular Imaging Studies of Brightly Luminescent Osmium(II) Pyridyltriazole Complexes

The series of complexes [Os(bpy)3- n(pytz) n][PF6]2 (bpy = 2,2'-bipyridyl, pytz = 1-benzyl-4-(pyrid-2-yl)-1,2,3-triazole, 1 n = 0, 2 n = 1, 3 n = 2, 4 n = 3) were prepared and characterized and are rare examples of luminescent 1,2,3-triazole-based osmium(II) complexes. For 3 we present an attractive and particularly mild preparative route via an osmium(II) η6-arene precursor circumventing the harsh conditions that are usually required. Because of the high spin-orbit coupling constant associated with the Os(II) center the absorption spectra of the complexes all display absorption bands of appreciable intensity in the range of 500-700 nm corresponding to spin-forbidden ground-state-to-3MLCT transitions (MLCT = metal-to-ligand charge transfer), which occur at significantly lower energies than the corresponding spin-allowed 1MLCT transitions. The homoleptic complex 4 is a bright emitter (λmaxem = 614 nm) with a relatively high quantum yield of emission of ∼40% in deoxygenated acetonitrile solutions at room temperature. Water-soluble chloride salts of 1-4 were also prepared, all of which remain emissive in aerated aqueous solutions at room temperature. The complexes were investigated for their potential as phosphorescent cellular imaging agents, whereby efficient excitation into the 3MLCT absorption bands at the red side of the visible range circumvents autofluorescence from biological specimens, which do not absorb in this region of the spectrum. Confocal microscopy reveals 4 to be readily taken up by cancer cell lines (HeLa and EJ) with apparent lysosomal and endosomal localization, while toxicity assays reveal that the compounds have low dark and light toxicity. These complexes therefore provide an excellent platform for the development of efficient luminescent cellular imaging agents with advantageous photophysical properties that enable excitation and emission in the biologically transparent region of the optical spectrum.

Bimetallic Ru(ii) and Os(ii) complexes based on a pyrene-bisimidazole spacer: synthesis, photophysics, electrochemistry and multisignalling DNA binding studies in the near infrared region

We report in this paper the synthesis, characterization, photophysical and electrochemical properties, and detailed DNA binding affinities of two homobimetallic Ru(ii) and Os(ii) complexes derived from a new bridging ligand consisting of two pyridyl-imidazole coordinating units rigidly coupled with a central pyrene moiety. The structure of the diruthenium complex was confirmed by X-ray crystallography. Both complexes exhibit luminescence at room temperature from their ³MLCT states, with lifetimes of τ₁ = 12.6 ns and τ₂ = 48.8 ns for the Ru(ii) complex (1) and τ₁ = 23.7 ns for the Os(ii) complex (2). For 2, the luminescence maximum stretches to the NIR region, which is suitable for potential biological applications. Both complexes exhibit two successive one-electron reversible metal-centered oxidations in the positive potential window. Computational studies employing DFT and TD-DFT methods were also performed to assign the experimentally observed optical spectral bands in the complexes. The binding affinities of the complexes towards DNA were thoroughly investigated through a variety of techniques, viz. absorption, luminescence, excited state lifetime, circular dichroism, thermal denaturation, viscosity measurement, and relative DNA binding studies using ethidium bromide. Finally, molecular docking studies were also carried out to visualize the modes of interaction between the complexes and DNA.

New Ruthenium-Based Probes for Selective G-Quadruplex Targeting

Telomeric regions containing G-quadruplex (G4) structures play a pivotal role in the development of cancers. The development of specific binders for G4s is thus of great interest in order to gain a deeper understanding of the role of these structures, and to ultimately develop new anticancer drug candidates. For several years, Ru^II complexes have been studied as efficient probes for DNA. Interest in these complexes stems mainly from the tunability of their structures and properties, and the possibility of using light excitation as a tool to probe their environment or to selectively trigger their reaction with a biological target. Herein, we report on the synthesis and thorough study of new Ru^II complexes based on a novel dipyrazino[2,3-a:2',3'-h]phenazine ligand (dph), obtained through a Chichibabin-like reaction. Luminescence experiments, surface plasmon resonance (SPR), and computational studies have demonstrated that these complexes behave as selective probes for G-quadruplex structures.

Luminescent osmium(ii) bi-1,2,3-triazol-4-yl complexes: photophysical characterisation and application in light-emitting electrochemical cells

The series of osmium(ii) complexes [Os(bpy)3-n(btz)n][PF6]2 (bpy = 2,2'-bipyridyl, btz = 1,1'-dibenzyl-4,4'-bi-1,2,3-triazolyl, n = 0, n = 1, n = 2, n = 3), have been prepared and characterised. The progressive replacement of bpy by btz leads to blue-shifted UV-visible electronic absorption spectra, indicative of btz perturbation of the successively destabilised bpy-centred LUMO. For , a dramatic blue-shift relative to the absorption profile for is observed, indicative of the much higher energy LUMO of the btz ligand over that of bpy, mirroring previously reported data on analogous ruthenium(ii) complexes. Unlike the previously reported ruthenium systems, heteroleptic complexes and display intense emission in the far-red/near-infrared (λmax = 724 and 713 nm respectively in aerated acetonitrile at RT) as a consequence of higher lying, and hence less thermally accessible, (3)MC states. This assertion is supported by ground state DFT calculations which show that the dσ* orbitals of to are destabilised by between 0.60 and 0.79 eV relative to their Ru(ii) analogues. The homoleptic complex appears to display extremely weak room temperature emission, but on cooling to 77 K the complex exhibits highly intense blue emission with λmax 444 nm. As complexes to display room temperature luminescent emission and readily reversible Os(ii)/(iii) redox couples, light-emitting electrochemical cell (LEC) devices were fabricated. All LECs display electroluminescent emission in the deep-red/near-IR (λmax = 695 to 730 nm). Whilst devices based on and show inferior current density and luminance than LECs based on , the device utilising shows the highest external quantum efficiency at 0.3%.

Homo- and Heterobimetallic Ruthenium(II) and Osmium(II) Complexes Based on a Pyrene-Biimidazolate Spacer as Efficient DNA-Binding Probes in the Near-Infrared Domain

We report in this work a new family of homo- and heterobimetallic complexes of the type [(bpy)2M(Py-Biimz)M'(II)(bpy)2](2+) (M = M' = Ru(II) or Os(II); M = Ru(II) and M' = Os(II)) derived from a pyrenyl-biimidazole-based bridge, 2-imidazolylpyreno[4,5-d]imidazole (Py-BiimzH2). The homobimetallic Ru(II) and Os(II) complexes were found to crystallize in monoclinic form with space group P21/n. All the complexes exhibit strong absorptions throughout the entire UV-vis region and also exhibit luminescence at room temperature. For osmium-containing complexes (2 and 3) both the absorption and emission band stretched up to the NIR region and thus afford more biofriendly conditions for probable applications in infrared imaging and phototherapeutic studies. Detailed luminescence studies indicate that the emission originates from the respective (3)MLCT excited state mainly centered in the [M(bpy)2](2+) moiety of the complexes and is only slightly affected by the pyrene moiety. The bimetallic complexes show two successive one-electron reversible metal-centered oxidations in the positive potential window and several reduction processes in the negative potential window. An efficient intramolecular electronic energy transfer is found to occur from the Ru center to the Os-based component in the heterometallic dyad. The binding studies of the complexes with DNA were thoroughly studied through different spectroscopic techniques such as UV-vis absorption, steady-state and time-resolved emission, circular dichroism, and relative DNA binding study using ethidium bromide. The intercalative mode of binding was suggested to be operative in all cases. Finally, computational studies employing DFT and TD-DFT were also carried out to interpret the experimentally observed absorption and emission bands of the complexes.

Luminescence quenching by photoinduced charge transfer between metal complexes in peptide nucleic acids

A new scaffold for studying photoinduced charge transfer has been constructed by connecting a [Ru(Bpy)3](2+) donor to a bis(8-hydroxyquinolinate)2 copper [CuQ2] acceptor through a peptide nucleic acid (PNA) bridge. The luminescence of the [Ru(Bpy)3](2+*) donor is quenched by electron transfer to the [CuQ2] acceptor. Photoluminescence studies of these donor-bridge-acceptor systems reveal a dependence of the charge transfer on the length and sequence of the PNA bridge and on the position of the donor and acceptor in the PNA. In cases where the [Ru(Bpy)3](2+) can access the π base stack at the terminus of the duplex, the luminescence decay is described well by a single exponential; but if the donor is sterically hindered from accessing the π base stack of the PNA duplex, a distribution of luminescence lifetimes for the donor [Ru(Bpy)3](2+*) is observed. Molecular dynamics simulations are used to explore the donor-PNA-acceptor structure and the resulting conformational distribution provides a possible explanation for the distribution of electron transfer rates.

Dinuclear osmium(ii) probes for high-resolution visualisation of cellular DNA structure using electron microscopy

Dinuclear osmium(ii) complexes are excellent easy-to-handle probes for transmission electron microscopy, facilitating high-resolution intracellular imaging of sub-nuclear structures.

Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor

Detection of proteins and nucleic acids is dominantly performed using optical fluorescence based techniques, which are more costly and timely than electrical detection due to the need for expensive and bulky optical equipment and the process of fluorescent tagging. In this paper, we discuss our study of the electrical properties of nucleic acids and proteins at the nanoscale using a nanoelectronic probe we have developed, which we refer to as the Nanoneedle biosensor. The nanoneedle consists of four thin film layers: a conductive layer at the bottom acting as an electrode, an oxide layer on top, and another conductive layer on top of that, with a protective oxide above. The presence of proteins and nucleic acids near the tip results in a decrease in impedance across the sensing electrodes. There are three basic mechanisms behind the electrical response of DNA and protein molecules in solution under an applied alternating electrical field. The first change stems from modulation of the relative permittivity at the interface. The second mechanism is the formation and relaxation of the induced dipole moment. The third mechanism is the tunneling of electrons through the biomolecules. The results presented in this paper can be extended to develop low cost point-of-care diagnostic assays for the clinical setting.

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.

Label-free sensing of pH and silver nanoparticles using an "OR" logic gate

Many natural phenomena are associated with the presence of two or more separate variables. We report here an "OR" DNA logic gate based on a luminescent platinum(II) switch-on probe for silver nanoparticles and pH, both of which may be considered putative indicators of pollution. The modulation of metal complex/double-stranded DNA complex phosphorescence by Ag(+) and H(+) was used to construct a simple, rapid and label-free method for the label-free detection of pH and nanomolar Ag(+) ions and nanoparticles in aqueous solutions with high selectivity.

A highly selective, label-free, homogenous luminescent switch-on probe for the detection of nanomolar transcription factor NF-kappaB

Transcription factors are involved in a number of important cellular processes. The transcription factor NF-κB has been linked with a number of cancers, autoimmune and inflammatory diseases. As a result, monitoring transcription factors potentially represents a means for the early detection and prevention of diseases. Most methods for transcription factor detection tend to be tedious and laborious and involve complicated sample preparation, and are not practical for routine detection. We describe herein the first label-free luminescence switch-on detection method for transcription factor activity using Exonuclease III and a luminescent ruthenium complex, [Ru(phen)₂(dppz)]²⁺. As a proof of concept for this novel assay, we have designed a double-stranded DNA sequence bearing two NF-κB binding sites. The results show that the luminescence response was proportional to the concentration of the NF-κB subunit p50 present in the sample within a wide concentration range, with a nanomolar detection limit. In the presence of a known NF-κB inhibitor, oridonin, a reduction in the luminescence response of the ruthenium complex was observed. The reduced luminescence response of the ruthenium complex in the presence of small molecule inhibitors allows the assay to be applied to the high-throughput screening of chemical libraries to identify new antagonists of transcription factor DNA binding activity. This will allow the rapid and low cost identification and development of novel scaffolds for the treatment of diseases caused by the deregulation of transcription factor activity.

DNA interaction studies of cobalt (II) mixed-ligand complexes containing dimethyl-1, 10-phenanthroline and dipyrido[3,2-a:2',3'-c]phenazine: the role of methyl substitutions on the mode of binding

Two cobalt (II) complexes containing a dipyrido[3,2-a:2',3'-c]phenazine (dppz) base with the general formulation [Co(dppz)(dmp)(2)]Cl(2), where dmp is 4,7-dimethyl-1,10-phenanthroline ligand (4,7-dmp) (1) and 2,9-dimethyl-1,10-phenanthroline ligand (2,9-dmp) (2) were synthesized and characterized. Binding interactions of these complexes with calf thymus DNA were investigated by emission, absorption, circular dichroism, and viscosity studies, and the effects of the positions of methyl substitutions in phenanthroline coligands were investigated. The DNA binding constants obtained from the absorption spectral titrations decrease in the order of 1 > 2, which is consistent with the trend in apparent emission enhancement of the complexes on binding to calf thymus DNA. These observations were supported by circular dichroism spectroscopy and viscosity measurements and reveal that DNA binding affinity of the complexes depends on the position of methyl groups on the phenanthroline ligands.

A selective G-quadruplex-based luminescent switch-on probe for the detection of nanomolar silver(I) ions in aqueous solution

A G-quadruplex-based luminescent platinum(II) switch-on probe has been developed for the selective detection of nanomolar Ag(+) ions in aqueous solution.

Photophysical properties and singlet oxygen production by ruthenium(II) complexes of benzo[i]dipyrido[3,2-a:2',3'-c]phenazine: spectroscopic and TD-DFT study

The photophysical properties of a series of Ru(II) complexes containing benzo[i]dipyrido[3,2-a:2',3'-c]phenazine (dppn) as a ligand are reported. Transient absorption spectroscopy studies indicate that, in contrast to related Ru(dppz) complexes (dppz = dipyrido[3,2-a:2',3'-c]phenazine), the excited state of all the dppn systems is a long-lived pipi* triplet state. Computational studies (DFT and TD-DFT) confirm that the excited state is based on the dppn ligand. Near-infrared luminescence studies reveal that the complexes are efficient singlet oxygen sensitizers with yields of 70-83%.

Cooperative and noncooperative binding of *Ru(bpy)3(2+) to DNA and SB4.5G dendrimers

The process *Ru(bpy)(3)(2+) + S(2)O(8)(2-) in two different reaction media, the SB4.5G dendrimer and DNA solutions, was studied. In both media, the receptors have anionic characteristics. This fact will produce a binding of the ruthenium complex to the two receptors by attractive electrostatic interactions. On the contrary, the peroxodisulfate ions will be preferentially located in the aqueous solution due to electrostatic repulsions with the receptors. Despite the similarities of the receptors, some differences are observed in these two reaction media. These differences arise from the fact that the binding of the *Ru(bpy)(3)(2+) complex to DNA shows a negative cooperativity, whereas the binding to the dendrimer is noncooperative in character. The anticooperative character of the binding that happens in DNA solutions becomes noncooperative when an electrolyte, NaNO(3), is added to the medium. This is related to a condensation of the salt's counterions on the surface of the DNA which produces a decrease of the equilibrium constant corresponding to the binding of the complex to the receptor. Therefore, it is shown that the ionic strength of the reaction medium exerts a great influence on the cooperative nature of the ligand/receptor binding. This also explains the different behavior observed in DNA and dendrimer solutions.

A selective oligonucleotide-based luminescent switch-on probe for the detection of nanomolar mercury(II) ion in aqueous solution

An oligonucleotide-based luminescent platinum(II) switch-on probe has been developed for selective detection of nanomolar Hg(2+) ions.

Synthesis and characterization of iridium(III) cyclometalated complexes with oligonucleotides: insights into redox reactions with DNA

Heteroleptic cyclometalated complexes of Ir(III) containing the dipyridophenazine ligand are synthesized through the direct introduction of a functionalized dipyridophenazine ligand onto a bis(dichloro)-bridged Ir(III) precusor and characterized by 1H NMR, mass spectrometry, as well as spectroscopic and electrochemical properties. The excited state of the Ir(III) complexes have sufficient driving force to oxidize purines and to reduce pyrimidine nucleobases. Luminescence and EPR measurements of the Ir(III) complex with an unmodified dppz bound to DNA show the formation of a guanine radical upon irradiation, resulting from an oxidative photoinduced electron-transfer process. Evidence is also obtained indirectly for reductive photoinduced electron transfer from the excited complex to the thymine base in DNA. We have also utilized cyclopropylamine-substituted nucleosides as ultrafast kinetic traps to report transient charge occupancy in oligonucleotides when DNA is irradiated in the presence of noncovalently bound complexes. These experiments establish that the derivatized Ir(III) complexes, with photoactivation, can trigger the oxidation of guanine and the reduction of cytosine.

DNA biosensor for detection of Helicobacter pylori using phen-dione as the electrochemically active ligand in osmium complexes

A surface-based method for the study of the interactions of DNA with redox-active 1,10-phenantroline-5,6-dione (phen-dione) osmium complexes is described. The study was carried out using gold electrodes modified with DNA via adsorption and [Os(bpy)(2)(phe-dione)](3+/2+) (bpy = 2,2'-bipyridyl) or [Os(phen)(2)(phen-dione)](3+/2+) (phen = 1,10-phenantroline) as electrochemical reported molecules. The method, which is simple and reagent-saving, allows the accumulation of osmium complexes within the DNA layer. The amount of osmium complex bound by the adsorbed layer of DNA was determined from the voltammetric charge associated with the osmium redox process of the immobilized metal complex. The quinone moiety of the phen-dione ligand was useful as an indicator for electrochemical DNA sensing because of its redox response at low potentials. A thiol-linked single-stranded Helicobacter pylori DNA probe was immobilized, through S-Au bonds on to a gold electrode (density of modification 86 pmol/cm(2)). Following hybridization with the complementary DNA sequence, the osmium complex was electrochemically accumulated within the double-stranded DNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range where the quinone moiety was redox active (i.e., at very low potentials, -0.020 V vs SSCE); with this approach, a sequence of the H. pylori could be quantified over the range from 5 to 20 pmol with a linear correlation of r = 0.9888 and a detection limit of approximately 6 pmol.

The two modes of binding of Ru(phen)2dppz2+ to DNA: Thermodynamic evidence and kinetic studies

The binding of Ru(phen)(2)dppz(2+) (dppz=dipyrido[3,2-a:2',3'-c]phenazine) to DNA was investigated at pH 7.0 and 25 degrees C using stopped-flow and spectrophotometric methods. Equilibrium measurements show that two modes of binding, whose characteristics depend on the polymer to dye ratio (C(P)/C(D)), are operative. The binding mode occurring for values of C(P)/C(D) higher than 3 exhibits positive cooperativity, which is confirmed by kinetic experiments. The reaction parameters are K=2 x 10(3)M(-1), omega=550, n=1, k(r)=(1.9+/-0.5) x 10(7)M(-1)s(-1) and k(d)=(9.5+/-2.5)x10(3)s(-1) at I=0.012 M. The results are discussed in terms of prevailing surface interaction with DNA grooves accompanied by partial intercalation of the dppz residue. The other binding mode becomes operative for C(P)/C(D)<3 and the equilibria analysis shows this is an ordinary intercalation mode (K=1.3 x 10(6) M(-1), n=1.5 at I=0.012 M and K=2 x 10(5) M(-1), n=1.2 at I=0.21 M). Similar behaviour is displayed by double-stranded poly(A).

Dinuclear Monointercalating RuII Complexes That Display High Affinity Binding to Duplex and Quadruplex DNA

The DNA duplex binding properties of previously reported dinuclear Ru(II) complexes based on the ditopic ligands tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2'',3''-j]phenazine (tppz) and tetraazatetrapyrido[3,2-a:2'3'-c:3'',2''-l:2''',3'''-n]pentacene (tatpp) are reported. Photophysical and biophysical studies indicate that, even at high ionic strengths, these complexes bind to duplex DNA, through intercalation, with affinities that are higher than any other monointercalating complex and are only equalled by DNA-threaded bisintercalating complexes. Additional studies at high ionic strengths using the 22-mer d(AG(3)[T(2)AG(3)](3)) [G3] human telomeric sequence reveal that the dinuclear tppz-based systems also bind with high affinity to quadruplex DNA. Furthermore, for these complexes, quadruplex binding is accompanied by a distinctive blue-shifted "light-switch" effect, characterized by higher emission enhancements than those observed in the analogous duplex effect. Calorimetry studies reveal that the thermodynamics of duplex and quadruplex binding is distinctly different, with the former being entirely entropically driven and the latter being both enthalpically and entropically favored.

Quantum mechanical description of the interactions between DNA and water

In recent years, a lot of attention has been focused on the electronic properties of DNA. With recent advances in linear scaling quantum mechanics there are now new tools available to enhance our understanding of the electronic properties of DNA among other biomolecules. Using both explicit solvent models and implicit (continuum) solvent models, the electronic characteristics of a dodecamer duplex DNA have been fully studied using both divide and conquer (D&C), semi-empirical quantum mechanics and non-D&C semi-empirical quantum mechanics. According to the AM1 Hamiltonian, approximately 3.5 electrons (approximately 0.3 electron/base pair) are transferred from the duplex to the solvent. According to the density of state (DOS) analysis, in vacuo DNA has a band gap of approximately 1 eV showing that in the absence of solvent, the DNA may exhibit similar properties to those of a semiconductor. Upon increasing solvation (2.5-5.5 A), the band gap ranges from approximately 3 eV to approximately 6 eV. For the implicit solvent model, the band gap continues this widening trend to approximately 7 eV. Therefore, upon solvation and in the absence of dopants, the DNA should begin to loose its conductive properties. Finally, when one considers the energy and localization of the frontier orbitals (HOMO and LUMO), solvent has a stabilizing effect on the DNA system. The energy of the HOMO drops from approximately 15 eV in vacuo to approximately 2 eV for 5.5 A of water to approximately -8 eV for the implicit solvent model. Similarly, the LUMO drops from approximately 16 eV for in vacuo to approximately 9 eV for 5.5 A of water to approximately -1 eV for the implicit model. Beyond the importance of the computed results on the materials properties of DNA, the present work also shows that the behavior of intercalators will be affected by the electronic properties of DNA. This could have an impact on our understanding of how DNA based drugs interact with DNA and on the design of new DNA based small molecule drugs.

Ruthenium(II) Complexes of 1,12-Diazaperylene and Their Interactions with DNA

Four complexes of the ligand 1,12-diazaperylene (DAP) have been prepared, [Ru(bpy)n(DAP)(3-n)]2+ where n = 0-2 and [Ru(DAP)3]2+. The [Ru(DAP)3]2+ complex was characterized by X-ray analysis and was found to exhibit the expected propeller-like structure with significant intermolecular pi-stacking interactions. The three Ru(II) complexes showed self-consistent optoelectronic properties with similar ligand-centered pi-pi* absorptions in the range of 333-468 nm and MLCT bands associated with the DAP which increased in intensity and decreased in energy as the number of DAP ligands varied from 1 to 3. Hypochromicity and viscosity changes were observed that were consistent with DAP intercalation into DNA, and binding constants were measured in the range of 1.4-1.6 x 10(6) M(-1) for the mixed ligand complexes. Furthermore, the complex [Ru(bpy)2(DAP)]2+ was found to photocleave plasmid DNA upon irradiation with visible light.

DNA binding of an organic dppz-based intercalator

An improved synthesis of a water-soluble derivative of dipyrido[3,2-a:2',3'-c]phenazine (dppz) is reported. The structures of both dppz and the cation ethylene-bipyridyldiylium-phenazine dinitrate [[1][(PF(6))(2)]] have been obtained via X-ray crystallography. Metal complex derivatives of dppz are very well studied. However, using the water soluble [1][(NO(3))(2)], the nature of the interaction of a simple dppz unit with duplex DNA has been investigated for the first time. In both organic solvents and water, 1 displays unstructured luminescence, assigned to an intramolecular charge transfer. The emission is quenched on binding to natural and synthetic duplex DNA, including poly(dA).poly(dT). A variety of techniques reveal that the cation binds to DNA with an affinity comparable to those of many metal dppz complexes, via an intercalative binding mode.