DNA Sequence and Ancillary Ligand Modulate the Biexponential Emission Decay of Intercalated [Ru(L)2dppz]2+ Enantiomers

The bi‐exponential emission decay of [Ru(L)₂dppz]²⁺ (L=N,N′‐diimine ligand) bound to DNA has been studied as a function of polynucleotide sequence, enantiomer, and nature of L (phenanthroline vs. bipyridine). The lifetimes (τ_i) and pre‐exponential factors (α_i) depend on all three parameters. With [poly(dA‐dT)]₂, the variation of α_i with [Nu]/[Ru] has little dependence on L for Λ‐[Ru(L)₂dppz]²⁺ but a substantial dependence for Δ‐[Ru(L)₂dppz]²⁺. With [poly(dG‐dC)]₂, by contrast, the Λ‐enantiomer α_i values depend strongly on the nature of L, whereas those of the Δ‐enantiomer are relatively unaffected. DNA‐bound linked dimers show similar photophysical behaviour. The lifetimes are identified with two geometries of minor‐groove intercalated [Ru(L)₂dppz]²⁺, resulting in differential water access to the phenazine nitrogen atoms. Interplay of cooperative and anti‐cooperative binding resulting from complex–complex and complex–DNA interactions is responsible for the observed variations of α_i with binding ratio. [Ru(phen)₂dppz]²⁺ emission is quenched by guanosine in DMF, which may further rationalise the shorter lifetimes observed with guanine‐rich DNA.     

Synthesis,characterization and DNA binding and photocleavage studies of [Ru(bpy)2BDPPZ]2+, [Ru(dmb)2BDPPZ]2+ and [Ru(phen)2BDPPZ]2+ complexes and their antimicrobial activity

Polypyridyl ligand 9a,13a‐dihydro‐4,5,9,14‐tetraaza‐benzo[b]triphenylene‐11‐yl)‐phenyl‐methanone (BDPPZ) and its complexes [Ru(bpy)₂BDPPZ]²⁺, [Ru(dmb)₂BDPPZ]²⁺ and [Ru(phen)₂BDPPZ]²⁺ (where bpy = 2,2′‐bipyridine, dmb = 4,4′‐dimethyl‐2,2′‐bipyridine, phen = 1,10‐phenanthroline) have been synthesized and characterized by elemental analysis, IR, UV–vis, ¹H‐NMR, ¹³C‐NMR and mass spectra. The DNA‐binding properties of the complexes were investigated by absorption, emission, melting temperature and viscosity measurements. Experimental results indicate that the three complexes can intercalate into DNA base pairs. Photo activated cleavage of pBR‐322 DNA by the three complexes was also studied. Further, all three Ru(II) complexes synthesized were screened for their antimicrobial activity. Copyright © 2009 John Wiley & Sons, Ltd.     

Influence of pH on the photochemical and electrochemical reduction of the dinuclear ruthenium complex, [(phen)2Ru(tatpp)Ru(phen)2)Cl4, in water: proton-coupled sequential and concerted multi-electron reduction

The dinuclear ruthenium complex [(phen)2Ru(tatpp)Ru(phen)2]4+ (P; in which phen is 1,10-phenanthroline and tatpp is 9,11,20,22-tetraaza tetrapyrido[3,2-a:2'3'-c:3',2'-l:2',3']-pentacene) undergoes a photodriven two-electron reduction in aqueous solution, thus storing light energy as chemical potential within its structure. The mechanism of this reduction is strongly influenced by the pH, in that basic conditions favor a sequential process involving two one-electron reductions and neutral or slightly acidic conditions favor a proton-coupled, bielectronic process. In this complex, the central tatpp ligand is the site of electron storage and protonation of the central aza nitrogen atoms in the reduced products is observed as a function of the solution pH. The reduction mechanism and characterization of the rich array of products were determined by using a combination of cyclic and AC voltammetry along with UV-visible reflectance spectroelectrochemistry experiments. Both the reduction and protonation state of P could be followed as a function of pH and potential. From these data, estimates of the various reduced species' pKa values were obtained and the mechanism to form the doubly reduced, doubly protonated complex, [(phen)2Ru(H2tatpp)Ru(phen)2]4+ (H2P) at low pH (< or =7) could be shown to be a two-proton, two-electron process. Importantly, H2P is also formed in the photochemical reaction with sacrificial reducing agents, albeit at reduced yields relative to those at higher pH.     

Base-Modified DNA Labeled by [Ru(bpy)3]2+ and [Os(bpy)3]2+ Complexes: Construction by Polymerase Incorporation of Modified Nucleoside Triphosphates,Electrochemical and Luminescent Properties,and Applications

Modified 2′-deoxynucleoside triphosphates (dNTPs) bearing [Ru(bpy)₃]²⁺ and [Os(bpy)₃]²⁺ complexes attached via an acetylene linker to the 5-position of pyrimidines (C and U) or to the 7-position of 7-deazapurines (7-deaza-A and 7-deaza-G) have been prepared in one step by aqueous cross-couplings of halogenated dNTPs with the corresponding terminal acetylenes. Polymerase incorporation by primer extension using Vent (exo-) or Pwo polymerases gave DNA labeled in specific positions with Ru²⁺ or Os²⁺ complexes. Square-wave voltammetry could be efficiently used to detect these labeled nucleic acids by reversible oxidations of Ru^2+/3+ or Os^2+/3+. The redox potentials of the Ru²⁺ complexes (1.1–1.25 V) are very close to that of G oxidation (1.1 V), while the potentials of Os²⁺ complexes (0.75 V) are sufficiently different to enable their independent detection. On the other hand, Ru²⁺-labeled DNA can be independently analyzed by luminescence. In combination with previously reported dNTPs bearing ferrocene, aminophenyl, and nitrophenyl tags, the Os-labeled dATP has been successfully used for “multicolor” redox labeling of DNA and for DNA minisequencing.     

Interaction studies of DNA binding of ruthenium(II) mixed-ligand complexes: [Ru(phen)2(dtmi)]2+ and [Ru(phen)2(dtni)]2+

Two new ligands, 3-(pyrazin-2-yl)-as-triazino[5,6-f]-5-methoxylisatin (dtmi), 3-(pyrazin-2-yl)-as-triazino[5,6-f]-5-nitroisatin (dtni) and their ruthenium(II) complexes [Ru(phen)2(dtmi)](ClO4)2 (1) and [Ru(phen)2(dtni)](ClO4)2 (2) have been prepared and characterized by elemental analysis, FAB-MS, ES-MS and 1H NMR. The DNA-binding behaviors of complexes have been studied by spectroscopic titration, viscosity measurements, thermal denaturation and circular dichromism (CD). The results indicate that the complexes 1 and 2 interact with calf thymus DNA (CT-DNA) by intercalative mode. The DNA-binding affinity of the complexes 2 is larger than that complex 1 does.     

Enantioselective luminescence quenching of DNA light-switch [Ru(phen)2dppz]2+ by electron transfer to structural homologue [Ru(phendione)2dppz]2+

The quenching of the luminescence of [Ru(phen)(2)dppz](2+) by structural homologue [Ru(phendione)(2)dppz](2+), when both complexes are bound to DNA, has been studied for all four combinations of Delta and Lambda enantiomers. Flow linear dichroism spectroscopy (LD) indicates similar binding geometries for all the four compounds, with the dppz ligand fully intercalated between the DNA base pairs. A difference in the LD spectrum observed for the lowest-energy MLCT transition suggests that a transition, potentially related to the final localization of the excited electron to the dppz ligand in [Ru(phen)(2)dppz](2+), is overlaid by an orthogonally polarized transition in [Ru(phendione)(2)dppz](2+). This would be consistent with a low-lying LUMO of the phendione moiety of [Ru(phendione)(2)dppz](2+) that can accept the excited electron from [Ru(phen)(2)dppz](2+), thereby quenching the emission of the latter. The lifetime of excited Delta-[Ru(phen)(2)dppz](2+) is decreased moderately, from 664 to 427 ns, when bound simultaneously with the phendione complex to DNA. The 108 ns lifetime of opposite enantiomer, Lambda-[Ru(phen)(2)dppz](2+), is only shortened to 94 ns. These results are consistent with an average rate constant for electron transfer of approximately 1.10(6) s(-1) between the phenanthroline- and phendione-ruthenium complexes. At binding ratios close to saturation of DNA, the total emission of the two enantiomers is lowered equally much, but for the Lambda enantiomer, this is not paralleled by a decrease in luminescence lifetime. A binding isotherm simulation based on a generalized McGhee-von Hippel approach shows that the Delta enantiomer binds approximately 3 times stronger to DNA both for [Ru(phendione)(2)dppz](2+) and [Ru(phen)(2)dppz](2+). This explains the similar decrease in total emission, without the parallel decrease in lifetime for the Lambda enantiomer. The simulation also does not indicate any significant binding cooperativity, in contrast to the case when Delta-[Rh(phi)(2)bipy](3+) is used as quencher. The very slow electron transfer from [Ru(phen)(2)dppz](2+) to [Ru(phendione)(2)dppz](2+), compared to the case when [Rh(phi)(2)phen](3+) is the acceptor, can be explained by a much smaller driving free-energy difference.     

Λ-及Δ-[Ru(phen)2dppz]n+对错配DNA的识别作用的分子模拟

本文通过在ESFF(Extensible Systematic Force Field)力场下对其作用中的体系势能进行分子力学计算，分析了手性金属配合物Λ－及Δ-[Ru(phen)2dppz]^n 对错配DNA d(CCGAATGAGG)2的识别机理，并在分子水平上对其做了详细解释。     

联吡啶和邻菲咯啉混配的钌配合物的核磁共振氢谱分析

合成了Ru(bpy)2(phen)(PF6)2 和Ru(bpy)(phen)2(PF6)2 (bpy和phen分别为2,2′-联吡啶和1,10 -邻菲咯啉)两种电化学发光物质,以 1HNMR谱研究这两种配合物的立体结构,利用 1H - 1HCOSY(同核相关谱)核磁共振技术详细分析并归属了它们的氢谱峰。     

The ligand-ligand and spin-orbit interactions in Fe(phen) 3 +2 and Ru(phen) 3 +2 ions

To explain the differences in the spectral properties of the complex ions (–)-Fe(phen) ₃ ⁺² and (–)-Ru(phen) ₃ ⁺² the interaction between the ligands and spin-orbit coupling energies have been calculated. It is shown that the spinorbit coupling energy in case of Ru(II) complex is more important than the ligand-ligand interaction. This leads to a sequence of the lowest excited states ³A₂<¹A₂<¹E.     

Synthesis and spectroscopic DNA binding studies of [Ru(phen)2(tbtc)]2+ and [Ru(2,9-dmp)2(tbtc)]2+

A new polypyridyl ligand tbtc (tbtc=4,5,9,14-tetraaza-benzo[b]triphenylene-11-carboxylic acid methyl ester) and its complexes [Ru(phen)2(tbtc)]2+ (1) (phen=1,10-phenanthroline) and [Ru(2,9-dmp)2(tbtc)]2+ (2) (2,9-dmp=2,9-dimethyl-1,10-phenanthroline) were synthesized and characterized by element analysis, MS, and 1H NMR. The DNA binding properties of both complexes to calf thymus DNA (CT-DNA) were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that both complexes bind to DNA via an intercalative mode, and the DNA binding affinity of complex 1 is much greater than that of complex 2. This difference in binding affinity probably was caused by the different ancillary ligands. Also, when irradiated at 365 nm, complex 1 was found to be a more-effective DNA-cleaving agent than complex 2.     

Ru(TAP)3]2+-photosensitized DNA cleavage studied by atomic force microscopy and gel electrophoresis: a comparative study

Topological modifications of plasmid DNA adsorbed on a variety of surfaces were investigated by using atomic force microscopy (AFM). On mica modified with 3-aminopropyltriethoxysilane (APS) or poly-L-lysine, the interaction between the plasmid DNA and the surface "freezes" the plasmid DNA conformation deposited from solution, and the AFM images resemble the projection of the three-dimensional conformation of the plasmid DNA in solution. Modified mica with low concentrations of Mg(2+) leads to a decrease in the interaction strength between plasmid DNA and the substrate, and the AFM images reflect the relaxed or equilibrium conformation of the adsorbed plasmid DNA. Under these optimized deposition conditions, topological modifications of plasmid DNA were produced under irradiation in the presence of [Ru(TAP)(3)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene), which is a non-intercalating complex, and were followed as a function of illumination time. The observed structural changes correlate well with the conversion of the supercoiled covalently closed circular form (ccc form) into the open circular form (oc form), induced by a single-strand photocleavage. The AFM results obtained after fine-tuning of the plasmid DNA-substrate interaction compare well with those observed from gel electrophoresis, indicating that under the appropriate deposition conditions, AFM is a reliable technique to investigate irradiation-induced topological changes in plasmid DNA.     

Templated synthesis of a rotaxane with a [Ru(diimine)3]2+ core

A rotaxane containing a ruthenium bisphenanthroline complex, acting as an axis, and a macrocycle incorporating a 2,2'-bipyridine (bpy) unit, threaded by the axis, has been synthesized. The bisphenanthroline ligand is such that its ruthenium(II) complexes possess a clearly identified axis, making such compounds ideal components of rotaxanes constructed around an octahedral ruthenium(II) center, which serves as a template. The ring is threaded by the axial ruthenium(II) precursor complex, to afford the corresponding pseudorotaxane in moderate yield. The X-ray structure analysis of this compound reveals the threaded nature of the complex. The length of the threaded ring (35 atoms in the periphery) is too short to allow easy threading of the axis through the macrocycle. As a consequence, an isomer is also obtained for which the axial ruthenium complex is attached in an exo fashion. (1)H NMR studies have been carried out, which reveal various conformational equilibria for the pseudorotaxane. Light-induced decoordination of the bpy-containing cyclic fragment was shown to be quantitative and to lead to the free ring and the axial ruthenium(II) complex, regardless of the starting compound (pseudorotaxane or exo isomer). Finally, the real rotaxane could be prepared, although it could not be separated from its exo isomer.     

Caught in the Loop: Binding of the [Ru(phen)2(dppz)]2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy

Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)₂(dppz)]²⁺ “light-switch” complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K⁺ and Na⁺ containing solutions. TRIR permits the simultaneous monitoring both of the “dark” and “bright” states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na⁺ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.     

Ru(phen)3 2+-SDBS-KMnO4化学发光体系检测半胱氨酸的研究

在20mmol·L-1硫酸-1.2mmol.L-1十二烷基苯磺酸钠(SDBS)介质中,半胱氨酸可以增强三(1,10-菲咯啉)钌(Ⅱ)[Ru(phen)32+]-KMnO4化学发光体系的发光强度.基于此,建立了一种化学发光直接检测半胱氨酸的新方法.在优化的实验条件下,该方法的线性范围和检测限分别为2.5×10-2-2.0μg·mL-1和2.1×10-2μg·mL-1,对11份含半胱氨酸0.5μg·mL-1的溶液平行测定的相对标准偏差(R.S.D.)为5.3%.将其用于合成样品中半胱氨酸含量的测定,结果令人满意.并提出了可能的化学发光机理.     

Symmetrical dinuclear complexes with high DNA affinity based on [Ru(dpq)2(phen)]2+

Symmetrical homometallic dinuclear complexes of the type [(Ru(dpq)2)2(phen-SOS-phen)]4+, with a flexible 2-mercaptoethyl ether linker joining the two [Ru(dpq)2(phen)]2+-based sub-units, have DNA dissociation constants (Kd) in the nM range.     

Ru(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and undergoes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate

The lowest excited state of [Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine) 1 is strongly luminescent, even in water, and very oxidizing. Therefore it is able to oxidise not only guanosine-5'-monophosphate (GMP), as demonstrated by laser flash photolysis, but also guanine-containing polynucleotides such as calf thymus DNA and [poly(dG-dC)]2. The luminescence quenching was found to be faster in H2O than in D2O, as is the back reaction, indicating that both processes probably proceed by proton-coupled electron transfer. These properties, that are controlled by the triplet MLCT state in which the charge has been transferred from the Ru to a TAP ligand, contrast with those of the well known [Ru(phen)2(dppz)]2+ 2.