Study on Triplex DNA by Use of Molecular “Light Switch“ Complex of Ru(phen)2(dppx)^2

A new method for the study of triplex DNA is established according the fluorescence enhancement of molecular “Light Switch“ complex of Ru(phen)2(dppx)^2 when it intercalate into triplex DNA.Because the fluorescence intensity of Ru(phen)2(dppx)^2 bonded to triplex DNA is in ths case higher than that bonded to duplex DNA in certain range of DNA concentration,the method is much more sensitive than other methods reported previously.     

Sensitive detection of H(2)O(2) and H(2)O(2)-related reactant with Ru(bipy)(2)(7,8-dimethyl-dipyridophenazine)(2+) and oligodeoxyribonucleotide

A sensor for H(2)O(2) and H(2)O(2)-related reactant was constructed with oligonucleotides and Ru(bipy)(2)dppx(2+) (bipy = 2,2'-bipyridine, dppx = 7,8-dimethyl-dipyridophenazine), which was performed by converting the H(2)O(2)-induced DNA cleavage into the change of luminescence. The 'DNA light switch' Ru(bipy)(2)dppx(2+) could emit strong luminescence in the presence of dsDNA. DNA cleavage occurred upon addition of H(2)O(2) due to the Fenton reaction, which resulted in the decrease of the luminescence of Ru(bipy)(2)dppx(2+). Therefore, the luminescence intensity depended on the concentration of H(2)O(2) and H(2)O(2)-related reactants, and the detection limits for H(2)O(2), uric acid and cholesterol were 0.20 μM, 0.46 μM and 1.25 μM, respectively. The recovery varied between 94.0% and 105.0% when the assay was applied to the determination of uric acid and cholesterol in biological samples, which demonstrated the good practicability of the assay.     

荧光探针Ru(phen)2(dppx)2+测定H1N1禽流感病毒DNA

利用荧光探针Ru(phen)2dppx2+与ssDNA作用时不产生荧光或荧光很弱,而与dsDNA作用时荧光增强的机理,将H1N1禽流感病毒ssDNA与其完全互补ssDNA杂交形成dsDNA实现Ru(phen)2dppx2+对H1N1禽流感病毒DNA特定序列（5’-CTA CCA TGC GAA CAA TTC AAC CGA CAC TGT T-3’）的定量检测。在优化的实验条件下,测定H1N1禽流感病毒 DNA的线性范围为9.3×10-10～7.4×10-8 mol/L,线性关系：y = 3.3829x + 8.3948,R2 =0.9982,检出限为5.3×10-10 mol/L。该方法具有操作简单,检测快速,灵敏度高和选择好等优点。     

DNA对Ru(bpy)_2(dppx)~(2+)-SDS体系共振光散射的猝灭作用及其应用

研究了Ru(bpy)2(dppx)2+-SDS-DNA(bpy=2,2′-联吡啶,dppx=7,8-二甲基-吡啶并[3,2-a:2′,3′-c]吩嗪)体系的共振光散射光谱。结果表明,在阴离子表面活性剂十二烷基硫酸钠(SDS)预胶束聚集体存在下,Ru(bpy)2(dppx)2+-SDS体系具有很强的共振光散射,DNA的加入使其共振散射光猝灭。探讨了反应机理。基于DNA对Ru(bpy)2(dppx)2+-SDS体系共振光散射的猝灭作用,建立了共振光散射法测定DNA的新方法。在最佳实验条件下,体系在393nm处的共振光散射猝灭程度与DNA的浓度呈线性关系,线性范围为0.01～1.2mg/L,检出限为1.5μg/L。     

Exploring the interaction of ruthenium(II) polypyridyl complexes with DNA using single-molecule techniques

Here we explore DNA binding by a family of ruthenium(II) polypyridyl complexes using an atomic force microscope (AFM) and optical tweezers. We demonstrate using AFM that Ru(bpy)2dppz2+ intercalates into DNA (K(b) = 1.5 x 10(5) M(-1)), as does its close relative Ru(bpy)2dppx2+ (K(b) = 1.5 x 10(5) M(-1)). However, intercalation by Ru(phen)3(2+) and other Ru(II) complexes with K(b) values lower than that of Ru(bpy)2dppz2+ is difficult to determine using AFM because of competing aggregation and surface-binding phenomena. At the high Ru(II) concentrations required to evaluate intercalation, most of the DNA strands acquire a twisted, curled conformation that is impossible to measure accurately. The condensation of DNA on mica in the presence of polycations is well known, but it clearly precludes the accurate assessment by AFM of DNA intercalation by most Ru(II) complexes, though not by ethidium bromide and other monovalent intercalators. When stretching individual DNA molecules using optical tweezers, the same limitation on high metal concentration does not exist. Using optical tweezers, we show that Ru(phen)2dppz2+ intercalates avidly (K(b) = 3.2 x 10(6) M(-1)) whereas Ru(bpy)3(2+) does not intercalate, even at micromolar ruthenium concentrations. Ru(phen)3(2+) is shown to intercalate weakly (i.e., at micromolar concentrations (K(b) = 8.8 x 10(3) M(-1))). The distinct differences in DNA stretching behavior between Ru(phen)3(2+) and Ru(bpy)3(2+) clearly illustrate that intercalation can be distinguished from groove binding by pulling the DNA with optical tweezers. Our results demonstrate both the benefits and challenges of two single-molecule methods of exploring DNA binding and help to elucidate the mode of binding of Ru(phen)3(2+).     

DNA intercalating studies of [Ru(bpy)<Subscript>2</Subscript>HPIP]<Superscript>2+</Superscript> with intramolecular hydrogen bond ligand based on introduction of copper ion

The effects of copper ion on the interaction of [Ru(bpy)₂HPIP]²⁺(bpy = 2,2′-bipyridine, HPIP = 2-(2-hydroxyphenyl) imidazo [4,5-f] [1, 10] phenanthroline) with DNA have been investigated by electronic absorption spectroscopy and fluorescence spectroscopy. HPIP ligand of the complex with an intramolecular hydrogen bond can bind Cu²⁺ in the absence of DNA, as revealed by the absorbance and fluorescence decrease for [Ru(bpy)₂HPIP]²⁺. The resultant heterometallic complex binds to DNA via intercalation of HPIP into the DNA base pairs and its DNA-binding ability is stronger than [Ru(bpy)₂HPIP]²⁺ itself. The DNA bound [Ru(bpy)₂HPIP]²⁺ cannot bind Cu²⁺ at low Cu²⁺ concentration and the intramolecular hydrogen bond in HPIP is located inside the DNA helix. While the Cu²⁺ concentration is relative high, Cu²⁺ can quench the fluorescence of DNA bound [Ru(bpy)₂HPIP]²⁺. The quenching reason is proposed.     

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.     

Kinetics and mechanism of oxidation of excited state Tris-(2,2′-bipyridyl)-ruthenium (II) complex by peroxomonosulfate,peroxodisulfate, and peroxodiphosphate

Excitation of Ru(bipy)₃²⁺ ion by visible radiation of wavelength λ = 436 nm in aqueous medium in presence of inorganic peroxides, peroxomonosulfate (PMS), peroxodisulfate (PDS), and peroxodiphosphate (PDP) was found to generate Ru(bipy)₃³⁺. The kinetics of this photochemical oxidation of Ru(bipy)₃²⁺ by each peroxide was followed spectrophotometrically and found to obey a total second-order, first-order each in [Ru(bipy)₃²⁺] and [peroxide]. In the absence of light, thermal reaction of PMS and PDS with Ru(bipy)₃²⁺ occurred but only when at 1.0 M [H⁺] and > 10^?2M [peroxide]. The reaction of PMS with the complex is found to be cyclic, ie., Ru(bipy)₃³⁺ formed oxidizes PMS itself and such a reaction was not observed in the case of PDS and PDP. The effects of pH, [peroxide], and [Ru(bipy)₃²⁺] on the visible light induced oxidation of Ru(bipy)₃²⁺ by these peroxides are investigated. The results are discussed with suitable reaction mechanisms.     

Ru(Ⅲ)、Rh(Ⅲ)、Pd(Ⅱ)离子与ct-DNA的相互作用研究

本文以中药小檗碱作为分子探针，在0.01mol·L^-1醋酸-醋酸钠缓冲体系中，用紫外-可见吸收及荧光光谱法研究了Ru(Ⅲ)、Rh(Ⅲ)、Pd(Ⅱ)三种贵金属离子与DNA的键合相互作用。实验发现Ru(Ⅲ)离子对小檗碱-DNA二元体系的荧光有较强的猝灭作用;而Rh(Ⅲ)、Pd(Ⅱ)两种离子则对该二元体系产生显著的荧光敏化作用。考察了EDTA对贵金属离子、小檗碱及DNA三元混合体系的荧光光谱的影响，初步探讨了贵金属离子与DNA可能的键合机理。     

A Novel Method to Determine DNA by Use of Molecular “Light Switch” of Ru(phen)2(dppz)

A novel fluorimetric method was developed for selective determination of DNA with the molecular “light switch” complex of Ru(phen)₂(dppz)²⁺. The maximum fluorescence intensity was produced in the pH range 9.3–11.5, with the maximum excitation and emission wavelength of 453.0 and 598.0 nm, respectively. Under the optimum conditions, the fluorescence intensity was in proportion to the concentration of DNA. The linear range for calfthymus DNA, salmon sperm DNA, and herring sperm DNA are 0–0.9 μg/mL. The limits of detection for calfthymus DNA, salmon sperm DNA, and herring sperm DNA are 2.0, 1.8, and 5.4 ng/mL, separately. When the proposed method was used to determine DNA in the presence of some coexisting substances, a satisfactory result was obtained.     

Rolling cycle amplification based single-color quantum dots–ruthenium complex assembling dyads for homogeneous and highly selective detection of DNA

In this work, a new, label-free, homogeneous, highly sensitive, and selective fluorescent biosensor for DNA detection is developed by using rolling-circle amplification (RCA) based single-color quantum dots–ruthenium complex (QDs–Ru) assembling dyads. This strategy includes three steps: (1) the target DNA initiates RCA reaction and generates linear RCA products; (2) the complementary DNA hybridizes with the RCA products to form long double-strand DNA (dsDNA); (3) [Ru(phen)₂(dppx)]²⁺ (dppx = 7,8-dimethyldipyrido [3,2-a:2′,3′-c] phenanthroline) intercalates into the long dsDNA with strong fluorescence emission. Due to its strong binding propensity with the long dsDNA, [Ru(phen)₂(dppx)]²⁺ is removed from the surface of the QDs, resulting in restoring the fluorescence of the QDs, which has been quenched by [Ru(phen)₂(dppx)]²⁺ through a photoinduced electron transfer process and is overlaid with the fluorescence of dsDNA bonded Ru(II) polypyridyl complex (Ru-dsDNA). Thus, high fluorescence intensity is observed, and is related to the concentration of target. This sensor exhibits not only high sensitivity for hepatitis B virus (HBV) ssDNA with a low detection limit (0.5 pM), but also excellent selectivity in the complex matrix. Moreover, this strategy applies QDs–Ru assembling dyads to the detection of single-strand DNA (ssDNA) without any functionalization and separation techniques.     

DNA interaction of platinum(II) complexes with 1,10-phenanthroline and extended phenanthrolines

The interaction with DNA of the platinum(II) square planar complexes [Pt(N-N)(py)(2)](2+) (N-N = 1,10-phenanthroline (phen), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), dipyrido[3,2-a:2',3'-c]phenazine (dppz), benzodipyrido[b:3,2-h:2'3'-f]phenazine (bdppz)) has been investigated by means of absorption, circular and linear dichroism spectroscopy, DNA melting, and viscosity. In the presence of excess [DNA] all the complexes intercalate to the double helix. For those with the most extended phenanthrolines the binding mode depends on the [DNA]/[complex] ratio (q); at low q values the substances bind externally to DNA probably self-aggregating along the double helix. When the DNA concentration is large enough, the aggregate breaks up and the complex intercalates within the nucleobases. The complexes self-aggregate, without added DNA, in the presence of a large salt concentration.     

Meta-linked poly(phenylene ethynylene) conjugated polyelectrolyte featuring a chiral side group: helical folding and guest binding

A water soluble, meta-linked poly(phenylene ethynylene) featuring chiral and optically active side groups based on L-alanine (mPPE-Ala) has been studied by using absorption, fluorescence, and circular dichroism spectroscopy. Studies of mPPE-Ala in methanol/water solvent mixtures show that the polymer folds into a helical conformation, and the extent of helical folding increases with the volume % water in the solvent. The presence of the helical conformation is signaled by the appearance of a broad, excimer-like visible fluorescence band, combined with a strong bisignate circular dichroism signal in the region of the pi,pi absorption of the polymer backbone. The circular dichroism signal exhibits negative chirality, suggesting that the left-handed (M-form) of the helix is in enantiomeric excess. Binding of the metallointercalator [Ru(bpy)2(dppz)]2+ (where bpy = 2,2-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) with the helical polymer is accompanied by the appearance of the orange-red photoluminescence from the metal complex. This effect is directly analogous to that observed when [Ru(bpy)2(dppz)]2+ binds to DNA via intercalation, suggesting that the metal complex binds to mPPE-Ala by intercalating between the pi-stacked phenylene ethynylene residues. Cationic cyanine dyes also bind to the periphery of the helical polymer in a manner that is interpreted as "groove binding". A circular dichroism signal is observed that is believed to arise from exciton coupling within the chiral cyanine dye chromophore aggregate that is formed as the dye molecules are oriented by the helical mPPE-Ala "template".     

Single-mismatch detection using nucleic acid molecular 'light switch'

A novel nucleic acid molecular ‘light switch’ method is developed for the sensitive recognition and detection of a single-base mismatched oligonucleotides. The detection limit of oligonucleotide of perfect double stranded and that with single-base, two-base and three-base mismatched are 0.11, 0.17, 0.34 and 1.5 ng ml⁻¹, respectively. It was found that Ru(phen)₂(dppx)²⁺ (phen=1,10-phenanthroline, dppx=7,8-dimethyl-dipyridophenazine) can be used to detect and recognize the perfect double stranded oligonucleotides from mismatched and random targets by the intensity of fluorescence and temperature. This method can be used to recognize and quantitatively detect target DNA with specific sequence. The advantage of this method is that no requisites are needed to separate the coexisting random targets in the case of a mixed solution containing perfect, mismatched and random targets, which make the recognition analysis of oligonucleotide simple and fast. Moreover, it has potential in the study of dynamic process of DNA hybridization.     

From model compounds to protein binding: syntheses, characterizations and fluorescence studies of [RuII(bipy)(terpy)L]2+ complexes (bipy = 2,2'-bipyridine; terpy = 2,2':6',2''-terpyridine; L = imidazole, pyrazole and derivatives, cytochrome c)

Compounds [RuII(bipy)(terpy)L](PF6)2 with bipy = 2,2'-bipyridine, terpy = 2,2':6',2"-terpyridine, L = H2O, imidazole (imi), 4-methylimidazole, 2-methylimidazole, benzimidazole, 4,5-diphenylimidazole, indazole, pyrazole, 3-methylpyrazole have been synthesized and characterized by 1H NMR, ESI-MS and UV/Vis (in CH3CN and H2O). For L = H2O, imidazole, 4,5-diphenylimidazole and indazole the X-ray structures of the complexes have been determined with the crystal packing featuring only few intermolecular C-H...pi or pi-pi interactions due to the separating action of the PF6-anions. Complexes with L = imidazole and 4-methylimidazole exhibit a fluorescence emission with a maximum at 662 and 667 nm, respectively (lambdaexc= 475 nm, solvent CH3CN or H2O). The substitution of the aqua ligand in [Ru(bipy)(terpy)(H2O)]2+ in aqueous solution by imidazole to give [Ru(bipy)(terpy)(imi)]2+ is fastest at a pH of 8.5 (as followed by the increase in emission intensity). Coupling of the [Ru(bipy)(terpy)]2+ fragment to cytochrome c(Yeast iso-1) starting from the Ru-aqua complex was successful at 35 degrees C and pH 7.0 after 5 d under argon in the dark. The [Ru(bipy)(terpy)(cyt c)]-product was characterized by UV/Vis, emission and mass spectrometry. The location where the [Ru(bipy)(terpy)] complex was coupled to the protein was identified as His44 (corresponding to His39 in other numbering schemes) using digestion of the Ru-coupled protein by trypsin and analysis of the tryptic peptides by HPLC-high resolution MS.     

Spectral studies of the binding of lucigenin,a bisacridinium derivative,with double-helix DNA

The non-covalent binding of the cationic reagent lucigenin to DNA has been investigated by spectroscopic methods. Results from absorption, circular dichroism, and fluorescence studies revealed that lucigenin could intercalate into the helix of DNA. Polarization and melting studies provided further evidence of the intercalation binding of lucigenin with DNA. The binding constant was obtained by varying the DNA concentration while keeping the concentration of lucigenin constant. It was of the order of 10(4) mol(-1) L in DNA base pairs. The experiment also showed that electrostatic interaction played a significant role in the intercalation of lucigenin with DNA. It is suggested that lucigenin can be intercalated into the interior of the DNA double helix because it is initially attracted by the anionic DNA. This research offers a new intercalation functional group for DNA-targeted drug design.     

Synthesis, characterization and interaction with DNA of ruthenium(II) mixed-ligand complexes containing pyridino[3,2-f] [1,7]phenanthroline

Summary A series of new complexes [RuL₂(pdphen)]²⁺, where pdphen is the planar ligand pyridino[3,2-f] [1,7]phenanthroline and L = 2,2-bipyridine, phenanthroline, 2,9-dimethylphenanthroline or 5-nitrophenanthroline, were prepared and characterized. The binding of [RuL₂-(pdphen)] ²⁺ to calf thymus DNA was investigated using absorption, fluorescence and circular dichroism (c.d.) spectroscopies. All of the complexes show absorption hypochromicity associated with binding to calf thymus DNA. [Ru(bipy)₂pdphen]²⁺ and [Ru(phen)₂pdphen]²⁺ also show fluorescence intensities and excited state life-time increases. The c.d. spectra of dialyzates from solutions of racemic complexes versus calf thymus DNA indicate enantioselectivity associated with binding to DNA.     

Structural and photophysical properties of adducts of [Ru(bipy)(CN)4]2- with different metal cations: metallochromism and its use in switching photoinduced energy transfer

We show in this paper how the 3MLCT luminescence of [Ru(bipy)(CN)4]2-, which is known to be highly solvent-dependent, may be varied over a much wider range than can be achieved by solvent effects, by interaction of the externally directed cyanide ligands with additional metal cations both in the solid state and in solution. A series of crystallographic studies of [Ru(bipy)(CN)4]2- salts with different metal cations Mn+ (Li+, Na+, K+, mixed Li+/K+, Cs+, and Ba2+) shows how the cyanide/Mn+ interaction varies from the conventional "end-on" with the more Lewis-acidic cations (Li+, Ba2+) to the more unusual "side-on" interaction with the softer metal cations (K+, Cs+). The solid-state luminescence intensity and lifetime of these salts is highly dependent on the nature of the cation, with Cs+ affording the weakest luminescence and Ba2+ the strongest. A series of titrations of the more soluble derivative [Ru(tBu2bipy)(CN)4]2- in MeCN with a range of metal salts showed how the cyanide/Mn+ association results in a substantial blue-shift of the 1MLCT absorptions, and 3MLCT energies, intensities, and lifetimes, with the complex varying from essentially non-luminescent in the absence of metal cation to showing strong (phi = 0.07), long-lived (1.4 micros), and high-energy (583 nm) luminescence in the presence of Ba2+. This modulation of the 3MLCT energy, over a range of about 6000 cm-1 depending on the added cation, could be used to reverse the direction of photoinduced energy transfer in a dyad containing covalently linked [Ru(bipy)3]2+ and [Ru(bipy)(CN)4]2- termini. In the absence of a metal cation, the [Ru(bipy)(CN)4]2- terminus has the lower 3MLCT energy and thereby quenches the [Ru(bipy)3]2+-based luminescence; in the presence of Ba2+ ions, the 3MLCT energy of the [Ru(bipy)(CN)4]2- terminus is raised above that of the [Ru(bipy)3]2+ terminus, resulting in energy transfer to and sensitized emission from the latter.     

DNA interactions of ruthenium(II) complexes with a polypyridyl ligand: 2-(2, 5-dimethoxyphenyl)-1<Emphasis Type="Italic">H</Emphasis>-imidazo[4,5-<Emphasis Type="Italic">f</Emphasis>]1,10-phenanthroline

This article describes the synthesis of a polypyridyl ligand, namely 2-(2, 5-dimethoxyphenyl)-1H-imidazo[4,5-f]1,10-phenanthroline (DMPIP) and its Ru(II) complexes, namely [Ru(bipy)₂DMPIP]²⁺ (1), [Ru(dmb)₂DMPIP]²⁺ (2) and [Ru(phen)₂DMPIP]²⁺ (3) ((bipy = 2,2′-bipyridine, dmb = 4,4′-dimethyl-2,2′-bipyridine, phen = 1,10-phenanthroline). The complexes were characterized by elemental analysis, plus IR, ¹H-NMR and ¹³C [¹H]-NMR spectra. The interactions of the complexes with calf thymus DNA were investigated. The results indicate that the three complexes can intercalate into DNA. Under irradiation at 365 nm, all three complexes promote the photocleavage of plasmid pBR 322 DNA. Inhibitor studies suggest that singlet oxygen plays a significant role in the cleavage mechanism for the complexes.     

Role of electronic structure on DNA light-switch behavior of Ru(II) intercalators

A series of ruthenium(II) complexes possessing ligands with an extended pi system were synthesized and characterized. The complexes are derived from [Ru(bpy)3](2+) (1, bpy = 2,2'-bipyridine) and include [Ru(bpy)2(tpphz)](2+) (2, tpphz = tetrapyrido[3,2-a:2',3'-c:3',2'-h:2',3'-j]phenazine), [Ru(bpy)2(dppx)](2+) (3, dppx = 7,8-dimethyldipyrido[3,2-a:2',3'-c]phenazine), [Ru(bpy)2(dppm2)](2+) (4, dppm2 = 6-methyldipyrido[3,2-a:2',3'-c]phenazine), and [Ru(bpy)2(dppp2)](2+) (5, dppp2 = pyrido[2',3':5,6]pyrazino[2,3-f][1,10]phenanthroline). The excited-state properties of these complexes, including their DNA "light-switch" behavior, were compared to those of [Ru(bpy)2(dppz)](2+) (6, dppz = dipyrido[3,2-a:2',3'-c]phenazine). Whereas 2, 3, and 4 can be classified as DNA light-switch complexes, 5 exhibits negligible luminescence enhancement in the presence of DNA. Because relative viscosity experiments show that 2-6 bind to DNA by intercalation, their electronic absorption and emission spectra, electrochemistry, and temperature dependence of the luminescence were used to explain the observed differences. The small energy gap between the lowest-lying dark excited state and the bright state in 2-4 and 6 is related to the ability of these complexes to exhibit DNA light-switch behavior, whereas the large energy gap in 5 precludes the emission enhancement in the presence of DNA. The effect of the energy gap among low-lying states on the photophysical properties of 1-6 is discussed. In addition, DFT and TD-DFT calculations support the conclusions from the experiments.