Effect of DNA and bivalent metal ions on the interaction of thermostable DNA polymerase <Emphasis Type="Italic">Tte</Emphasis> with dNTPs

The interaction of DNA polymerase Tte from Thermus thermophilus B35 with dUTP analog containing a fluorescein residue bound to C(5) of the base (Flu-dUTP) was studied by fluorescence titration. The dissociation constants of the enzyme—substrate complexes in the absence and in the presence of a DNA duplex containing an extended template and bivalent metal ions and the kinetic parameters of polymerization by DNA polymerase Tte in the presence of Flu-dUTP were determined. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1268–1272, May, 2005.     

Study of non-covalent interactions of luotonin A derivatives and the DNA minor groove as a first step in the study of their analytical potential as DNA probes

The interaction between DNA and several newly synthesized derivatives of the natural anticancer compound luotonin A has been studied. The results from our work reveal an effective and selective alkaloid/double-stranded DNA (ds-DNA) interaction. In the presence of increasing amounts of ds-DNA, a noticeable fluorescence quenching of the luotonin A derivatives under study was observed. However, this effect did not take place when single-stranded DNA (ss-DNA) was employed. The association constant alkaloids/ds-DNA was calculated by quantitation of such a quenching effect. The influence of other quenchers, namely Co²⁺ and Br⁻ on the native fluorescence of luotonin A and derivatives was also studied, and a remarkable quenching effect was observed for both ions. We have also investigated how by binding DNA the alkaloids could get protected from the external Co²⁺ and Br⁻ quenchers. The Stern–Volmer constants (K _SV) for Co²⁺ and Br⁻ quenching effect on the studied alkaloids were considerably reduced (10–50%) after incubation of the compounds in the presence of DNA with regard to the K _SV values in absence of DNA. An increase in the fluorescence anisotropy values of luotonins was also produced only in the presence of ds-DNA but not in the case of ss-DNA. To better characterize the nature of that interaction, viscosimetry assays and ethidium bromide displacement studies were conducted. With regard to DNA reference solutions, the viscosity of solutions containing DNA and luotonin A derivatives was reduced or not significantly increased. It was also observed that the studied compounds were unable to displace the intercalating agent ethidium bromide. All of these results, together with the obtained association constants values (K _ass = 2.2 × 10² – 1.3 × 10³), support that neither covalent nor intercalating interactions luotonin A derivatives/ds-DNA are produced, leading to the conclusion that these alkaloids bind ds-DNA through the minor groove. The specific changes in the fluorescence behavior of luotonin A and derivatives distinguishing between ss-DNA and ds-DNA binding, lead us to propose these compounds as attractive turn-off probes to detect DNA hybridization.     

Structural studies of benzophenanthridine alkaloid free bases by NMR spectroscopy

The free bases of eight quaternary benzo[c]phenanthridine alkaloids (chelerythrine, sanguilutine, chelirubine, chelilutine, sanguirubine, sanguinarine, nitidine and fagaronine) were investigated by ¹H and ¹³C NMR spectroscopy. The pseudobases (the 6‐hydroxy‐5,6‐dihydro derivatives) were found to be the only products of the alkalization of these alkaloids using sodium carbonate in DMSO‐d₆ solution. This observation differs from the measurements of preparative free bases in CDCl₃ solution, where the structures of the bimolecular aminoacetals were unequivocally confirmed. According to the results obtained, in biological systems, in the presence of excess of water and ions, free bases of the investigated alkaloids are assumed to adopt the pseudobase (6‐hydroxy derivative) structure. In contrast, in less polar media (C₆D₆, CDCl₃), the formation of the bimolecular aminoacetal structure is preferred. Copyright © 2001 John Wiley & Sons, Ltd.     

DNA binding and antibacterial properties of ternary lanthanide complexes with salicylic acid and phenanthroline

Twelve ternary lanthanide complexes RE(sal)₃phen (RE³⁺ = La³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺, Dy³⁺, Ho³⁺, Tm³⁺, Yb³⁺, Lu³⁺, sal = salicylic acid, phen = phenanthroline) were prepared. Interactions between the complexes and calf thymus DNA (ct‐DNA) were investigated using UV–visible spectrophotometry, fluorescence quench experiment and viscosity measurement. Hypochromicity and red shift of the absorption spectra of complexes were observed in the presence of DNA. The enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by the addition of lanthanide complexes, which indicated that the lanthanide complexes displaced EB from its binding sites in DNA. Based on the systematic research of the binding constant (K_b) and the fluorescence quenching constant (K_q) of the 12 complexes, we found that the complexes with smaller lanthanide ion radius had stronger binding abilities with DNA. Viscosity measurement showed that the relative viscosity of the DNA solution was enhanced with increasing the amounts of the complexes. All these results suggested that the complexes could bind to DNA and the major binding mode was intercalative binding. Moreover, all these complexes exhibited excellent antibacterial abilities against Escherichia coli. Also, the antibacterial activities of complexes with heavy rare earth were higher than those of complexes with light rare earth. Copyright © 2014 John Wiley & Sons, Ltd.     

Cavity size effect on ICT-dual emission of p-(N,N-dimethylamino)-2-styrylquinoline: complexation with cyclodextrin derivatives

The effect of cyclodextrin inclusion complex formation on the intramolecular charge transfer (ICT) of the included 4-N,N-dimethylamino-2-strylquinoline (2-StQ-NMe₂) has been studied in detail. 2-StQ-NMe₂ in presence of α-, β-, γ- and HP-α- and Hp-β-CDs predominantly exhibits ICT fluorescence predominantly than the emission from locally excited state, whereas in presence of HP-γ-CD the later is observed. In presence of α-CD, 2:1 complexation of the 2-StQ-NMe₂ is observed in addition to 1:1 complexation. The observed results are explained by the CD cavity size and an active role for the secondary hydroxyl groups present in the wider rim of the CD cavity and also which finds support from absorption, emission, lifetime and molecular modeling studies. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users.     

Asymmetric hydrogenation of acetophenone catalyzed by cinchonidine stabilized Ir/SiO2

A series of silica (SiO₂) supported iridium catalysts stabilized by cinchona alkaloids was prepared and applied in the heterogeneous asymmetric hydrogenation of acetophenone. Cinchona alkaloids exhibited a marked ability to stabilize and disperse the Ir particles. In the presence of (1S,2S)-diphenylethylenediamine ((1S,2S)-DPEN)) as chiral modifier, the cinchonidine (CD) stabilized catalyst 5%Ir/2CD-SiO₂ exhibited excellent catalytic performance in the asymmetric hydrogenation of acetophenone in MeOH. Under the optimum conditions, the ee value of (R)-phenylethanol achieved 79.8% and no other product was produced, a higher enantioselectivity than that reported up to now for acetophenone hydrogenation catalyzed by the supported metal catalysts modified by chiral reagents. In particular, a synergistic effect between (1S,2S)-DPEN and CD was observed, which significantly accelerated the reaction rate and enhanced the enantioselectivity. The catalyst can be reused several times without a significant loss of activity and enantioselectivity.     

Binding behaviour and solubilisation of p-sulfonatocalixarenes to cinchona alkaloids

In this study, we investigated the binding behaviours of three water-soluble p-sulfonatocalixarenes with four cinchona alkaloids in aqueous and phosphate buffer solutions (pH 7.2 and 2.0). The complexation stability constants obtained by fluorescence titrations were comparatively discussed from several aspects: host cavity, pH effect and ionic strength. Among three hosts, p-sulfonatocalix[4]arene (SC4A) forms the most stable complexes with cinchona alkaloids, especially in acidic aqueous conditions. Furthermore, SC4A was elected as model drug carrier for cinchona alkaloids, where solubilisation by the complexation of SC4A and mimic release from the calixarene cavity in the presence of negatively charged micelles were initially studied.     

Complexation Study and Spectrofluorimetric Determination of Pipemidic Acid with γ-Cyclodextrin

The fluorimetric characteristics of pipemidic acid (PIPE) have been investigated. It has been proven that the fluorescence emission band of pipemidic acid at 439 nm is significantly intensified in the presence of γ-cyclodextrin. The inclusional complexation between the antibacterial pipemidic acid and γ-cyclodextrin (γ-CD) has been studied. A 1:1 stoichiometry of the complex was established and its association constant was calculated by a nonlinear regression method, monitoring the changes in the fluorescence signal of pipemidic acid in the presence of γ-CD. According to the results obtained, a spectrofluorimetric method for the determination of PIPE has been proposed. The best limits of detection and quantification were obtained in presence of γ-CD, in acidic media. The dynamic range of the method was comprised between 0.18 and 1.40 μg/ml.     

Tetrahydrofuran Activates Fluorescence Resonant Energy Transfer from a Cationic Conjugated Polyelectrolyte to Fluorescein‐Labeled DNA in Aqueous Media

A cationic water‐soluble conjugated polyelectrolyte, poly[9,9‐bis(6′′‐(N,N,N‐trimethylammonium)hexyl)fluorene‐co‐alt‐2,5‐bis(6′‐(N,N,N‐trimethylammonium)hexyloxyphenylene) tetrabromide], was synthesized. Fluorescence resonant energy transfer (FRET) experiments between the polymer and fluorescein‐labeled single‐stranded DNA (ssDNA‐Fl) were conducted in aqueous buffer and THF/buffer mixtures. Weak fluorescence emission in aqueous buffer was observed upon excitation of the polymer, whereas addition of THF turned on the fluorescence. Fluorescence self‐quenching of ssDNA‐Fl in the ssDNA‐Fl/polymer complexes as well as electron transfer from the polymer to fluorescein may account for the low fluorescence emission in buffer. The improved sensitization of fluorescence by the polymer observed in THF/buffer could be attributed to the weaker binding between the polymer and ssDNA‐Fl and a decrease in dielectric constant of the solvent mixture, which disfavors electron transfer. THF‐assisted signal sensitization was also observed for the polymer and fluorescein‐labeled double‐stranded DNA (dsDNA‐Fl). These results indicate that the use of cosolvent provides a strategy to improve the detection sensitivity for biosensors based on the optical amplification provided by conjugated polymers.     

健那绿B的荧光猝灭研究及作为核酸测定探针的应用

用紫外可见光谱、稳态荧光发射及荧光寿命测定研究了核酸猝灭十二烷基磺酸钠胶束中的健那绿荧光。水溶液中弱的健那绿荧光在十二烷基磺酸钠胶束中被大大加强，其最大发射从425纳米移至410纳米，核酸的加入将猝灭健那绿的荧光，当健那绿浓度为2.5×10^–5 mol•L^-1时，荧光猝灭(F₀/F)分别与小牛胸腺DNA及鱼精DNA在2.4×10^–8 到 1.08×10^–7及 1.9×10^–8 到 3.8×10^–8 mol•L^-1范围内成正比, 检测限分别为1.3×10^–8 mol•L^-1 (小牛胸腺DNA)及6.3×10^–9 mol•L^-1 (鱼精DNA)。当DNA浓度较高时, 将系统偏离Stern-Volmer方程。这是因为动态猝灭和静态猝灭同时存在。方法已应用于鸡血提取液中DNA的测定, 测定结果与紫外法一致。     

Fluorescence Quenching Study on the Interaction of Some Schiff Base Complexes with Bovine Serum Albumin

The interaction of Schiff base ligand A and its three metal complexes [A‐Fe(II), A‐Cu(II), and A‐Zn(II)] with bovine serum albumin (BSA) was investigated using a tryptophan fluorescence quenching method. The Schiff base ligand A and its three metal complexes all showed quenching of BSA fluorescence in a Tris‐HCl buffer. Quenching constants were determined for quenching BSA by the Schiff base ligand A and its metal complexes in a Tris‐HCl buffer (pH=7.4) at different temperatures. The experimental results show that the dynamic quenching constant (K_SV) was increased with increasing temperature, whereas the association constant (K) was decreased with the increase of temperature. The thermodynamic parameters ΔH, ΔG and ΔS at different temperatures were calculated. The ionic strength of the Tris‐HCl buffer had a great influence on the wavelength of maximum emission of BSA. Under low ionic strength, the emission spectra of BSA influenced by A‐Zn(II) had a small blue shift. Compared to A‐Zn(II), the emission spectra of BSA in the presence of the Schiff base ligand A and A‐Cu(II) had no significant λ_em shift. At high ionic strength, the emission spectra of BSA upon addition of the Schiff base A, A‐Fe(II), and A‐Zn(II) all had a red shift, but the emission spectra of BSA had λ_em shift neither at low ionic strength, nor at high ionic strength in the presence of A‐Cu(II). Furthermore, the temperature did not affect the λ_em shift of BSA emission spectra.     

Investigations on the Synthesis,Reactivity, and Properties of Perfluoro-α-Benzo-Fused BOPHY Fluorophores

The synthesis and reactivity of 3,8-dibromo-dodecafluoro-benzo-fused BOPHY 2 are reported, via S_NAr with O-, N- S- and C-nucleophiles, and in Pd(0)-catalyzed cross-coupling reactions (Suzuki and Stille). The resulting perfluoro-BOPHY derivatives were investigated for their reactivity in the presence of various nucleophiles. BOPHY 3 displays reversible color change and fluorescence quenching in the presence of bases (Et₃N, DBU), whereas BOPHY 7 reacts preferentially at the α-pyrrolic positions, and BOPHY 8 undergoes regioselective fluorine substitution in the presence of thiols. The structural and electronic features of the fluorinated BOPHYs were studied by TD-DFT computations. In addition, their spectroscopic and cellular properties were investigated; BOPHY 10 shows the most red-shifted absorption/emission (λ_max 659/699 nm) and 7 the highest fluorescence (Φ_f=0.95), while all compounds studied showed low cytotoxicity toward human HEp2 cells and were efficiently internalized.     

微量热法比较黄连中四种生物碱的抗菌作用

采用微量热法研究和比较中药黄连中四种生物碱(BAs)的抗菌(大肠杆菌)作用。这四种生物碱分别为小檗碱、黄连碱、巴马汀和药根碱。用LKB-2277生物活性检测系统,以停留法测定了37 ℃时大肠杆菌在BAs作用下的热流功率-时间曲线,并记录生长速率常数k, 指数生长期和稳定期的最大热功率Pm, log、Pm, stat, 生长抑制率I, 传代时间tg,指数生长期的总产热量Qt, log,半数抑菌浓度IC50等热动力学参数。结果显示这四种生物碱具有相异的抗大肠杆菌生长代谢的作用,k, Pm, log和Qt, log值随BAs浓度的增加而相应的减少。综合分析k, Pm, log, Qt, log, I 和IC50值可以看出,BAs抑制大肠杆菌生长代谢强度按小檗碱、黄连碱、巴马汀、药根碱的顺序依次减弱。构效关系研究表明,母环C-2和C-3上连接的亚甲二氧基比甲氧基更能显著增强相应化合物的抗菌作用,而C-9和C-10上连接的亚甲二氧基或甲氧基对这种抗菌作用影响不大。     

Studies on Intramolecular Charge Transfer Fluorescence Probe and DNA Binding Characteristics

An intramolecular charge transfer fluorescence probe of 4′-N,N-dimethylamino-4-amino-chalcone(DMAC) exhibits characteristics clearly correlated with the polarity of solvents. The interaction of this fluorescence probe with calf thymus DNA has been investigated. Generally, DMAC bound to DNA shows marked changes in fluorescence and absorbance properties compared to the spectral characteristics of the free form in solution phase. In the presence of DNA the fluorescence intensity of DMAC is greatly increased with a large bathochromic shift of excitation and emission wavelengths. A hypochromism in absorption spectrum was also observed. The absorption and fluorescence spectra, salt concentration effect, and KI quenching experiments demonstrate that DMAC molecule as an intercalator is inserted into the base-stacking domain of DNA double helix, and the interaction of the nucleobases with DMAC molecule causes the increase of fluorescence intensity and hypochromism in absorption spectrum. The intrinsic binding constant and the binding site number were estimated to be 7.04 × 10⁶ mol L⁻¹ in base pairs and 0.065, respectively. The I/I₀ vs DNA concentration plot shows a linear range covering 1.98 × 10⁻⁶ to 2.08 × 10⁻⁴ mol L⁻¹ in base pairs which can be used for determining DNA with a detection limit of 6.0 × 10⁻⁷ mol L⁻¹ in base pairs (0.6 μg ml⁻¹).     

Synthesis and Fluorescence Properties of α,α′-Bis(substituted-benzylidene)cycloalkanones Catalyzed by 1-Methyl-3(2-(sulfooxy)ethyl)-1H-imidazol-3-ium Chloride

α,α′-Bis(substituted-benzylidene)cycloalkanones were synthesized via a solvent-free cross-aldol condensation of aromatic aldehydes with cycloalkanones in the presence of a catalytic amount 1-methyl-3(2-(sulfooxy)ethyl)-1H-imidazol-3-ium chloride at room temperature with excellent yields. The screening for optical properties indicated that the size of cycloalkanone has an influence on the fluorescence emission of products. Products coming from cyclohexanone have stronger fluorescence emission than those from cyclopentanone.     

Phytochemical screening,total phenolic content and phytotoxic activity of corn (Zea mays) extracts against some indicator species

Allelopathic effects of corn (Zea mays) extracts was studied, against seed germination and seedling growth of Phalaris minor, Helianthus annuus, Triticumaestivum, Sorghum halepense, Z. mays. Bioassay results showed that aqueous extracts of corn root and shoot, markedly affected seed germination, and other parameters compared with related controls. Preliminary phytochemical screening revealed the presence of various phytochemicals such as tannins, phlobatannins, flavonoids, terpenoids and alkaloids in both roots and shoot aqueous extracts. However, saponins were only present in the shoot aqueous extract, while in shoot ethanol extracts, only terpenoids and alkaloids were detected. Additionally, total polyphenolic (TPC) content in aqueous extracts of corn root and shoot, plus ethanol extracts of corn shoot were determined using an Ultraviolet–visible spectroscopy. Results revealed TPC content of the corn shoot aqueous extract showed the highest yield, compared to other extracts. These findings suggest that phytochemicals present in Z. mays extracts may contribute to allelopathy effect.     

Ultrafast excited-state dynamics of RNA and DNA C tracts

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)₁₈ were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5′-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)₁₈ at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of 100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.     

Blue-luminescent poly(p-phenylenevinylene) derivatives: Synthesis and effect of side-group size on the optical properties

New conjugated polymers based on separated PPV-type chromophores and incorporating different types of solubilizing side-groups (ethoxy: P1, hexyloxy: P2, dodecyloxy: P3 and benzyloxy: P4) were synthesized via Wittig polycondensation, using a series of bisphenol A-derived di(triphenylphosphonium) salts as starting monomers. The polymers are soluble in common organic solvents and their structures were confirmed by ¹H NMR, ¹³C NMR and FTIR spectroscopies. The optical properties of these materials were investigated by UV–vis absorption and fluorescence spectroscopies. In dilute solution, quasi-identical fluorescence spectra were obtained and all the polymers showed a blue emission (420, 445 nm) and a narrow spectrum. In thin solid films, the polymers show side-group-dependent optical behavior and, whereas the emission remains blue in the case of P2, P3 and P4, a green fluorescence was observed for the ethoxylated polymer P1. From cyclic voltammetry analysis, the electrochemical band gaps were estimated to be 2.99, 3.07, 3.15 and 3.06 eV for P1, P2, P3 and P4, respectively. Single-layer diode devices of the [indium tin oxide/polymer/aluminum] configuration have been fabricated and show relatively low turn-on voltages between 2.6 and 4.9 V.     

Study of cis-trans equilibrium of oxacarbocyanine dyes in solution and in a complex with DNA

Cis-trans equilibrium for a number of meso-substituted oxacarbocyanine dyes, 3,3′-diethyloxacarbocyanine iodide (K1), 3,3′-diethyl-9-methyloxacarbocyanine iodide (K2), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K3), 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K4), and 3,3′,9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), has been studied in solutions and in a complex with DNA by spectral and fluorescent methods. A shift of the cis-trans isomer equilibrium toward the formation of the trans-isomer was observed in the presence of DNA, which determined in many respects the spectral effects observed upon the complexation of the oxacarbocyanine dyes. A steep rise of fluorescence (due to binding of the trans-isomer) in a complex with DNA is favorable for using oxacarbocyanine dyes to determine DNA.     

Unfolding of Bovine Heart Cytochrome c Induced by Urea and Guanidine Hydrochloride

The unfolding of bovine heart cytochrome c induced by urea and guanidine hydrochloride was studied through their intrinsic fluorescence emission spectra, fluorescence phase diagrams, fluorescence quenching, size‐exclusion chromatographies, native polyacrylamide gel electrophoreses and deactivation profiles. The results showed that during their unfolding in urea and guanidine hydrochloride solutions, bovine heart cytochrome c molecules existed only in a unimolecular form and their bi‐molecular and/or poly‐molecular aggregates and aggregate precipitates were not formed all along. When the urea and guanidine hydrochloride concentrations in denaturation solution were separately about 6.0 and 3.0 mol/L, they could be completely deactivated and almost all of the tryptophan residues originally embedded in the interior of their molecules were exposed to the surface of their molecules. Different from the unfolding of the most often used horse heart cytochrome c, that of bovine heart cytochrome c induced by urea and guanidine hydrochloride was separately a completely co‐operative procedure and followed a two‐state model.