Spectral properties and G-quadruplex DNA binding selectivities of a series of unsymmetrical perylene diimides

A series of new unsymmetrical perylene diimides have been synthesized to investigate their binding selectivities to G-quadruplex DNA structure, a unique four-stranded DNA motif, which is significant to the regulation of telomerase activity. The structures of the perylene diimides have been characterized by IR spectrophotometer, ¹H NMR, ¹³C NMR, MS, TGA and time-resolved instruments. Spectrochemical behaviors have been investigated by visible absorption and fluorescence emission spectra. The spectral characterization of the compounds has been investigated in five common organic solvents of different polarity and in water (in 170 mM phosphate buffer at pH 6). Marked red shifts of absorbance and fluorescence emission bands of the compounds in aqueous solution are compared with the other organic solutions. The fluorescence quantum yields are determined low in more polar solvents and also calculated to be about less than about 0.05 in aqueous solution because of the aggregation effects. Photodegradation rate constants (k_p) of the synthesized compounds have been compared under xenon lamp irradiation in acetonitrile solution.Binding abilities of the synthesized perylene diimides to different form of DNA strands have been investigated by visible absorption and fluorescence spectroscopy in the phosphate buffer solutions. Also, pH-dependent aggregation and G-quadruplex DNA binding selectivity of these ligands have been compared. Among these ligands, N-(2,6-diisopropylphenyl)-N′-(4-pyridyl)-perylene-3,4,9,10-tetracarboxylic diimide (PYPER) has been found to be the most selective interactive ligand for G-quadruplex formed in the G4′-DNA structure. PYPER has shown a significant selectivity to G4′-DNA which is comprised of d(TTAGGG) repeats, known as human telomeres, in the phosphate buffer at pH 6. The absorption maximum of the PYPER/G4′-DNA complex has given bathochromic shift of 7 nm with respect to the absorption maximum of DNA-free solution of PYPER in phosphate buffer at pH 6. Fluorescence quenching experiments between PYPER and G4′-DNA show that PYPER demonstrates about a 9.3-fold selectivity for binding to G4′-DNA versus ds-DNA base pairs with the bimolecular rate constant of 0.95 × 10¹² M⁻¹ s⁻¹.     

Evaluation of binding of perylene diimide and benzannulated perylene diimide ligands to dna by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the self-association, G-quadruplex DNA binding, and selectivity of a series of perylene diimides (PDIs) (PIPER, Tel01, Tel11, Tel12, and Tel18) or benzannulated perylene diimide ligands (Tel34 and Tel32). Fluorescence and resonance light scattering spectra of Tel01, Tel12, Tel32, and Tel34 reveal that these analogs undergo self-association in solution. UV-Vis and fluorescence titrations with G-quadruplex, duplex, or single-stranded DNA demonstrate that all the analogs, with the exception of Tel32, bind to G-quadruplex DNA, with those PDIs that are self-associated in solution showing the highest degree of selectivity for binding G-quadruplex DNA. Parallel ESI-MS analysis of the stoichiometries demonstrates the ability of the ligands, with the exception of Tel32, to bind to G-quadruplex DNA. While most ligands show major 1:1 and 2:1 binding stoichiometries as expected in the case of end-stacking, interestingly, three of the most quadruplex-selective ligands show a different behavior. Tel01 forms 3:1 complexes, while Tel12 and Tel32 only form 1:1 complexes. Collisional activation dissociation patterns are compatible with ligand binding to G-quadruplex DNA via stacking on the ends of the terminal G-tetrads. Experiments with duplex and single strand DNA were performed to assess the binding selectivities of the ligands. PIPER, Tel11, and Tel18 demonstrated extensive complexation with duplex DNA, while Tel11 and Tel18 bound to single strand DNA, confirming the lack of selectivity of these two ligands. Our results indicate that Tel01, Tel12, and Tel34 are the most selective for G-quadruplex DNA.     

A novel biomimetic logic gate for sensitive and selective detection of Pb(II) base on porous alumina nanochannels

A novel biomimetic logic gate sensor for Pb^2 + is established using porous alumina membrane nanochannels modified with morpholino and DNA. It is based on electrochemical detection, and the current response from the diffusion flux of Fe(CN)₆^3 − is influenced by the steric blockage and charge repulsion in nanochannels. A limit of detection (0.1 nM) and good linear range (0.1 nM–5 μM) for Pb^2 + analysis are achieved in the tenth cycle. The sensing strategy shows prospective application in drug release, artificial ion channels, DNA logic gates for controlling biomolecule, and ion translocation.     

Study on electrochemical performance of activated carbon in aqueous Li2SO4, Na2SO4 and K2SO4 electrolytes

The electrochemical performances of activated carbon (AC) in 0.5 mol/l Li₂SO₄, Na₂SO₄ and K₂SO₄ aqueous electrolytes were investigated. The cyclic voltammetric results at different scan rates show that the rate behaviors of AC in the three electrolytes improve in the order of Li₂SO₄ < Na₂SO₄ < K₂SO₄. This improvement can be mainly ascribed to the following two reasons: (1) the decreasing equivalent series resistance in the order of Li₂SO₄ > Na₂SO₄ > K₂SO₄, which is the main factor influencing the maximum output power, and (2) the increasing migration speed of hydrated ions in the bulk electrolyte and in the inner pores of AC electrode in the order of Li⁺ < Na⁺ < K⁺. Their cycling behaviors do not show any differences in capacitive fading. The above results provide valuable information to explore new hybrid supercapacitors.     

Multivariate investigation of interaction between porphyrin ligands and human telomeric DNA

G-quadruplexes are formed by association of DNA strands containing multiple contiguous guanines. The capability of drugs to induce formation or stabilize G-quadruplexes is an active area of cancer therapy investigation. We evaluated interaction between two cationic tetrapyridinoporphyrazines with Na⁺ and K⁺ forms of human telomeric G-quadruplex DNA by chemometrics method. An antiparallel quadruplex structure was found to be stabilized more greatly by these two isomers in the presence of K⁺ and Na⁺ ions. Equilibrium model of a ligand binding with DNA oligomer has been considered as a process of small molecule adsorption on to a lattice of multiple binding sites. In multivariate analysis methods, it is accounted this assertion that during saturation of the macromolecule by a ligand should expect effect of cooperativity due to changes in DNA conformation or the mutual influence between bound ligands. Such phenomenon cannot be entirely described by the classical stepwise complex formation model. From the results of absorption and circular dichroism measurements, the unique site for the ligand binding is suggested to be the intercalating in guanine tetrad plane quadruplex. We found a 2:1 binding stoichiometry for both ligands and Tel22.     

Simple and sensitive fluorescence sensor for detection of potassium ion in the presence of high concentration of sodium ion using berberine–G-quadruplex complex as sensing element

In this work, a novel potassium ion (K⁺) sensor is presented using berberine–G-quadruplex complex as a fluorescent probe. This sensor is based on the K⁺that can induce the G-rich DNA to form G-quadruplex conformation. The G-quadruplex can bind berberine to form berberine–G-quadruplex complex, resulting in remarkable enhancement of fluorescence emission of the berberine–G-quadruplex system. In the presence of 800 mM sodium ion (Na⁺), the fluorescence of the berberine–G-quadruplex complex increased linearly with increasing K⁺ concentration in the range of 0.005–1.0 mM. The turn-on fluorescent assay is simple, inexpensive, and highly sensitive. We observed that Na⁺ in 10,000-fold molar excess does not interfere. The molecular mechanisms which produce enhanced fluorescence of berberine were discussed.     

Synthesis,characterization and biological studies of some homodinuclear complexes of zinc with second-generation quinolone drug and neutral bidentate ligands

The novel homodinuclear zinc(II) complexes with the quinolone antibacterial drugs ciprofloxacine and neutral bidentate ligands have been synthesized and characterized by elemental analysis, TG analyses and various spectroscopic techniques. The metal ion exhibits octahedral geometry with two water molecule in the inner sphere cavity environment. The interaction of complexes with DNA was determined using absorption titration, viscosity measurements and electrophoresis technique. The intrinsic binding constants (K_b) of complexes were determined, which were ranging from 1.0 × 10⁴ to 3.5 × 10⁴ per mole. Suggesting that complexes bind more strongly to DNA. Effect on viscosity has also been checked to authenticate the binding of metal complexes with DNA. An antimicrobial activity of all the ligands and metal complexes has been examined by minimum inhibitory concentration method (MIC).     

DNA binding of benzophenanthridine compounds sanguinarine versus ethidium: Comparative binding and thermodynamic profile of intercalation

There is compelling evidence that cellular DNA is the target of many small molecule anticancer agents. Consequently, elucidation of the molecular nature governing the interaction of small molecules to DNA is paramount to the progression of the rational drug design strategies. In this study, we have compared the binding and thermodynamic aspects of two known DNA binding agents, ethidium and sanguinarine with calf thymus DNA. The study revealed non-cooperative binding phenomena for both the drugs to DNA with an affinity similar for ethidium and sanguinarine as observed from different techniques. The binding phenomena analyzed from isothermal titration calorimetry showed exothermic binding for both compounds that was favoured by negative enthalpy and positive entropy changes typical of intercalative binding. The binding of both the drugs was further characterized by strong stabilization of DNA against thermal strand separation in optical melting as well as differential scanning calorimetry studies. The data of the salt dependence of binding of sanguinarine and ethidium from the plot of log K versus log [Na⁺] revealed a slope of ?0.711 and ?0.875, respectively, consistent with the values predicted by the theories for the binding of monovalent cations and the binding free energy has been analyzed for contributions from polyelectrolytic and non-polyelectrolytic forces. The salt dependence of the binding was also evident from the conformational changes in the circular dichroism where both extrinsic and induced changes were lowered on increasing the salt concentration. The heat capacity changes obtained from temperature dependence of enthalpy change gave values of (?590 and ?670) J · mol^?1 · K^?1, respectively for the binding of sanguinarine and ethidium to DNA. Overall the DNA binding of ethidium was slightly more favoured over sanguinarine.     

Conductometric study of some alkali metal halides in (dimethyl sulfoxide + acetonitrile) at T = 298.15 K

Electrolytic conductivities of some alkali metal halides, MX (M⁺ = Li⁺, Na⁺, and K⁺; X^? = Cl^?, Br^?, and I^?), NaBPh₄ and Bu₄NBr have been investigated in (20, 40, and 60) mass% {dimethyl sulfoxide (DMSO) in DMSO + acetonitrile} at T = 298.15 K. The conductance results have been analyzed by the Fuoss-conductance-concentration equation in terms of the limiting molar conductance Λ° the association constant K_A and the association diameter R. The ionic contributions to the limiting molar conductance have been estimated using Bu₄NBPh₄ as the “reference electrolyte”. The association constant K_A tends to increase in the order mass percent 20 < 40 < 60 DMSO in (DMSO + acetonitrile) which is explained by the thermodynamic parameter ΔG° and Walden product Λ°η. The results have been interpreted in terms of ion–solvent interactions and structural changes in the mixed solvents.     

A novel method for Co(Ⅱ) and Cu(Ⅱ) analysis by capillary electrophoresis with chemiluminescence detection

Based on the fact that some metal ions can catalyze the chemiluminescence(CL)reaction of luminol with K_3Fe(CN)_6,a novel capillary electrophoresis CL method was developed for the determination of Co(Ⅱ)and Cu(Ⅱ).The separation was carried out with a 10 mmol/L sodium acetate solution containing 0.8 mmol/L luminol and 2.0 mmol/Lα-HIBA(adjusted to pH 4.8 by HAc solution).The post-capillary reagent was 2.0 mmol/L K_3Fe(CN)_6 which was adjusted to pH 13.0 by NaOH solution.Under the optimum conditions,the detection limits(S/N=3)for Co(Ⅱ)and Cu(Ⅱ)were 7.5×10~(-11)mol/L and 7.5×10~(-9)mol/L,with the linear range of 7.5×10~(-9)mol/L to 1.0×10~(-6)mol/L and 7.5×10~(-8)mol/L to 5.0×10~(-5)mol/L, respectively.     

Needle-like IrO/Ag combined pH microelectrode

In this study, a combined pH microelectrode has been developed consisting of an indicator electrode made of IrO₂ prepared using the polymeric precursor method and deposited in a platinum microwire. This electrode was mounted inside a stainless steel needle, the external surface of which was painted with conductive silver ink which is used as reference electrode. This device was compared with a conventional glass electrode, and the results presented linear behavior in the pH range from 2.0 to 12.5, in Na⁺ and K⁺ solutions, exceeding glass electrodes in the alkaline range. The sensitivity was 56.9 ± 0.2 mV pH^? 1 and using ANOVA test we conclude that the electrode is not sensitive to the presence of alkaline cations such as Li⁺, Na⁺ or K⁺. Finally, the response time (t₉₅) was 4.9 to 9.0 s depending on the solution pH. The combined pH microelectrode can be used several times and, after three years, continues to have a response similar to that of a freshly produced one.     

Thermodynamics of the hydrolysis reactions of adenosine 3′,5′-(cyclic)phosphate(aq) and phosphoenolpyruvate(aq); the standard molar formation properties of 3′,5′-(cyclic)phosphate(aq) and phosphoenolpyruvate(aq)

Molar calorimetric enthalpy changes Δ_rH_m(cal) have been measured for the biochemical reactions {cAMP(aq) + H₂O(l)=AMP(aq)} and {PEP(aq) + H₂O(l)=pyruvate(aq) + phosphate(aq)}. The reactions were catalyzed, respectively, by phosphodiesterase 3^′,5^′-cyclic nucleotide and by alkaline phosphatase. The results were analyzed by using a chemical equilibrium model to obtain values of standard molar enthalpies of reaction Δ_rH_m^∘ for the respective reference reactions {cAMP⁻(aq) + H₂O(l)=HAMP⁻(aq)} and {PEP³⁻(aq) + H₂O(l)=pyruvate⁻(aq) + HPO²⁻₄(aq)}. Literature values of the apparent equilibrium constants K^′ for the reactions {ATP(aq)=cAMP(aq) + pyrophosphate(aq)}, {ATP(aq) + pyruvate(aq)=ADP(aq) + PEP(aq)}, and {ATP(aq) + pyruvate(aq) + phosphate(aq)=AMP(aq) + PEP(aq) + pyrophosphate(aq)} were also analyzed by using the chemical equilibrium model. These calculations yielded values of the equilibrium constants K and standard molar Gibbs free energy changes Δ_rG_m^∘ for ionic reference reactions that correspond to the overall biochemical reactions. Combination of the standard molar reaction property values (K, Δ_rH_m^∘, and Δ_rG_m^∘) with the standard molar formation properties of the AMP, ADP, ATP, pyrophosphate, and pyruvate species led to values of the standard molar enthalpy Δ_fH_m^∘ and Gibbs free energy of formation Δ_fG_m^∘ and the standard partial molar entropy S_m^∘ of the cAMP and PEP species. The thermochemical network appears to be reasonably well reinforced and thus lends some confidence to the accuracy of the calculated property values of the variety of species involved in the several reactions considered herein.     

Impact of the alkali cation on the electrocatalytic oxidation of urea and benzyl alcohol on nickel electrode

The effect of electrolyte alkali metal cations (Li⁺, Na⁺, or K⁺) on the electro-oxidation of urea and benzyl alcohol on NiOOH catalyst has been investigated by means of cyclic voltammetry and chronoamperometry in the presence of an electrolyte containing LiOH, NaOH, or KOH. The catalytic activity toward the electro-oxidation of urea and benzyl alcohol was found to increase in the sequence Li⁺ < Na⁺ < K⁺. This activity's difference is partly caused by different surface blockage abilities by OH–M⁺(H₂O)_x (M: Li, Na, K) clusters, which is similar to many electrocatalytic reactions on Pt reported previously, additionally, incorporation of various cations to the catalyst may induce the activities difference as well.     

Direct electrochemistry of myoglobin based on DNA accumulation on carbon ionic liquid electrode

Poly-anionic deoxyribonucleic acid (DNA) was accumulated on the positively charged surface of carbon ionic liquid electrode (CILE) with N-butylpyridinium hexafluorophosphate (BPPF₆) as binder, and then myoglobin (Mb) was immobilized onto the DNA film by electrostatic interaction to form Mb/DNA/CILE electrode. The direct electrochemistry of Mb was then investigated in detail. A pair of well-defined, quasi-reversible cyclic voltammetric peaks of Mb was obtained with the formal potentials (E⁰′) at ?0.304 V (vs. SCE) in phosphate buffer solution (PBS, pH 7.0). The Mb/DNA/CILE electrode showed excellent electrocatalytic activity to H₂O₂ and trichloroacetic acid (TCA) in the range of 1.0–160 μmol/L and 0.5–40.0 mmol/L, respectively. The apparent Michaelis–Menten constants (K_M) toward H₂O₂ and TCA were calculated as 0.42 and 0.82 mmol/L. So, the DNA/CILE had potential to study other proteins.     

Voltammetric study on the mechanism of ion transfer caused by weak acids in the bilayer lipid membrane

The mechanism has been investigated by cyclic voltammetry for the ion transfer from one aqueous phase (W1) to another (W2) across a bilayer lipid membrane (BLM) in the presence of a typical uncoupler, carbonylcyanide p-trifluoromethoxyphenylhydrazone (FCCP). Voltammograms for the ion transfer were in steady-state and showed rotated sigmoidal and symmetrical shape about the origin (0 V, 0 A). The magnitude of the ion transfer current at a given applied potential increased linearly with the concentration of FCCP in W2 up to 10⁻⁶ M and then became saturated. The ion transfer current also showed a bell-type dependence on pH centered around pH ≅ pK_a + 1, K_a being the dissociation constant of FCCP in aqueous phase. These properties have been well explained by our proposed model that the ion transfer current is attributable to the transfers of H⁺ and Na⁺ distributed in BLM. The hydrophilic counter ions, H⁺ and Na⁺, compensate the negative charge of the dissociated FCCP in BLM. The current intensity is predominantly governed by the concentration and the ion mobility of the counter cations.     

Thermodynamics of the oxidation–reduction reaction {2 glutathionered(aq) + NADPox(aq)=glutathioneox(aq) + NADPred(aq)}

Microcalorimetry, spectrophotometry, and high-performance liquid chromatography (h.p.l.c.) have been used to conduct a thermodynamic investigation of the glutathione reductase catalyzed reaction {2 glutathione_red(aq) + NADP_ox(aq)=glutathione_ox(aq) + NADP_red(aq)}. The reaction involves the breaking of a disulfide bond and is of particular importance because of the role glutathione_red plays in the repair of enzymes. The measured values of the apparent equilibrium constant K^′ for this reaction ranged from 0.5 to 69 and were measured over a range of temperature (288.15 K to 303.15 K), pH (6.58 to 8.68), and ionic strength I_m (0.091 mol · kg⁻¹ to 0.90 mol · kg⁻¹). The results of the equilibrium and calorimetric measurements were analyzed in terms of a chemical equilibrium model that accounts for the multiplicity of ionic states of the reactants and products. These calculations led to values of thermodynamic quantities at T=298.15 K and I_m=0 for a chemical reference reaction that involves specific ionic forms. Thus, for the reaction {2 glutathione_red⁻(aq) + NADP_ox³⁻(aq)=glutathione_ox²⁻(aq) + NADP_red⁴⁻(aq) + H⁺(aq)}, the equilibrium constant K=(6.5±4.4)·10⁻¹¹, the standard molar enthalpy of reaction Δ_rH^o_m=(6.9±3.0) kJ · mol⁻¹, the standard molar Gibbs free energy change Δ_rG^o_m=(58.1±1.7) kJ · mol⁻¹, and the standard molar entropy change Δ_rS^o_m=−(172±12) J · K⁻¹ · mol⁻¹. Under approximately physiological conditions (T=311.15 K, pH=7.0, and I_m=0.25 mol · kg⁻¹ the apparent equilibrium constant K^′≈0.013. The results of the several studies of this reaction from the literature have also been examined and analyzed using the chemical equilibrium model. It was found that much of the literature is in agreement with the results of this study. Use of our results together with a value from the literature for the standard electromotive force E^o for the NADP redox reaction leads to E^o=0.166 V (T=298.15 K and I=0) for the glutathione redox reaction {glutathione_ox²⁻(aq) + 2 H⁺(aq) + 2 e⁻=2 glutathione_red⁻(aq)}. The thermodynamic results obtained in this study also permit the calculation of the standard apparent electromotive force E^′o for the biochemical redox reaction {glutathione_ox(aq) + 2 e⁻=2 glutathione_red(aq)} over a wide range of temperature, pH, and ionic strength. At T=298.15 K, I=0.25 mol · kg⁻¹, and pH=7.0, the calculated value of E^′o is −0.265 V.     

Measurement and modelling of mean activity coefficients of aqueous mixed electrolyte solution containing glycine

Electrochemical measurements were made on (H₂O + NaBr + K₃PO₄ + glycine) mixtures at T = 298.15 K by using ion selective electrodes. The mean ionic activity coefficients of NaBr at molality 0.1 were determined at five K₃PO₄ molalities (0.01, 0.03, 0.05, 0.07, and 0.1) mol · kg⁻¹. The activity coefficients of glycine were evaluated from mean ionic activity coefficients of NaBr. The modified Pitzer equation was used to model the experimental data.     

Anthroneamine based chromofluorogenic probes for Hg2+ detection in aqueous solution

Anthroneamine derivatives 1–3 (H₂O:DMSO; 9:1, HEPES buffer, pH 7.0 ± 0.1) undergo highly selective fluorescence quenching with Hg²⁺. The observed linear fluorescence intensity change allows the quantitative detection of Hg²⁺ between 200 nM/40 ppb—12 μM/2.4 ppm even in the presence of interfering metal ions viz. Na⁺, K⁺, Mg²⁺, Ca²⁺, Ba²⁺, Cr³⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Ag⁺, Cd²⁺, Pb²⁺. Probes 1–3 and their Hg²⁺ complexes also show the broad pH resistance for their practical applicability.     

Zeptomolar detection of Hg2 + based on label-free electrochemical aptasensor: One step closer to the dream of single atom detection

An ultra-sensitive and highly selective electrochemical label-free aptasensor is proposed for the quantitation of Hg^2 + based on the hybridization/dehybridization of double-stranded DNA (dsDNA) on a gold electrode. Thiol-substituted single-stranded DNA (ssDNA) is self-assembled on the gold electrode surface through the SAu interaction. The hybridization of ssDNA with complementary DNA (cDNA) and the consequences of dehybridization in the presence of mercury ions are followed through differential pulse voltammetry (DPV) responses using a [Fe(CN)₆]^{3 −/4 −} redox probe. The formation of a thymine–Hg^2 +–thymine (T–Hg^2 +–T) complex is the key to producing a highly selective and sensitive aptasensor for Hg^2 + determination. Specifically, the present electrochemical aptasensor is able to quantify Hg^2 + ions in concentrations from 5 zeptomolar (zM) to 55 picomolar (pM) with a limit of detection of 0.6 zM, close to the dream of single atom detection, without requiring a complicated procedure or expensive materials.     

Triggering G-Quadruplex Conformation Switching with [7]Helicenes

The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K⁺) and antiparallel (Na⁺) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K⁺) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na⁺). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2 , and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.