Electrochemical DNA biosensor for the study of ciprofloxacin-DNA interaction

The interaction of ciprofloxacin with DNA was studied by using an electrochemical DNA biosensor. The binding mechanism of ciprofloxacin was elucidated by using constant current potentiometry and differential pulse voltammetry at DNA-modified glassy carbon electrode. The decrease in the guanine oxidation peak area or peak current at +0.9 V was used as an indicator for the interaction mechanism in 0.2M acetate buffer (pH 5). The binding constant (K) values obtained were 1.33+/-0.02 x 10(4) and 1.32+/-0.08 x 10(4) M(-1) with constant current potentiometry and differential pulse voltammetry, respectively. A linear dependence of the guanine peak area or peak currents was observed in the range of 40-80 microM ciprofloxacin, with a detection limit of 24 microM with r=0.995 and 9 microM with r=0.999 by using constant current potentiometry and differential pulse voltammetry, respectively. Moreover, the influence of sodium and calcium ions was also studied to elucidate the mechanism of ciprofloxacin-DNA interaction at different solution conditions, and this proved to be helpful in understanding the ciprofloxacin-DNA interaction.     

Electrochemical biosensor evaluation of the interaction between DNA and metallo-drugs

Electrochemical techniques were used to study the interaction between a panel of antiproliferative metallo-drugs and double-stranded DNA immobilized on screen-printed electrodes as a model of the analogous interaction occurring in solution. The propensity of a given metal drug to interact with DNA was measured as a function of the decrease of guanine oxidation signal, which was detected by square wave voltammetry. Estimates of variations in experimental parameters, such as the concentration of complexes, time following dissolution (ageing time) and the presence of chloride, are provided. Presented at the IV Symposium on Pharmaco-Bio- Metallics, October, 29–31, 2004, Lecce (Italy)     

Features of the interaction of antitumor mitoxantrone compounds with sarcoma 45 tumor DNA]

The interaction of antitumoral drug mitoxantrone with DNA of the tumor sarcoma 45 and healthy animals liver has been investigated according to the character of changes on the absorption spectra at binding at 30 degrees C and 0.11 M NaCl. The investigation shows that the interaction of mitoxantrone with DNA of sarcoma 45 differs from that with DNA of healthy animals liver. The calculations show that the saturation stoichiometry by both DNA is one mitoxantrone molecule per 2.5 base pairs with the binding constant k = 4 x 10(5) M-1 (for binding mitoxantrone with liver DNA) and k = 3 x 10(6) M-1 (with tumor DNA). Possible reason of such a difference is discussed on the basis of structural peculiarities of tumor DNA.     

Ill-conditioning associated with the "end-point" method for the determination of kinetic parameters describing irreversible enzyme inactivation by an unstable inhibitor

Study of the complete time-course of irreversible enzyme inhibition by an unstable inhibitor yields more information than can be obtained by recording data only at the end point of reaction. Time-course analysis of co-operative irreversible enzyme inhibition by an unstable inhibitor has been shown to be considerably less susceptible to ill-conditioning than the "end-point" method for the determination of kinetic parameters describing inactivation. As a result, mechanisms that cannot be distinguished by the "end-point" method are readily differentiated by time-course analysis without the need to isolate intermediate species.     

Electrochemical studies of kanamycin immobilization on self-assembled monolayer and interaction with DNA

The electrochemical characteristics of kanamycin onto self-assembled monolayer (SAM) modified gold electrode (SAM/Au) is investigated by cyclic voltammetry. In the potential range 0-0.6 V, Cu(II) yields a pair of stable redox waves at the bare gold electrode. E(pa) is located at 0.189 V and E(pc) at 0.254 V. In contrast, Cu(II) is reduced at a more positive potential and a decreasing current at the kanamycin SAM/Au electrode. Cu(II) and kanamycin can form a stoichiometry complex with chemical ratio of 2:1. The interaction of Cu(II)-kanamycin complex with calf thymus DNA is also studied in the solution. And the interactive mode between Cu(II)-kanamycin complex and DNA is verified by the fluorescence method. Binding constants (K) of the Cu(II)-kanamycin complex to DNA and binding site size (s) are calculated from voltammetric data and equal to 1.5 x 10(7) l/mol and 4 bp, respectively.     

Evaluation of parameters for monitoring an anaerobic co-digestion process

The system investigated in this study is an anaerobic digester at a municipal wastewater treatment plant operating on sludge from the wastewater treatment, co-digested with carbohydrate-rich food-processing waste. The digester is run below maximum capacity to prevent overload. Process monitoring at present is not extensive, even for the measurement of on-line gas production rate and off-line pH. Much could be gained if a better program for monitoring and control was developed, so that the full capacity of the system could be utilised without the risk of overload. The only limit presently set for correct process operation is that the pH should be above 6.8. In the present investigation, the pH was compared with alkalinity, gas production rate, gas composition and the concentration of volatile fatty acids (VFA). Changes in organic load were monitored in the full-scale anaerobic digester and in laboratory-scale models of the plant. Gas-phase parameters showed a slow response to changes in load. The VFA concentrations were superior for indicating overload of the microbial system, but alkalinity and pH also proved to be good monitoring parameters. The possibility of using pH as a process indicator is, however, strongly dependent on the buffering capacity. In this study, a minor change in the amount of carbohydrates in the substrate had drastic effects on the buffering effect of the system. Received: 21 January 2000 / Received revision: 10 July 2000 / Accepted: 16 July 2000     

Myotrophin-kappaB DNA interaction in the initiation process of cardiac hypertrophy

To investigate how cardiac hypertrophy and heart failure develop, we isolated and characterized a candidate initiator, the soluble 12-kDa protein myotrophin, from rat and human hearts. Myotrophin stimulates protein synthesis and myocardial cell growth associated with increased levels of hypertrophy marker genes. Recombinant myotrophin from the cloned gene showed structural/functional motifs, including ankyrin repeats and putative phosphorylation sites for protein kinase C (PKC) and casein kinase II. One repeat, homologous with I kappaB, interacts with rel/NF-kappaB in vitro. We analyzed the interaction of recombinant myotrophin and nuclear extracts prepared from neonatal and adult cardiomyocytes; gel mobility shift assay showed that myotrophin bound to kappaB DNA. To define PKC's role in myotrophin-induced myocyte growth, we incubated neonatal rat myocytes (normal and stretch) with specific inhibitors and found that myotrophin inhibits [3H]leucine incorporation into myocytes and different hypertrophic gene expression in neonatal myocytes. Using confocal microscopy, we observed that a basal level of myotrophin was present in both cytoplasm and nucleus under normal conditions, but under cyclic stretch, myotrophin levels became elevated in the nucleus. Myotrophin gene levels were upregulated when myocytes underwent cyclic stretch or were treated with tumor necrosis factor-alpha (TNF-alpha) or interleukin-1beta and also when excised beating hearts were exposed to high pressure. Our data showed that the myotrophin-kappaB interaction was increased with age in spontaneously hypertensive rats (SHRs) only. Our data provide evidence that myotrophin-kappaB DNA interaction may be an important step in initiating cardiac hypertrophy.     

Electrochemical investigation on interaction between DNA with quercetin and Eu-Qu3 complex

The interactions of quercetin (Qu) and Eu-Qu3 complex with calf thymus DNA were studied using cyclic voltammetry (CV) and double potential step chronocoulometry (DPSCC) at glass carbon electrode (GCE) for the surface method. The method is simple, convenient, reliable, reagent saving. Information such as intrinsic binding constant (K), and binding numbers (n) of bound species per DNA (bp), ratio (K(Ox)/K(Red)) of the binding constants for the oxidized and reduced forms of a bound species and interaction mode was obtained using dsDNA-modified GCE. Quercetin and Eu-Qu3 can both bind to DNA, but quercetin binds to DNA mainly by electrostatic attraction and the complex bind to DNA by both intercalation and electrostatic attraction. For the quercetin/dsDNA-modified GCE systems, a K of (3.80+/-0.3) x 10(4) M(-1), saturation coverage value (Gammas) of (2.28+/-0.2) x 10(-10) mol/cm2 and n of 1.2 were obtained. For the complex system, a saturation coverage value (Gammas) of 1.65 x 10(-10) mol/cm2 and n of 1.8 were obtained.     

Electrochemical spectroscopic investigations on the interaction of an ytterbium complex with DNA and their analytical applications such as biosensor

Metal ion-DNA interactions are important in nature, often changing the genetic material's structure and function. A new Yb complex of YbCl₃ (tris(8-hydroxyquinoline-5-sulfonic acid) ytterbium) was synthesized and utilized as an electrochemical indicator for the detection of DNA oligonucleotide based on its interaction with Yb(QS)₃. Cyclic voltammetry (CV) and fluorescence spectroscopy were used to investigate the interaction of Yb(QS)₃ with ds-DNA. It was revealed that Yb(QS)₃ presented an excellent electrochemical activity on glassy carbon electrode (GCE) and could intercalate into the double helix of double-stranded DNA (ds-DNA). The binding mechanism of interaction was elucidated on glassy carbon electrode dipped in DNA solution and DNA modified carbon paste electrode by using differential pulse voltammetry and cyclic voltammetry. The binding ratio between this complex and ds-DNA was calculated to be 1:1. The extent of hybridization was evaluated on the basis of the difference between signals of Yb(QS)₃ with probe DNA before and after hybridization with complementary DNA. With this approach, this DNA could be quantified over the range from 1 × 10⁻⁸ to 1.1 × 10⁻⁷ M. The interaction mode between Yb(QS)₃ and DNA was found to be mainly intercalative interaction. These results were confirmed with fluorescence experiments.     

Electrochemical study on behavior of EuMo2 complex and its interaction with DNA

The electrochemical behavior of complex EuMo2 (Mo = Morin, 2',3,4'5,7-pentahydroxyflavone) and its interactions with calf thymus DNA were studied using cyclic voltammetry (CV) and double potential step chronocoulometry (DPSCC) at glass carbon electrode (GCE) and DNA modified GCE, respectively. Information such as diffusion coefficient (D), rate constant (ks) of EuMo2 and intrinsic binding constant (K), binding numbers (n) of bound species per DNA (bp) were obtained. EuMo2 can bind to DNA, and the binding mode is intercalation. By nonlinear fitting with Langmuir equation, a K of 1.02 x 10(6) M-1 and an n of 1 were obtained.     

The antitumor agent mitoxantrone binds cooperatively to DNA: evidence for heterogeneity in DNA conformation

The equilibrium binding of the antitumor compound DHAQ, or mitoxantrone [1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]ethyl]amino]-9,10- anthracenedione], to various DNAs has been examined by optical titration and equilibrium dialysis methods. At low r (bound drug/DNA base pair) values, r less than 0.03, DHAQ binds, in a highly cooperative manner, to calf thymus and Micrococcus lysodeikticus DNAs. The binding isotherms for the interaction of DHAQ with Clostridium perfringens DNA and poly(dA-dT).poly(dA-dT) exhibit a small positive slope at low r values, suggestive of cooperative binding. In contrast, the binding of DHAQ to poly(dG-dC).poly(dG-dC) shows no evidence of cooperative binding even at very low r values. At higher r values (r greater than 0.05), the binding of DHAQ to all the DNAs studied is characterized by a neighbor-exclusion process. A model is proposed to account for the two modes of binding exhibited in the cooperative binding isotherms. The main feature of the proposed model is that local sequence and structural heterogeneity of the DNA give rise to sets of binding sites to which DHAQ binds in a highly cooperative manner, while the majority of the DNA sites bind DHAQ via a neighbor-exclusion process. This two-site model reproduces the observed binding isotherms and leads to the conclusion that DHAQ binds in clusters to selected regions of DNA. It is suggested that clustering may play a role in the physiological activity of drugs.     

Deciphering molecular aspects of interaction between anticancer drug mitoxantrone and tRNA

Mitoxantrone (1,4-dihydroxy-5,8-bis[[2-[(2-hydroxyethyl)amino]ethyl]amino]-9,10-anthracenedione) is a synthetically designed antineoplastic agent and structurally similar to classical anthracyclines. It is widely used as a potent chemotherapeutic component against various kinds of cancer and possesses lesser cardio-toxic effects with respect to naturally occurring anthracyclines. In the present study, we have investigated the binding features of mitoxantrone–tRNA complexation at physiological pH using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and UV–visible absorption spectroscopic techniques. FTIR analysis reveals that mitoxantrone interacts mainly with heterocyclic base residues of tRNA along with slight external binding with phosphate–sugar backbone. In particular, mitoxantrone binds at uracil (C=O) and adenine (C=N) sites of biomolecule (tRNA). CD spectroscopic results suggest that there is no major conformational transition in native A-form of tRNA upon mitoxantrone–tRNA adductation except an intensification in the secondary structure of tRNA is evident. The association constant calculated for mitoxantrone–tRNA association is found to be 1.27?×?10⁵ M^?1 indicating moderate to strong binding affinity of drug with tRNA. Thermodynamically, mitoxantrone–tRNA interaction is an enthalpy-driven exothermic reaction. Investigation into drug–tRNA interaction can play an essential role in the rational development of RNA targeting chemotherapeutic agents, which also delineate the structural–functional relationship between drug and its target at molecular level.     

Electrochemical studies of DNA immobilization onto the azide-terminated monolayers and its interaction with taxol

A surface modification procedure for the creation of self-assembled monolayers (SAMs) that can be used as a scaffold for double-stranded DNA (dsDNA) incorporation onto the gold surfaces is described. The SAMs of an azidohexane thiol derivative were prepared on the Au electrode and then used for the immobilization of dsDNA. The electrochemical characteristics of dsDNA onto the SAM-modified gold electrode were investigated by cyclic voltammetry and electrochemical impedance spectroscopy, and the surface concentration of dsDNA onto the SAMs surface was estimated. The interaction of dsDNA with the anticancer drug, taxol (paclitaxel), was also studied on the surface of DNA/SAM/Au electrode. The observed decrease in the guanine oxidation peak current was used to monitor the interaction of taxol with DNA. The resulting Langmuir isotherm for taxol binding to DNA at the modified electrode was used to evaluate the binding constant of taxol-DNA. The results obtained supported the groove binding interaction of taxol with DNA. The modified electrode was used as a sensitive sensor for quantification of taxol in human serum sample.     

Electrochemical selective determination of ascorbic acid at redox active polymer modified electrode derived from direct blue 71

A simple selective method for determination of ascorbic acid using polymerized direct blue 71 (DB71) is described. Anodic polymerization of the azo dye DB71 on glassy carbon (GC) electrode in 0.1M H(2)SO(4) acidic medium was found to yield thin and stable polymeric films. The poly(DB71) films were electroactive in wide pH range (1-13). A pair of symmetrical redox peaks at a formal redox potential, E('0)=-0.02V vs. Ag/AgCl (pH 7.0) was observed with a Nernstian slope -0.058V, is attributed to a 1:1 proton+electron involving polymer redox reactions at the modified electrode. Scanning electron microscope (SEM), atomic force microscope (AFM) and electrochemical impedance spectroscopy (EIS) measurements were used for surface studies of polymer modified electrode. Poly(DB71) modified GC electrode showed excellent electrocatalytic activity towards ascorbic acid in neutral buffer solution. Using amperometric method, linear range (1x10(-6)-2x10(-3)M), dynamic range (1x10(-6)-0.01M) and detection limit (1x10(-6)M, S/N=3) were estimated for measurement of ascorbic acid in pH 7.0 buffer solution. Major interferences such as dopamine and uric acid are tested at this modified electrode and found that selective detection of ascorbic acid can be achieved. This new method successfully applied for determination of ascorbic acid in commercial tablets with satisfactory results.     

Kinetics of irreversible dissociation for proteins bound cooperatively to DNA

We consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one-dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22 , 1697–1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n?2) internal positions of an n-cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero-order dissociation kinetics predicted by the Lohman model.     

Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences

Equilibrium binding of EcoRI endonuclease to DNA has been analyzed by nitrocellulose filter and preferential DNA cleavage methods. Association constants for pBR322 and a 34-base pair molecule containing the EcoRI site of this plasmid in a central position were determined to be 1.9 X 10(11) M-1 and 1.0 X 10(11) M-1 at 37 degrees C, respectively, with the stoichiometry of binding being 0.8 +/- 0.1 mol of endonuclease dimer per mol of DNA. In contrast, the affinity of the enzyme for a pBR322 derivative from which the EcoRI site has been deleted is 3.2 X 10(9) M-1 as judged by competitive binding experiments. If it is assumed that each base pair can define the beginning of a nonspecific binding site, this value corresponds to an affinity for nonspecific sites of 7.4 X 10(5) M-1. Furthermore, the affinity of the endonuclease for the EcoRI-methylated sequence is at least three orders of magnitude less than that for the unmodified recognition site. The dependence on temperature and ionic strength of the equilibrium constant governing specific interactions has also been examined. The temperature dependence of the reaction indicates that entropy increase accounts for 70% of the free energy of specific binding at 37 degrees C. Affinity of the endonuclease for the EcoRI site is highly dependent on NaCl concentration. Analysis of this dependence according to the theory of Record and colleagues (Record, T. M., Jr., Lohman, T. M., and deHaseth, P. (1976) J. Mol. Biol. 107, 145-158) has implicated 8 ion pairs in the stability of specific complexes, a value identical with the number of phosphate contacts determined by ethylation interference analysis (Lu, A. L., Jack, W. E., and Modrich, P. (1981) J. Biol. Chem. 256, 13200-13206). Extrapolation to 1 M NaCl suggests that nonelectrostatic interactions account for 40% of the free energy change associated with specific complex formation.     

Single-sample preparation for simultaneous cellular redox and energy state determination

A simple and reliable method for the preparation of biological samples for the evaluation of biochemical parameters representative of the redox and energy states, such as glutathione (GSH), oxidized glutathione (GSSG), oxidized nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), oxidized nicotinamide adenine dinucleotide phosphate (NADP+), reduced nicotinamide adenine dinucleotide phosphate (NADPH), coenzyme A (CoASH), oxidized CoASH, ascorbate, malondialdehyde, oxypurines, nucleosides, and energy metabolites, is presented. Fast deproteinization under nonoxidizing conditions is obtained by tissue homogenization in ice-cold, nitrogen-saturated CH3CN + 10 mM KH2PO4 (3:1; v:v), pH 7.40. After sample centrifugation to pellet precipitated proteins, organic solvent removal is performed on clear supernatants by three washings with large volumes of high-performance liquid chromatography (HPLC)-grade chloroform. The remaining aqueous phase, free of solvent and any lipid-soluble substances that may interfere with the further metabolite analysis, is used for the simultaneous ion-pairing HPLC determination of 39 compounds by means of a Kromasil C-18, 250 x 4.6-mm, 5-microm-particle-size column with tetrabutylammonium hydroxide as the pairing reagent. Results obtained by using the present method to prepare different rat tissue extracts demonstrate that it is possible to perform a single tissue preparation only for monitoring, in the same sample, compounds representative of the redox state (through the direct determination of GSH, GSSG, NAD+, NADH, NADP+, NADPH, CoASH, and oxidized CoASH) and of the cell energy state (by the analysis of oxypurines, nucleosides, and energy metabolites). Applicability of this sample processing procedure to quantify variations of the aforementioned compounds under pathological conditions was effected in rats subjected to moderate closed-head trauma.     

Electrochemical study of the interaction between cytochrome c and DNA at a modified gold electrode

The direct electron transfer of surface-confined horse heart cytochrome c (Cyt c) was achieved using COOH-terminated alkanethiolate-modified gold electrode. Later DNA was immobilized on the two-layer modified electrode. The quantitative determination of DNA was explored and the interaction between cytochrome c and DNA was studied. The binding site sizes were determined to be 15 bp per Cyt c molecule with double-stranded (ds) DNA and 30 nucleotides binding one Cyt c molecule with single-stranded (ss) DNA. At the dsDNA/Cyt c/MUA/Au electrode, the rate constant of oxidation electron transfer k(s,ox)=1.59x10(-3)cms-1 was obtained, at the ssDNA/Cyt c/MUA/Au electrode, the value was 2.43x10(-3)ms-1 when the scan rate was 1.0V/s. The different electrodes were characterized with electrochemical quartz crystal microbalance and atomic force microscope.