Study of Ni(II) ion-DNA interactions with methylene blue as fluorescent probe

Spectroscopic studies of the interactions of Ni(II) ion with herring sperm DNA have been performed in this contribution using methylene blue (MB) as the fluorescent probe molecule. MB binds to double helical DNA via the intercalative mode, and its fluorescence is efficiently quenched by the DNA nucleobases. The fluorescence intensity of the probe molecule increases distinctly when Ni(II) ion is added to the MB-DNA solution system. These results indicate that the Ni(II) ions may be complexed with the DNA helix and probably bind at N-7 of adenine or guanine; consequently, some intercalated MB molecules are released due to the binding of Ni(II) ions to N-7 nitrogen of the purines. The Ni(II) ion-DNA interactions are further investigated by performing the photobleaching experiments of the MB-DNA complex in the presence and absence of Ni(II) ion. The bi-exponential decay functions of the fluorescence intensity have been observed in both cases and the shortening of the slow decay component when added Ni(II) ion also agrees with the release of MB from the DNA duplex.     

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent interactions, which are assumed to be nearly constant for the compared complexes of MB with DNA, seem to be justified by the results.     

Gel filtration studies of methylene blue–heparin interactions in aqueous solution

The gel filtration method was applied to the study of the interaction of the metachromatic cationic dye methylene blue (MB) with heparin in aqueous solution. This method requires the determination of the total MB concentration in the effluent. It was found that (i) MB in aqueous solution can be extracted quantitatively with benzyl alcohol (BzlOH), (ii) the metachromatic effect of MB is not observed in BzlOH, and (iii) the presence of heparin in aqueous solution does not interfere in the BzlOH extraction of MB. Accurate determination of MB concentration in the effluent can be made by extraction of MB with BzlOH, followed by the usual absorption spectroscopy. In addition, the use of the spectrophotometric method with this procedure entailed no serious problem relating to adsorption of MB on the glass walls. Gel filtration binding experiments were successfully carried out on a Sephadex LH-20 column using 0.005M acetate buffer as effluent. The binding data obtained were analyzed in terms of the cooperativity parameter according to the method of Schwarz. The thermodynamic parameters for the binding process of MB were also evaluated. It is shown that the binding of MB to heparin is highly cooperative, exothermic, and stabilized by entropic factors.     

Methylene Blue Binding to DNA with Alternating AT Base Sequence: Minor Groove Binding is Favored over Intercalation

Abstract

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5′-YpR-3′ intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent interactions, which are assumed to be nearly constant for the compared complexes of MB with DNA, seem to be justified by the results.     

Analysis of calorimetric data for the binding of monomeric bis-benzimidazole,an analog of the Hoechst 33258 dye,to poly(dA) · poly(dT)

Monomeric bis-benzimidazole (MB) is an analog of the Hoechst 33258 dye. The enthalpy and entropy of MB binding were evaluated by analyzing the calorimetric data on MB reverse titration with poly(dA) · poly(dT). A mathematical model was developed to estimate the thermodynamic parameters of binding on the basis of calorimetric data. The results agree well with spectrophotometric data on the binding of analogous compounds. The model was used to estimate the parameters of binding with poly(dA) · poly(dT) for dimeric bis-benzimidazole (DB), which consists of two bis-benzimidazole monomers linked via a flexible chain. The ligand was assumed to produce different types of complexes with the polymer.     

The identification of antigenic determinants on Mycobacterium bovis using monoclonal antibodies

Murine hybridomas secreting monoclonal antibodies to Mycobacterium bovis were produced and three soluble antigens were identified using radioimmunoassays and immunoblotting from polyacrylamide electrophoresis gels. Antibody MB3 (IgM, k chain) reacted with 20-100 kDal antigens produced by all mycobacterial strains examined while antibody MB5 (IgG2a, k chain) identified a 29.8 kDal antigen detected in field isolates of M. bovis and M. bovis strains Vallée and AN5. There was insignificant binding to M. bovis BCG, M. tuberculosis, M. microti, M. africanum, M. avium or M. paratuberculosis. Monoclonal antibody MB17 (IgA, k chain) reacted with a 17.4 kDal antigen present in M. bovis, M. tuberculosis and M. microti. Absorption of monoclonal antibodies with antigens from different species of Mycobacterium confirmed the specificities of MB3 and MB5 but the binding of MB17 was inhibited to some extent by all the extracts examined. The antigen identified by MB3 was present in purified protein derivative (PPD) from M. bovis, M. paratuberculosis and M. avium but antigens identified by MB5 and MB17 were not detected in these reagents.     

Enhancement of the binding affinity of methylene blue to site I in human serum albumin by cupric and ferric ions

In this work, the binding characteristics of methylene blue (MB) to human serum albumin (HSA) and the influence of Cu²⁺ and Fe³⁺ on the binding affinity of MB to HSA were investigated using fluorescence, absorption, circular dichroism (CD) spectroscopy and molecular modelling. The results of competitive binding experiments using the site probes ketoprofen and ibuprofen as specific markers suggested that MB was located in site I within sub‐domain IIA of HSA. The molecular modelling results agreed with the results of competitive site marker experiments and the results of CD spectra indicated that the interaction between MB and HSA caused the conformational changes in HSA. The binding affinity of MB to HSA was enhanced but to a different extent in the presence of Cu²⁺ and Fe³⁺, respectively, which indicated that the influence of different metal ions varied. Enhancement of the binding affinity of MB to HSA in the presence of Cu²⁺ is due to the formation of Cu²⁺–HSA complex leading to the conformational changes in HSA, whereas in the presence of Fe³⁺, enhancement of the binding affinity is due to the greater stability of the Fe³⁺–HSA–MB complex compared with the MB–HSA complex. Copyright © 2015 John Wiley & Sons, Ltd.     

Cocaine-induced changes in 3H-naloxone binding in brain membranes isolated from spontaneously hypertensive and Wistar-Kyoto rats

Effects of sub-acute cocaine treatment on 3H-naloxone binding to 6 brain regions were examined in spontaneously hypertensive (SHR) and Wistar-Kyoto (WKY) rats. Cocaine hydrochloride (3 mg/kg, i.v.) was given by bolus injection daily for five days. Rats were decapitated 24 hr following the final injection and crude membrane fractions prepared from the cortex (CT), hippocampus (HI), striatum (ST), hypothalamus (HY), midbrain (MB) and medulla/pons (MD). Binding of 3H-naloxone was consistent with a single site model in CT, HI, HY, MB and MD from vehicle-treated SHR and WKY. Cocaine treatment of SHR significantly decreased the maximal binding capacity (Bmax) of 3H-naloxone in the HI, ST and HY and the binding affinity was increased in HI. In contrast, a significant increase in Bmax was noted in CT and HI membranes isolated from cocaine-treated WKY. The binding affinity of 3H-naloxone to MB membranes of WKY was significantly decreased by cocaine treatment. The binding characteristics of 3H-naloxone in MD membranes were not different following cocaine treatment or between strains. Scatchard analysis indicated biphasic binding of 3H-naloxone binding to ST membranes from both SHR and WKY. Our results indicate that cocaine produces complex and differential changes in opiate receptors and, presumably, opioid peptide neuronal function in SHR and WKY.     

Developmental and dominance-associated differences in mushroom body structure in the paper wasp Mischocyttarus mastigophorus

Primitively eusocial paper wasps exhibit considerable plasticity in their division of labor. Dominance interactions among nest mates play a strong role in determining the task performance patterns of adult females. We asked whether dominance status and task performance differences were associated with the development of subregions of the mushroom bodies (MB) of female Mischocyttarus mastigophorus queens and workers. We found that the MB calycal neuropils were better developed (relative to the Kenyon cell body layer) in the dominant females that spent more time on the nest. Increased MB calyx development was more strongly associated with social dominance than with high rates of foraging. The MB of queens resembled those of dominant workers. The results suggest that social interactions are particularly relevant to M. mastigophorus females' cognition. By examining the MB of newly emerged females, we also found evidence for significant age-related changes in MB structure.     

Exciplexes or ground state complexes of (dibenzoylmethanato)boron difluoride and benzene derivatives? A study of their optical properties revisited via liquid state investigations and structure calculations.

(Dibenzoylmethanato)boron difluoride (DBMBF2) was found to form with benzene (B) and its methylated derivatives (MB) in cyclohexane (cHex) two types of ground state complexes. The first complexes with low stoichiometries 2 : 1, 1 : 1 and 1 : 2 do not fluoresce when they are excited. On the other hand, the ground state complexes with high stoichiometry, DBMBF2-(B)(n) or DBMBF2-(MB)(n) (with n> 2), exhibit a strong fluorescence in their excited states. These findings differ from the previous results, where the strongly fluorescing complexes have been argued to be the 1 : 1 and 1 : 2 exciplexes, complexes of the singlet excited state of DBMBF2 with one or two B or MB molecules. These differences are discussed in terms of the solute-solute and solute-solvent interactions when DBMBF2 and MB are solutes in cyclohexane or when MB is a co-solvent of cyclohexane in binary mixtures of DBMBF2. We also argue that the use of well-suited analytical methods is important for the determination of the nature of the various complexes. Furthermore, to understand the nature of the interactions between benzene and DBMBF2 molecules, we attempt to predict the sites of interaction between DBMBF2 and benzene molecules by determining theoretically the structure of the 1 : 1 complex.     

Effects of methyl bromide concentration, fumigation time, and fumigation temperature on Mediterranean and oriental fruit fly (Diptera: Tephritidae) egg and larval survival

The effects of methyl bromide (MB) concentration (16, 32,48, or 64 g/m3), fumigation temperature (15, 20, 25, or 30 degrees C), and fumigation time interactions on the survival of Mediterranean fruit fly, Ceratitis capitata (Wiedemann), and oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), eggs and first and third instars were recorded. Increasing the fumigation temperature from 15 to 20 degrees C or from 20 to 25 degrees C resulted in a significant reduction in fumigation time required for equivalent egg and larval mortalities at all studied MB concentrations; no further reductions in fumigation time resulted from increasing the temperature from 25 to 30 degrees C. Conversely, increasing temperature and time allowed for a reduction in MB concentration to obtain equivalent mortality. Thus, the optimum fumigation temperature for Mediterranean and oriental fruit fly eggs and larvae was 25 degrees C. Reducing MB concentrations required for phytosanitary fumigations would save time and expense, and reduce the amount of MB released into the atmosphere during aeration. Mediterranean fruit fly was as or more tolerant to MB than oriental fruit fly in MB tolerance for eggs and first instars. The egg stage was generally more tolerant to MB regardless of concentration. However, Mediterranean fruit fly eggs showed similar tolerance to first instars at 25 degrees C for the three highest concentrations and to third instars at 25 and 30 degrees C for the highest concentration, with no significant difference between them. Therefore, eggs alone can be used to obtain MB fumigation efficacy and quarantine security data at fumigation temperatures between 15 and 30 degrees C for Mediterranean and oriental fruit fly.     

Purification and immunological characterization of human myocardial MB creatine kinase

Elevated plasma MB creatine kinase (CK) is considered the most sensitive and specific diagnostic indicator of myocardial infarction. However, attempts to purify human MB CK have been unsuccessful. The need for purified human MB CK was further enhanced with the development of a radioimmunoassay for CK isoenzymes which would provide more prompt and specific detection of myocardial infarction. The major protein contaminant of MB CK is albumin which has been difficult to separate due to their similar electrophoretic mobility. Human hearts were obtained within 2 h postmortem and the tissue homogenized in 50 mm Tris-HCl (pH 7.4), 2 mm mercaptoethanol. The CK was recovered from the supernatant (31,000g) by ethanol extraction (50–70%). The resuspended pellet was fractionated on DEAE Sephadex A-50 with a salt gradient (50–500 mm, pH 8.0). The MB fraction contained about 90% albumin. The preparation was bound to an Affigel blue column and contaminating proteins other than albumin were eluted with 50 mm Tris-HCl (pH 8.0), 2 mm mercaptoethanol. MB CK was eluted with 250 mm NaCl, but the albumin remained bound. The MB fraction with a specific activity of 453 IU/mg represented an 80-fold increase in purity and exhibited a single protein band on polyacrylamide gels. Purified MB CK labeled with ¹²⁵I exhibited no binding to human albumin antiserum, but bound to MB CK antiserum, and unlabeled MB CK competitively inhibited binding of ¹²⁵I-MB CK in the radioimmunoassay system exhibiting a sensitivity for detection of plasma MB CK at the nanogram level.     

Incorporation of acridine orange and methylene blue in Langmuir monolayers mimicking releasing nanostructures

The efficiency of methylene blue (MB) and acridine orange (AO) for photodynamic therapy (PDT) is increased if encapsulated in liposomes. In this paper we determine the molecular-level interactions between MB or AO and mixed monolayers of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dipalmitoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DPPG) and cholesterol (CHOL) using surface pressure isotherms and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). To increase liposome stability, the effects from adding the surfactants Span® 80 and sodium cholate were also studied. Both MB and AO induce an expansion in the mixed monolayer, but this expansion is less significant in the presence of either Span® 80 or sodium cholate. The action of AO and MB occurred via coupling with phosphate groups of DPPC or DPPG. However, the levels of chain ordering and hydration of carbonyl and phosphate in headgroups depended on the photosensitizer and on the presence of Span® 80 or sodium cholate. From the PM-IRRAS spectra, we inferred that incorporation of MB and AO increased hydration of the monolayer headgroup, except for the case of the monolayer containing sodium cholate. This variability in behaviour offers an opportunity to tune the incorporation of AO and MB into liposomes which could be exploited in the release necessary for PDT.     

Electrochemical properties of DNA-intercalating doxorubicin and methylene blue on n-hexadecyl mercaptan-doped 5'-thiol-labeled DNA-modified gold electrodes

Interactions between DNA-intercalating molecules, methylene blue (MB) and doxorubicin (DOX), and gold surface modified by various DNA species and n-hexadecyl mercaptan (HDM) were investigated by cyclic voltammetry (CV). Hydrophilic DOX was completely blocked by the HDM film from contacting the gold electrode whereas hydrophobic MB could readily partition into the film. Unlabeled single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) underwent non-specific adsorption on gold surface but the adsorbed DNA can be partially displaced by HDM. Thiol-labeled ssDNA and dsDNA adsorbed on gold surface via both thiol-gold linkage and non-specific interactions between DNA strands and gold. The non-specific interactions could be interrupted by the addition of HDM, forming a mixed monolayer containing both HDM and DNA attached to the gold surface at 5'-thiol termini. The presence of ssDNA and dsDNA in the monolayer facilitated the redox reaction of MB and DOX on the modified electrode. Both MB and DOX diffuse along the ssDNA in the ssDNA-containing monolayers, and they additionally intercalate into the dsDNA in the dsDNA-containing monolayers. No sufficient evidence is shown to indicate that an organized monolayer is formed by the thiol-labeled dsDNA on gold surface, and that the redox reactions of MB and DOX were carried out by electron transfer through DNA helix.     

Methyl-beta-cyclodextrin directly binds methylene blue and blocks both its cell staining and glucose uptake stimulatory effects

GLUT1, the most ubiquitously expressed member of the GLUT family of glucose transporters, can be acutely activated by a variety of cell stresses. Methylene blue activates glucose transport activity of GLUT1 in L929 fibroblast cells presumably by a redox cycling of MB, which generates an oxidative stress. Data shown here reveal that methyl-beta-cyclodextrin (MCD) blocks both the staining of cells and activation of glucose uptake by directly binding to MB. MCD binding to MB was qualitatively demonstrated by a significantly slower dialysis rate of MB in the presence of MCD. Analysis of the complete spectra of aqueous MB solutions and MB plus MCD solutions by a factor analysis program called SIVVU indicated that these equilibria can be modeled by three species: MB monomer, MB dimer, and MCD-MB inclusion complex. The molar extinction coefficients for each species from 500 to 700nm were determined. The equilibrium association constant (K(a)) for MB dimer formation was measured at 5846+/-30M(-1) and the K(a) for formation of the MCD-MB complex was 310+/-10M(-1). MCD also dramatically enhances the destaining rate of MB-stained cells. The loss of MB from the cell is tightly correlated with the loss of activated glucose uptake. This suggests that the MB activation of glucose uptake is likely not caused by its redox cycling, but more likely the result of a specific interaction between MB and a protein directly involved in the activation of GLUT1.     

93 Spectroscopic investigation of methylene blue binding to DNA

The interaction of methylene blue (MB) with DNA has been investigated by UV absorption spectra, Fluorescence spectra and UV-melting method. Analysis of the results of the melting experiments shows that melting temperature (T _m) of the complexes increases with the [total ligand]: DNA ratio (r) at two concentrations of Na⁺ (2?mM Na⁺ and 20?mM Na⁺) providing support for conclusion that MB is a stabilizer of DNA helix structure. By contrast, the shapes of dependences of width of transition (ΔT) on r at low and high [Na⁺] are different which points to the existence of different types of binding modes of MB with DNA. UV-spectroscopy experiments and fluorescence spectra indicated that the binding modes of MB with DNA depended on r. At high r (r?>?0.25), remarkable hypochromic effect with no shift of λ _max in the absorption spectra of MB was observed. The fluorescence of MB was quenched which indicated that MB was bound to phosphate groups of DNA by electrostatic interaction. At low r ratios (r?<?0.2), the absorption spectra of MB upon increasing the concentration of DNA showed gradually decrease in the peak intensities with a red shift. This phenomenon is usually associated with molecular intercalation into the base stack of the ds-DNA. Using the Scatchard’s model, the complex formation constants for MB with DNA were determined: the binding constant K?≈?6.5?×?10⁵ and binding site size n?≈?4. Obtained data are not typical for intercalation model of ligands to DNA. Moreover, comparison between these data and our early experimental results of interaction of ethidium bromide with DNA made it possible to suggest that this binding type of MB is, more probably, semi-intercalation mode (Vardevanyan et al., 2003). This conclusion is in accordance with the analysis of the model structures of MB–DNA complexes which clearly shows the importance of solvent contributions in suggested structural form (Tong et al., 2010).