Studies of the binding of ethidium bromide to cells before and after enzyme treatment

Summary Binding of ethidium bromide (EB) to cells before and after HCl, pepsin and RNase treatment was investigated by spectrophotometric and fluorimetric methods. Binding isotherms, calculated with the McGheevon Hippel equation, taking EB as a non-interacting ligand, revealed the influence of these treatments on the fluorescence characteristics of the cells which were measured by flow-through cytofluorimetry. Thus pepsin- and RNase-treated cells have a reduced intercalation capacity due to the loss of cytoplasmic RNA and RNA hydrolysis, respectively. HCl alone, or in association with pepsin, increased the equilibrium constant K considerably. Thus at low free EB concentrations the enhanced EB affinity of acid-pretreated cells generates a high fluorescence intensity, by comparison with treatments at neutral pH. This result contradicts the interpretation of high EB binding to acid pretreated cells which is commonly believed to be due to hydrolytic histone removal from potential intercalation sites.With increasing free EB concentrations the fluorescence intensities of RNase- and pepsin-treated cells culminate at the same level due to their almost identical intercalation capacities. Consequently, quantitative DNA analysis of pretreated cell suspensions with EB can only be performed if the alteration, induced by the pretreatment, has previously been studied.     

Ethidium-dependent uncoupling of substrate binding and cleavage by Escherichia coli ribonuclease III

Ethidium bromide (EB) is known to inhibit cleavage of bacterial rRNA precursors by Escherichia coli ribonuclease III, a dsRNA-specific nuclease. The mechanism of EB inhibition of RNase III is not known nor is there information on EB-binding sites in RNase III substrates. We show here that EB is a reversible, apparently competitive inhibitor of RNase III cleavage of small model substrates in vitro. Inhibition is due to intercalation, since (i) the inhibitory concentrations of EB are similar to measured EB intercalation affinities; (ii) substrate cleavage is not affected by actinomycin D, an intercalating agent that does not bind dsRNA; (iii) the EB concentration dependence of inhibition is a function of substrate structure. In contrast, EB does not strongly inhibit the ability of RNase III to bind substrate. EB also does not block substrate binding by the C-terminal dsRNA-binding domain (dsRBD) of RNase III, indicating that EB perturbs substrate recognition by the N-terminal catalytic domain. Laser photocleavage experiments revealed two ethidium-binding sites in the substrate R1.1 RNA. One site is in the internal loop, adjacent to the scissile bond, while the second site is in the lower stem. Both sites consist of an A-A pair stacked on a CG pair, a motif which apparently provides a particularly favorable environment for intercalation. These results indicate an inhibitory mechanism in which EB site-specifically binds substrate, creating a cleavage-resistant complex that can compete with free substrate for RNase III. This study also shows that RNase III recognition and cleavage of substrate can be uncoupled and supports an enzymatic mechanism of dsRNA cleavage involving cooperative but not obligatorily linked actions of the dsRBD and the catalytic domain.     

Microfluorometric assessment of the DNA-DNP complex in human spermatozoa

During spermiogenesis, the DNA-nucleoprotein complex undergoes alterations that are reflected in a decreasing capacity for binding DNA-specific dyes, such as ethidium bromide (EB). Human spermatozoa with a low or high capacity for EB binding were depleted of RNA and most nuclear proteins by exposure to RNAse, EDTA and trypsin, with and without additional high salt buffer (HSB) treatment. When treated with RNAse, EDTA and trypsin only, the haploid DNA fluorescence value (calculated from the diploid value of the standard cell population) was found at EB concentrations of 6.5 to 12.5 micrograms/mL. At these EB concentrations, a significantly lower fluorescence was found in the material also treated with HSB, probably reflecting an unwinding of the highly negatively supercoiled DNA loops that are induced by HSB treatment. Maximal fluorescence was not found until a concentration of 50 micrograms EB/mL. This may be due to an overwinding of the DNA by the positive supercoiling caused by EB. The significant difference in EB uptake initially found between the two groups whose spermatozoa showed low and high capacities for EB binding disappeared after removal of the nucleoproteins, suggesting that this compartment of the nucleoprotein-DNA complex is responsible for the different uptakes of EB.     

Induction of cytoplasmic petite in yeast by guanidine hydrochloride: Combined treatment with other inducing agents

We have studied the induction of ?^? mutants by guanidine hydrochloride (GuHCl) in combination with other known inducers: ethidium bromide (EB), berenil and ultraviolet light. Competition was observed when cells were simultaneously treated with optimal concentrations of EB and GuHCl; on the other hand, treatment of cells with EB in the presence of non-inducing concentrations of GuHCl resulted in the stimulation of ?^? induction by EB. Furthermore, using a strain which upon treatment with high EB concentrations shows recovery of respiratory competence, the presence of GuHCl did not interfere either with the early phase of induction or with the recovery phase, but it did interfere in a competitive fashion with the final irreversible phase of EB induction. In the case of berenil, a synergistic effect was seen when cells were pretreated with GuHCl. A synergistic induction was also observed when cells were submitted to UV prior to GuHCl treatment. These results suggest that GuHCl, EB and berenil act via some common step in their ?^? induction pathways. Moreover, GuHCl may somehow be decreasing the efficiency of dark repair of ultraviolet lesions on mitochondrial DNA.     

Fluorescence decay of ethidium bromide in the presence of the Z-conformation of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride

A time-resolved fluorescence study of ethidium bromide (EB) in the presence of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride is presented under solvent conditions in which these polymers adopt the Z-conformation (high ionic strength). It is shown that these polynucleotides can intercalate a very small quantity of EB. The binding parameters have been determined. The fluorescence lifetime of EB is slightly higher when bound to the Z-conformation (?25 ns) than when bound to the B-conformation (?23.7 ns). The nature of the salt has been checked. In the presence of 2.5M NaClO₄, no transition from the Z-conformation to another conformation is observed when EB is added. On the contrary, in the presence of 4.25M NaCl, EB induces a cooperative transition from the Z-conformation to a conformation characterized by a much higher affinity for EB intercalation. In the case of poly(dG-dC) this last conformation is identical to the one observed at low ionic strength (B-conformation), but in the case of the platinated polymer this conformation is slightly different, as judged by the smaller value of the fluorescence lifetime of the intercalated EB.     

Study on the mechanism of the interaction between acteoside and pepsin using spectroscopic techniques

The interaction of acteoside with pepsin has been investigated using fluorescence spectra, UV/vis absorption spectra, three‐dimensional (3D) fluorescence spectra and synchronous fluorescence spectra, along with a molecular docking method. The fluorescence experiments indicate that acteoside can quench the intrinsic fluorescence of pepsin through combined quenching at a low concentration of acteoside, and static quenching at high concentrations. Thermodynamic analysis suggests that hydrogen bonds and van der Waal's forces are the main forces between pepsin and acteoside. According to the theory of Förster's non‐radiation energy transfer, the binding distance between pepsin and acteoside was calculated to be 2.018 nm, which implies that energy transfer occurs between acteoside and pepsin. In addition, experimental results from UV/vis absorption spectra, 3D fluorescence spectra and synchronous fluorescence spectra imply that pepsin undergoes a conformation change when it interacts with acteoside. Copyright © 2015 John Wiley & Sons, Ltd.     

Interaction between azo dye Acid Red 14 and pepsin by multispectral methods and docking studies

The interaction of synthetic azo dye Acid Red 14 with pepsin was studied by fluorescence spectroscopy, UV–vis spectroscopy, circular dichroism and molecular docking. Results from the fluorescence spectroscopy show that Acid Red 14 has a strong capability to quench the intrinsic fluorescence of pepsin with static quenching. Binding constant, number of the binding sites and thermodynamic parameters were measured at different temperatures. The result indicates that Acid Red 14 interact with pepsin spontaneously by hydrogen bonding and van der Waals interactions. Three‐dimensional fluorescence spectra and circular dichroism spectra reveal that Acid Red 14 could slightly change the structure of pepsin. The hydrogen bond is formed between Acid Red 14 and Tyr‐189 and Thr‐218 residues of pepsin. Furthermore, the binding between Acid Red 14 and pepsin inhibits pepsin activity. The study can provide a way to analyze the biological safety of Acid Red 14 on digestive proteases or other proteins.     

Evidence for tertiary structure in natural single stranded RNAs in solution.

Binding isotherms (20 degrees C) of ethidium bromide to a number of tRNA species at various ionic strengths indicate that i) the number ni of intercalation sites is high 7 to 11 per molecule, in the low salt form III, but small, 2 to 1, at high Mg2+ or Na+ when form I predominates. ii) modification of tRNA at strategic positions for 3D folding prevents full expression of intercalation restriction iii) maximal restriction is obtained at salt concentrations higher than needed for full conversion to form I. It is inferred that restriction, which is not observed with bihelical RNA (or DNA), requires the native tRNA 3D structure but also some physical coupling between the region of 3D folding and bihelical arms. Ribosomal RNAs, some viral RNAs, mRNA from sheep mammary gland as well as the random copolymers Poly UG, Poly AUG, Poly AUCG all exhibit intercalation restriction. Hence 3D folding of the polyribonucleotide chains appears to be a feature common to single-stranded RNAs when free in solution under physiological conditions.     

Restrained torsional dynamics of nuclear DNA in living proliferative mammalian cells

Physical parameters, describing the state of chromatinized DNA in living mammalian cells, were revealed by in situ fluorescence dynamic properties of ethidium in its free and intercalated states. The lifetimes and anisotropy decays of this cationic chromophore were measured within the nuclear domain, by using the ultra-sensitive time-correlated single-photon counting technique, confocal microscopy, and ultra-low probe concentrations. We found that, in living cells: 1) free ethidium molecules equilibrate between extracellular milieu and nucleus, demonstrating that the cation is naturally transported into the nucleus; 2) the intercalation of ethidium into chromatinized DNA is strongly inhibited, with relaxation of the inhibition after mild (digitonin) cell treatment; 3) intercalation sites are likely to be located in chromatin DNA; and 4) the fluorescence anisotropy relaxation of intercalated molecules is very slow. The combination of fluorescence kinetic and fluorescence anisotropy dynamics indicates that the torsional dynamics of nuclear DNA is highly restrained in living cells.     

Incorporation of ethidium bromide in the Drosophila salivary gland approached by microspectrofluorometry: evidence for the presence of both free and bound dye in the nuclei of cells in viable conditions

The incorporation of 10^–6 M ethidium bromide (EB) was studied in viable Drosophila melanogaster salivary glands with a spatial resolution reaching a few µm³, using a confocal laser microspectrofluorometer designed for spectral analysis. Spectra were recorded with the 514 nm Argon laser line during excitation times of 1 second (20 µW on the preparation) at 5 min intervals for 30 or 60 min, either at points in determined cell sites or serially throughout the cells. The fluorescence intensity time-course indicated that the EB intake was not an all-or-none process, but rather a graded, sensitive indicator of the functional state of the cell. On the micrometer scale, the cytoplasm behaved as an homogeneous substrate with the fluorescence intensity depending on EB intake and intracellular diffusion. In the nucleus, however, localized enhancement of the emission intensity was observed. Spectral analysis allowed us to characterize the interactions. The mean values of λ _max in the cytoplasm (600 nm), in the nucleus (601 nm) and outside the glands (602 nm) were less than for free EB in aqueous solution (630 nm); values of full width at half maximum were between 92 and 96 nm, which is much lower than the 120 nm observed for free EB. The recorded spectra were analyzed using a linear combination of two spectral models, namely free and DNA intercalated EB. In the nucleus, the free EB model spectra was found to represent up to 10% of the recorded spectra whereas it was near zero in the cytoplasm. The present data suggest that the intranuclear concentration of free EB (allowing for its lower fluorescence quantum yield) might be at least equal to that of the bound EB.     

Energy migration in the poly(ra-rU)-ethidium complex. determination of the unwinding angle of the polyribonucleic helix

The polarized fluorescence of the ethidium bromide (EB)-poly(rA-rU) complex has been studied by pulse fluorometry. As expected for a polynucleotide snowing one single kind of intercalation site, the decay of the whole emission is a single exponential (time constant 27 ns). The anisotropy decay is analysed as follows: (1) A brownian contribution having two correlation times, one of which characterizes local motions and the other a macromolecular motion. (2) A contribution due to transfers between EB molecules fixed to the same polynucleotide molecule, is analysed by a method analogous to the method used in previous work on EB-DNA complexes. That method consists in choosing a molecular model of the complex depending on geometrical parameters, and in simulating the energy migration on that model with a Monte Carlo calculation. Poly(rA-rU) is assumed here to adopt the structure A of RNA. Intercalated EB molecules modify the anale between two consecutive base pairs by δ. The angular position of the EB transition moment is defined by an angle φ. One finds that the angle φ is situated between 0° and 30°, which corresponds to a whole intercalation of the chroniophore as opposed to the semi-intercalation which has been proposed for certain dyes. The angle δ is negative; therefore there is an unwinding of the polyribonucleotide helix. Its absolute value is about 38°, sensibly greater than The value previously found for EB-DNA complexes.     

Changes in the patching and capping of insulin receptors under the influence of hormonal imprinting

Binding of fluorescein-isothiocyanate-(FITC)-labeled insulin was followed up in the function of time in Chang liver cells pretreated and not pretreated with insulin. The not pretreated cells showed patching, but no capping of the receptors during the period of study (60 min), whereas the insulin-pretreated cells showed indications of capping already after 10 min. Patching of the insulin receptors was particularly conspicuous at the sites of cell-cell contact (at the intercellular junctions). Supra-nuclear patching occurred earlier in the control cultures, and on it followed the fluorescence of the nuclear chromatin.     

Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity

The equilibrium and kinetic aspects of the interaction between four anthracyclines and two synthetic self-complementary hexanucleotides was investigated by fluorescence detection. Two of the studied anthracyclines are widely used antitumor drugs: doxorubicin (1, formerly adriamycin) and daunorubicin (2, formerly daunomycin). The other two, 9-deoxydoxorubicin (3) and 3'-deamino-3'-hydroxy-4'-epidoxorubicin (4), are doxorubicin analogues with modifications of the chemical groups that have been proposed as responsible for sequence specificity (Chen, K.-X., Gresh, N. and Pullman, B. (1985). J. Biomol. Struct. Dyn. 3, 445-466). One of the oligonucleotides, d(CGTACG), is identical to that used in the high resolution x-ray structure determination of the daunorubicin intercalative complex (Wang, A. H.-J., Ughetto, G., Quigley, G. J. & Rich, A. (1987). Biochemistry 26, 1152-1163). Binding to this hexanucleotide is compared with intercalation into the d(CGCGCG) duplex, revealing sequence preferences of the four anthracyclines. Taking into account the anthracycline aggregation and the dissociation of the hexanucleotide double standard form, results can be interpreted with a model that assumes complete fluorescence quenching at intercalative sites containing the CG base pair, and a large residual fluorescence after intercalation within the TpA fragment. All four anthracyclines show preferential intercalation at sites near the ends of both hexanucleotide duplexes, partly as a result of positive cooperativity in the formation of di-intercalated species at these sites. Within the limits of experimental error, complete site specificity for the CpG fragment is found in the intercalation of 1 and 2 into d(CGTACG) duplex, whereas analogues 3 and 4 give increasing evidence of intercalation at other sites including the fluorescence-preserving TpA fragment. Site specificity is less pronounced in the association with d(CGCGCG), when cooperativity is taken into account. Kinetic data corroborate the results of equilibrium studies and are interpreted with a mechanism that includes formation of an intermediate bound species followed by drug redistribution to preferential sites. Finally, from a comparison of pertinent site binding constants, approximate free energy contributions to sequence specific DNA interaction, due to C9-OH on the aglycone and -NH3+ on daunosamine, are estimated not to exceed 2 kcal/mol.     

Peritoneal resorption of ethidium bromide, free or linked to DNA in rodents]

Ethidium bromide, either free (EB) or bound to DNA (EB-DNA), is injected into the peritoneal cavity of adult rats or mice. EB is then detected by fluorescence microscopy in peritoneal cells and by spectrophotometry in the peritoneal fluid. EB-DNA persists for a longer period of time in the peritoneal cavity than free EB does.     

Effect of hepcidin on intracellular calcium in human osteoblasts

Hepcidin is known to increase intracellular iron through binding to and degrading ferroportin, which is a transmembrane protein that transports iron from the intracellular to the outside. However, it is not clear whether hepcidin has a similar effect on intracellular calcium. Here, we investigated the influence of hepcidin on intracellular calcium in human osteoblasts, with or without high environmental iron concentrations. Our data showed that hepcidin (<100 nmol/L) could increase intracellular calcium, and this effect was more significant when cells were exposed to high environmental iron concentrations. To further explore its underlying mechanisms, we pretreated human osteoblasts with Nimodipine, a L-type calcium channel blocker, and Dantrolene, a ryanodine receptor antagonist to inhibit abnormal calcium release from the sarco-endoplasmic reticulum. These treatments had not resulted in any alteration of intracellular calcium in human osteoblasts. Thus, these findings indicate that the increase of intracellular calcium induced by hepcidin is probably due to calcium release from endoplasmic reticulum, which is triggered by calcium influx.     

Changes in the patching and capping of insulin receptors under the influence of hormonal imprinting

Summary Binding of fluorescein-isothiocyanate-(FITC)-labeled insulin was followed up in the function of time in Chang liver cells pretreated and not pretreated with insulin. The not pretreated cells showed patching, but no capping of the receptors during the period of study (60 min), whereas the insulin-pretreated cells showed indications of capping already after 10 min. Patching of the insulin receptors was particularly conspicuous at the sites of cell-cell contact (at the intercellular junctions). Supra-nuclear patching occurred earlier in the control cultures, and on it followed the fluorescence of the nuclear chromatin.     

Studies related to antitumor antibiotics. Part V. Reactions of mitomycin C with DNA examined by ethidium fluorescence assay.

The cytotoxic action of the antitumor antibiotic mitomycin C occurs primarily at the level of DNA. Using highly sensitive fluorescence assays which depend on the enhancement of ethidium fluorescence only when it intercalates duplex regions of DNA, three aspects of mitomycin C action on DNA have been studied: (a) cross-linking events, (b) alkylation without necessarily cross-linking, and (c) strand breakage. Cross-linking of DNA is determined by the return of fluorescence after a heat denaturation step at alkaline pH's. Under these conditions denatured DNA gives no fluorescence. The cross-linking was independently confirmed by S1-endonuclease (EC 3.1.4.-) digestion. At relatively high concentrations of mitomycin the suppression of ethidium fluorescence enhancement was shown not to be due to depurination but rather to alkylation, as a result of losses in potential intercalation sites. A linear relationship exists between binding ratio for mitomycin and loss of fluorescence. The proportional decrease in fluorescence with pH strongly suggests that the alkylation is due to the aziridine moiety of the antibiotic under these conditions. A parallel increase in the rate and overall efficiency of covalent cross-linking of DNA with lower pH suggests that the cross-linking event, to which the primary cytotoxic action has been linked, occurs sequentially with alkylation by aziridine and then by carbamate. Mitomycin C, reduced chemically, was shown to induce single strand cleavage as well as monoaklylation and covalent cross-linking in PM2 covalently closed circular DNA. The inhibition of this cleavage by superoxide dismutase (EC 1.15.1.1) and catalase (EC 1.11.1.6), and by free radical scavengers suggests that the degradation of DNA observed to accompany the cytotoxic action of mitomycin C is largely due to the free radical O2. In contrast to the behavior of the antibiotic streptonigrin, mitomycin C does not inactivate the protective enzymes superoxide dismutase or catalase. Lastly, mitomycin C is able to cross-link DNA in the absence of reduction at pH 4. This is consistent with the postulated cross-linking mechansims.     

Conformational properties of human and rat apolipoprotein A-IV

Apolipoprotein A-IV has been isolated from four sources: human and rat lymph and plasma. Conformational properties of the rat and human apoA-IV in solution and denaturation changes induced by guanidine hydrochloride (Gnd X HCl) were studied using circular dichroic and fluorescence spectroscopy, and analytical sedimentation equilibrium ultracentrifugation. We have shown that both rat and human apoA-IV have similar secondary structure with negative maxima in the circular dichroic spectra at 222 nm and 207 nm. Furthermore, we have found no significant difference in the alpha-helical content of the apoA-IV from rat plasma (33%), rat lymph (37%), human plasma (35%), or human lymph (35%). Our denaturation studies with Gnd X HCl demonstrated reversibility and the fact that each apoA-IV had a tendency to self-associate in solution and the self-association could be disrupted by low concentrations of Gnd X HCl (less than or equal to 0.4 M). Unfolding of the secondary structure of each apoA-IV occurred at higher concentrations of Gnd X HCl (midpoint less than or equal to 1.0 M). The apparent free energy of denaturation of the four apoA-IV proteins calculated from changes in the circular dichroic spectra upon addition of increasing concentrations of Gnd X HCl varied in a range from 3.0 to 4.2 kcal/mol. The fluorescence experiments revealed that apoA-IV from all sources had a maximum fluorescence emission at 342.5 nm, which shifted to the red region upon addition of increasing concentrations of Gnd X HCl.(ABSTRACT TRUNCATED AT 250 WORDS)     

Binding domain for laminin on type IV collagen

Binding of type IV collagen to laminin was studied by attaching one member of the ligand pair to a solid phase. When laminin was bound to a solid phase, type IV collagen exhibited saturable binding. Digestion of type IV collagen with high concentrations of pepsin destroyed the laminin binding activity. Type IV collagen was also found to bind to fibronectin but the binding activity was not destroyed by pepsin treatment. Rotary shadowing electron microscopy of the pepsin digested type IV collagen indicated that the carboxy terminal end region of about 100 nm is cleaved. Rotary shadowing electron microscopy studies demonstrate that the carboxy terminal end of type IV collagen has a major laminin binding site.     

Ethidium bromide (EB) binding to nucleosomal DNA : Effects on DNA cleavage patterns

Binding of ethidium bromide (EB) to chromatin DNA induces structural changes in nucleosomes. The characteristic cleavage patterns of nucleosomal DNA after digestion with either micrococcal nuclease or pancreatic deoxyribonuclease are altered in the presence of the intercalating dye. Instead, apparently random digestion occurs. Polylysine reduces the amount of EB-binding sites in nucleosomal DNA. Since the intercalation of EB is known to proceed from the minor groove of DNA, polylysine supposedly occupies the same site of the nucleosomal DNA moiety.