Propidium: induction of petites and recovery from ethidium mutagenesis in Saccharomyces cerevisiae.

It was shown that petite induction in growing cells of $\text{Saccharomyces}$$\text{cerevisiae}$ by ethidium was strongly stimulated by the presence of propidium, a phenanthridinium dye of similar structure to ethidium. Propidium itself also induced petites in growing but not in resting cells. Furthermore, propidium could prevent petite induction in resting cells and caused recovery from ethidium induction with prolonged incubation. A possible mode of action of propidium in the ethidium-induced petite mutagenesis is discussed.     

The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site

Ehrlich's pioneering chemotherapeutic experiments published in 1904 (Ehrlich, P., and Shiga, K. (1904) Berlin Klin. Wochenschrift 20, 329-362) described the efficacy of a series of dye molecules including trypan blue and trypan red to eliminate trypanosome infections in mice. The molecular structures of the dyes provided a starting point for the synthesis of suramin, which was developed and used as a trypanocidal drug in 1916 and is still in clinical use. Despite the biological importance of these dye-like molecules, the mode of action on trypanosomes has remained elusive. Here we present crystal structures of suramin and three related dyes in complex with pyruvate kinases from Leishmania mexicana or from Trypanosoma cruzi. The phenyl sulfonate groups of all four molecules (suramin, Ponceau S, acid blue 80, and benzothiazole-2,5-disulfonic acid) bind in the position of ADP/ATP at the active sites of the pyruvate kinases (PYKs). The binding positions in the two different trypanosomatid PYKs are nearly identical. We show that suramin competitively inhibits PYKs from humans (muscle, tumor, and liver isoenzymes, K(i) = 1.1-17 μM), T. cruzi (K(i) = 108 μM), and L. mexicana (K(i) = 116 μM), all of which have similar active sites. Synergistic effects were observed when examining suramin inhibition in the presence of an allosteric effector molecule, whereby IC(50) values decreased up to 2-fold for both trypanosomatid and human PYKs. These kinetic and structural analyses provide insight into the promiscuous inhibition observed for suramin and into the mode of action of the dye-like molecules used in Ehrlich's original experiments.     

Inhibition of cation-induced DNA condensation by intercalating dyes

Several intercalating dyes are shown to inhibit the cation-induced condensation of λ-DNA when Co³⁺(NH₃)₆ is the condensing agent. The dyes that have been studied are ethidium, propidium, proflavin, quinacrine, and actinomycin D. Earlier work has shown that intercalating dyes inhibit ψ-DNA condensation. [Lerman, L. S. (1971) Prog. Mol. Subcell. Biol. 2 , 382–391; Cheng, S. & Mohr, S. C. (1975) Biopolymers 14 , 663–674.] Dye-induced decondensation of intramolecularly condensed DNA has been studied by making use of conditions in which Co³⁺(NH₃)₆ produces intramolecular condensation without significant aggregation. Some aggregation is caused, however, during dye-induced decondensation. Dye titration curves of DNA decondensation have been measured by excess light scattering to monitor decondensation and by fluorescence to monitor intercalation. All of the dyes studied act as competing cations in displacing the condensing cation Co³⁺(NH₃)₆ from the DNA. Competition occurs both in and below the transition zone for condensation. The effectiveness of a dye as a competing cation increases with its net positive charge. Before decondensation begins, no intercalated dye can be detected, suggesting that intercalation might be incompatible with the proper helix packing needed for cation-induced DNA condensation. To test this last point, methidium–spermine was synthesized: it contains an intercalating methidium head group combined with a polyamine tail. Methidium–spermine is found to cause λ-DNA condensation, but aggregation accompanies condensation, as has been found earlier for spermine and spermidine. Fluorescence and absorption spectra indicate that the methidium group is intercalated when the DNA is condensed, indicating that intercalation need not be incompatible with DNA condensation. The presence of aggregates among the condensed DNA molecules makes this last conclusion tentative.     

Effects of ethidium bromide and berenil on protein synthesis

The effects of ethidium bromide, an intercalating dye and berenil, a nonintercalating dye on the biological activities ofEscherichia coli ribosomes have been studied. Ethidium bromide treatment drastically reduced both enzymatic and nonenzymatic initiation complex formation, enzymatic as well as nonenzymatic binding of phenylalanyl tRNA, peptidyl transferase, GTPase as well as the overall protein synthesising activity as measured by the poly U-dependent polymerization of phenylalanine. On berenil treatment, however, only enzymatic formation of the initiation complex is marginally reduced. Other reactions are not markedly affected except the enzymatic phenylalanyl tRNA binding which is slightly decreased only at high Mg²⁺ concentration; the treated ribosome has lowered polymerizing activity at sub-optimal Mg²⁺ concentration (10 mM). Although it has already been shown in this laboratory that treatment with either dye leads to the unfolding of the structure of the ribosome, the present studies indicate that berenil treatment does not alter the structure of the ribosome drastically in contrast to ethidium bromide treatment.     

Decolorization of sulfonated azo dyes with two photosynthetic bacterial strains and a genetically engineered Escherichia coli strain

Sulfonated azo dyes were decolorized by two wild type photosynthetic bacterial (PSB) strains (Rhodobacter sphaeroides AS1.1737 and Rhodopseudomonas palustris AS1.2352) and a recombinant strain (Escherichia coli YB). The effects of environmental factors (dissolved oxygen, pH and temperature) on decolorization were investigated. All the strains could decolorize azo dye up to 900 mg l⁻¹, and the correlations between the specific decolorization rate and dye concentration could be described by Michaelis–Menten kinetics. Repeated batch operations were performed to study the persistence and stability of bacterial decolorization. Mixed azo dyes were also decolorized by the two PSB strains. Azoreductase was overexpressed in E. coli YB; however, the two PSB strains were better decolorizers for sulfonated azo dyes.     

Binding of bifunctional ethidium intercalators to transfer RNA

Two bifunctional intercalating dimers, an ethidium homodimer and an acridine ethidium heterodimer, bind to yeast tRNA^phe through two classes of sites, I and II (K_I ≥ 10⁹ M^?1, K_II ～ 10⁶ M^?1), as indicated by fluorescence titration, fluorescence lifetime, “contact” energy transfer and equilibrium dialysis measurements. Binding appears to involve mono-intercalation of the phenanthridinium moiety of these dimers and it is sensitive to, or possibly coupled with, conformational changes within the tRNA macromolecule. These observations raise the possibility that tRNA may represent a pharmacological target of the bifunctional intercalators.     

Antagonism by propidium of petite induction by ethidium and ethidium azide in Saccharomyces cerevisiae.

Propidium, a phenanthridinium dye similar to ethidium, did not induce petite mutations in non-growing yeast cells in contrast to ethidium. Combined exposure to ethidium and an excess of propidium for periods up to 2 h resulted in the expected petite induction expressed after subsequent plating on growth medium. As incubation was continued with propidium, the numbers of petites declined on subsequent plating whether the drug had been added before, during, or after the mutagenic treatment by ethidium. Propidium decreased petite induction by the monoazide analog of ethidium when applied before but not after photolytic attachment of the drug.     

Electrical potential changes in the surface and the central region of chromatophore membranes of photosynthetic bacteria detected by the absorbance changes of ethidium and carotenoid

(1) Changes of local intramembrane electrical field in the surface and central region of the chromatophore membrane during energization were studied both by the measurement of absorbance changes of ethidium, a monovalent cationic dye, and of carotenoid, the intrinsic probe of electrical field. (2) Binding of ethidium to the chromatophore membrane of Rhodopseudomonas sphaeroides was found to be dependent on the energization of membrane as well as on the ionic condition of the medium. The dye was released from the membrane when salt was added to the suspension, indicating the electrostatic interaction between the positive dye and the net negative membrane surface. The result was explained by the surface-potential dependent distribution of the dye to the membrane surface, as seen with other charged dyes (Masamoto, K., Matsuura, K., Itoh, S. and Nishimura, M. (1981) Biophys. Acta 638, 108–115). (3) Energization of chromatophores by flash-light-induced absorbance change of ethidium showing a similar difference spectrum to that induced by the addition of salts. The release of ethidium by a single turn-over flash of saturating intensity was estimated to be 0.22 ethidium per reaction center. Addition of ethidium (at 200 μM) slightly affected the flash-induced absorbance change of carotenoid which responds to the intramembrane electricalfield change, indicating a low-membrane permeability of the dye. The extent of the absorbance change of ethidium was linear to that of carotenoid, and was abolished in the presence of valinomycin plus K⁺. However, the rise and decay kinetics of the absorbance change of ethidium was different from that of carotenoid. (4) These absorbance changes of ethidium and carotenoid can be explained by a model in which ethidium responds to the potential changes in the surface region and carotenoid in the central hydrophobic region of the chromatophore membrane.     

Brazilwood,sappanwood, brazilin and the red dye brazilein: from textile dyeing and folk medicine to biological staining and musical instruments

Abstract

Brazilin is a nearly colorless dye precursor obtained from the heartwood of several species of trees including brazilwood from Brazil, sappanwood from Asia and the Pacific islands, and to a minor extent from two other species in Central America, northern South America and the Caribbean islands. Its use as a dyeing agent and medicinal in Asia was recorded in the 2^nd century BC, but was little known in Europe until the 12^th century AD. Asian supplies were replaced in the 16^th century AD after the Portuguese discovered vast quantities of trees in what is now Brazil. Overexploitation decimated the brazilwood population to the extent that it never fully recovered. Extensive environmental efforts currently are underway to re-create a viable, sustainable population. Brazilin is structurally similar to the better known hematoxylin, thus is readily oxidized to a colored dye, brazilein, which behaves like hematein. Attachment of the dye to fabric is by hydrogen bonding or in conjunction with certain metallic mordants by coordinative bonding. For histology, most staining procedures involve aluminum (brazalum) for staining nuclei. In addition to textile dyeing and histological staining, brazilin and brazilein have been and still are used extensively in Asian folk medicine to treat a wide variety of disorders. Recent pharmacological studies for the most part have established a scientific basis for these uses and in many cases have elucidated the biochemical pathways involved. The principal use of brazilwood today is for the manufacture of bows for violins and other stringed musical instruments. The dye and other physical properties of the wood combine to produce bows of unsurpassed tonal quality.     

Molecular determinants for DNA minor groove recognition: design of a bis-guanidinium derivative of ethidium that is highly selective for AT-rich DNA sequences

The phenanthridinium dye ethidium bromide is a prototypical DNA intercalating agent. For decades, this anti-trypanosomal agent has been known to intercalate into nucleic acids, with little preference for particular sequences. Only polydA-polydT tracts are relatively refractory to ethidium intercalation. In an effort to tune the sequence selectivity of known DNA binding agents, we report here the synthesis and detailed characterization of the mode of binding to DNA of a novel ethidium derivative possessing two guanidinium groups at positions 3 and 8. This compound, DB950, binds to DNA much more tightly than ethidium and exhibits distinct DNA-dependent absorption and fluorescence properties. The study of the mode of binding to DNA by means of circular and electric linear dichroism revealed that, unlike ethidium, DB950 forms minor groove complexes with AT sequences. Accurate quantification of binding affinities by surface plasmon resonance using A(n)T(n) hairpin oligomer indicated that the interaction of DB950 is over 10-50 times stronger than that of ethidium and comparable to that of the known minor groove binder furamidine. DB950 interacts weakly with GC sites by intercalation. DNase I footprinting experiments performed with different DNA fragments established that DB950 presents a pronounced selectivity for AT-rich sites, identical with that of furamidine. The replacement of the amino groups of ethidium with guanidinium groups has resulted in a marked gain of both affinity and sequence selectivity. DB950 provides protection against DNase I cleavage at AT-containing sites which frequently correspond to regions of enhanced cleavage in the presence of ethidium. Although DB950 maintains a planar phenanthridinium chromophore, the compound no longer intercalates at AT sites. The guanidinium groups of DB950, just like the amidinium group of furamidine (DB75), are the critical determinants for recognition of AT binding sites in DNA. The chemical modulation of the ethidium exocyclic amines is a profitable option to tune the nucleic acid recognition properties of phenylphenanthridinium dyes.     

Maitotoxin-induced membrane blebbing and cell death in bovine aortic endothelial cells

Background

Maitotoxin, a potent cytolytic agent, causes an increase in cytosolic free Ca²⁺ concentration ([Ca²⁺]_i) via activation of Ca²⁺-permeable, non-selective cation channels (CaNSC). Channel activation is followed by formation of large endogenous pores that allow ethidium and propidium-based vital dyes to enter the cell. Although activation of these cytolytic/oncotic pores, or COP, precedes release of lactate dehydrogenase, an indication of oncotic cell death, the relationship between CaNSC, COP, membrane lysis, and the associated changes in cell morphology has not been clearly defined. In the present study, the effect maitotoxin on [Ca²⁺]_i, vital dye uptake, lactate dehydrogenase release, and membrane blebbing was examined in bovine aortic endothelial cells.

Results

Maitotoxin produced a concentration-dependent increase in [Ca²⁺]_i followed by a biphasic uptake of ethidium. Comparison of ethidium (M_w 314 Da), YO-PRO-1 (M_w 375 Da), and POPO-3 (M_w 715 Da) showed that the rate of dye uptake during the first phase was inversely proportional to molecular weight, whereas the second phase appeared to be all-or-nothing. The second phase of dye uptake correlated in time with the release of lactate dehydrogenase. Uptake of vital dyes at the single cell level, determined by time-lapse videomicroscopy, was also biphasic. The first phase was associated with formation of small membrane blebs, whereas the second phase was associated with dramatic bleb dilation.

Conclusions

These results suggest that maitotoxin-induced Ca²⁺ influx in bovine aortic endothelial cells is followed by activation of COP. COP formation is associated with controlled membrane blebbing which ultimately gives rise to uncontrolled bleb dilation, lactate dehydrogenase release, and oncotic cell death.     

Flow dichroism of capsid DNA phages. II. Effect of DNA deletions and intercalating dyes

The flow linear dichroism of bacteriophage λ and its deletion mutants, λ b2 and λ b221, was determined. The hydrodynamic behavior of the three phages differed slightly, but the magnitude of the dichroism was substantially the same with 〈cos²θ_μp〉 = 0.364, 0.368, and 0.372, respectively. The dichroism of intercalating dyes combined with bacteriophage was used as a further probe of phage structure. The reduced dichroism from proflavin with T4 showed no change with time during the reaction, but the interpretation of the ligand dichroism is complicated by an alteration of the hydrodynamic behavior of the phage–dye complex relative to the phage alone. Ethidium with λ also produced a stable reduced dichroism, but the signal indicated an average orientation of intercalated dye that is different from the average base orientation. The reduced dichroism of ethidium changes with time as it penetrates λ b2, eventually approaching the dichroism of the nucleotide bases. The implication of these findings on the plausibility of various simple DNA packing models is discussed.     

Ethidium and azidoethidium oligonucleotide derivatives: Synthesis,complementary complex formation and sequence-specific photomodification of the single-stranded and double-stranded target oligo- and polynucleotides

Oligodeoxyribonucleotide derivatives containing ethidium or azidoethidium residues attached to 3′ and/or 5′ end were prepared. These derivatives formed tight specific complexes with complementary oligodeoxyribonucleotides where each attached ethidium residue led to an increase of complex T_m by 20–30°C. Tandem complexes of two oligodeoxyribonucleotides containing ethidium residues with an oligodeoxyribonucleotide having two adjacent complementary sequences for these Oligonucleotide were investigated. Photoinduced reactions of a number of ethidium and azidoethidium oligodeoxyribonucleotide derivatives with target complementary single-stranded and double-stranded oligo- and polydeoxyribonucleotides were investigated. The irradiation led to direct photocleavage of the target oligo- or polynucleotide, to formation of hidden (piperidine cleavable) modifications of the target of formation of covalent adducts between ethidium oligodeoxyribonucleotide derivative and the target. In a number of experiments, azidoethidium dyes were demonstrated to be considerably stronger photosensitizers than ethidium ones. Depending on the nature of the target (single- or double-stranded DNA) and on the irradiation conditions, the total damages to the target oligo- or polydeoxyribonucleotides ranged from 10–70% (for ethidium dyes) to 30–80% (for azidoethidium dyes).     

Stacking interactions of ethidium bromide bound to a polyphosphate and phage DNA in situ

Ethidium bromide forms spectroscopically detectable aggregates in aqueous solution and at a high dye concentration larger than 1 × 10^?3 moles/ρ. At moderate concentration in the order of 1 × 10^?4 moles/ρ the dye interacts with inorganic polyphosphate Graham salt and with phage sd DNA in situ by formation of stacking complexes. Maximal stacking was found at a phosphate to dye ratio, P/D, of approximately 1 for Graham salt and 1.5–2 for phages. In going to a higher P/D ratio Graham salt dye complex dissociates again and free dye reappears, while phage dye binding changes from stacking (type II complex) to intercalation (type I complex). Stacking is accompanied by a decrease and intercalation by an increase of relative fluorescence intensity with respect to free dye. However, both binding types lead to hypechromism and a red shift of the dye absorption band in the visible spectral region. Thus spectral behavior of ethidium aggregates deviate clearly from that known for other dyes, i.e., acridines.     

The use of dyes in modern biomedicine

The discovery of the aniline dyes in the 19th century and contemporary investigation of their use as biological stains by scientists such as Koch and Ehrlich led to the idea of selectivity and formed the basis of modern chemotherapy; several of these dyes remain in pharmacopoeias. While the development of therapeutics has tended to avoid colored compounds due to unwanted coloration, the modern application of photosensitizing dyes, both in the fields of cancer therapy and anti-infection, depends on this phenomenon. In addition, the fluorescence of some anticancer photosensitizers allows their use as tumor localizing agents, which is particularly useful in precancerous conditions. It is also fitting that dyes employed in Ehrlich's original studies, such as the phenothiazinium dye, methylene blue, are now in clinical use for disinfecting donated blood products.     

The use of dyes in modern biomedicine

The discovery of the aniline dyes in the 19th century and contemporary investigation of their use as biological stains by scientists such as Koch and Ehrlich led to the idea of selectivity and formed the basis of modern chemotherapy; several of these dyes remain in pharmacopoeias. While the development of therapeutics has tended to avoid colored compounds due to unwanted coloration, the modern application of photosensitizing dyes, both in the fields of cancer therapy and anti-infection, depends on this phenomenon. In addition, the fluorescence of some anticancer photosensitizers allows their use as tumor localizing agents, which is particularly useful in precancerous conditions. It is also fitting that dyes employed in Ehrlich's original studies, such as the phenothiazinium dye, methylene blue, are now in clinical use for disinfecting donated blood products.     

The use of dyes in modern biomedicine.

The discovery of the aniline dyes in the 19th century and contemporary investigation of their use as biological stains by scientists such as Koch and Ehrlich led to the idea of selectivity and formed the basis of modern chemotherapy; several of these dyes remain in pharmacopoeias. While the development of therapeutics has tended to avoid colored compounds due to unwanted coloration, the modern application of photosensitizing dyes, both in the fields of cancer therapy and anti-infection, depends on this phenomenon. In addition, the fluorescence of some anticancer photosensitizers allows their use as tumor localizing agents, which is particularly useful in precancerous conditions. It is also fitting that dyes employed in Ehrlich's original studies, such as the phenothiazinium dye, methylene blue, are now in clinical use for disinfecting donated blood products.     

Optimized Staining and Proliferation Modeling Methods for Cell Division Monitoring using Cell Tracking Dyes

Fluorescent cell tracking dyes, in combination with flow and image cytometry, are powerful tools with which to study the interactions and fates of different cell types in vitro and in vivo .^1-5 Although there are literally thousands of publications using such dyes, some of the most commonly encountered cell tracking applications include monitoring of:

1. stem and progenitor cell quiescence, proliferation and/or differentiation^6-8
2. antigen-driven membrane transfer⁹ and/or precursor cell proliferation^3,4,10-18 and
3. immune regulatory and effector cell function^1,18-21.

Commercially available cell tracking dyes vary widely in their chemistries and fluorescence properties but the great majority fall into one of two classes based on their mechanism of cell labeling. "Membrane dyes", typified by PKH26, are highly lipophilic dyes that partition stably but non-covalently into cell membranes^1,2,11. "Protein dyes", typified by CFSE, are amino-reactive dyes that form stable covalent bonds with cell proteins^4,16,18. Each class has its own advantages and limitations. The key to their successful use, particularly in multicolor studies where multiple dyes are used to track different cell types, is therefore to understand the critical issues enabling optimal use of each class^2-4,16,18,24.The protocols included here highlight three common causes of poor or variable results when using cell-tracking dyes. These are:

1. Failure to achieve bright, uniform, reproducible labeling . This is a necessary starting point for any cell tracking study but requires attention to different variables when using membrane dyes than when using protein dyes or equilibrium binding reagents such as antibodies.
2. Suboptimal fluorochrome combinations and/or failure to include critical compensation controls . Tracking dye fluorescence is typically 10² - 10³ times brighter than antibody fluorescence. It is therefore essential to verify that the presence of tracking dye does not compromise the ability to detect other probes being used.
3. Failure to obtain a good fit with peak modeling software . Such software allows quantitative comparison of proliferative responses across different populations or stimuli based on precursor frequency or other metrics. Obtaining a good fit, however, requires exclusion of dead/dying cells that can distort dye dilution profiles and matching of the assumptions underlying the model with characteristics of the observed dye dilution profile.

Examples given here illustrate how these variables can affect results when using membrane and/or protein dyes to monitor cell proliferation.     

A study on the utility of immobilized cells of indigenous bacteria for biodegradation of reactive azo dyes

Abstract

Azo dyes are recalcitrant compounds used as a colorant in various industries. The pollution caused by their extensive usage has adversely affected the environment for years. The existing physicochemical methods for dye pollution remediation are rather inefficient and hence there is a dearth of low-cost, potential systems capable of dye degradation. The current research studies the biodegradation potential of immobilized bacterial cells against azo dyes Reactive Orange 16 (RO-16) and Reactive Blue 250 (RB-250). Two indigenous dye degrading bacteria Bacillus sp. VITAKB20 and Lysinibacillus sp. KPB6 was isolated from textile sludge sample. Free cells of Bacillus. sp. VITAKB20 degraded 92.38% of RO-16 and that of Lysinibacillus sp. KPB6 degraded 95.36% of RB-250 within 72?h under static conditions. Upon immobilization with calcium alginate, dye degradation occurred rapidly. Bacillus. sp. VITAKB20 degraded 97.5% of RO-16 and Lysinibacillus sp. KPB6 degraded 98.2% of RB-250 within 48?h under shaking conditions. Further, the nature of dye decolorization was biodegradation as evident by high-performance liquid chromatography (HPLC), and Fourier-transform infrared spectroscopy (FTIR) results. Phytotoxicity and biotoxicity assays revealed that the degraded dye products were less toxic in nature than the pure dyes. Thus, immobilization proved to be a highly likely alternative treatment for dye removal.     

Evidence on manganese peroxidase and tyrosinase expression during decolorization of textile industry dyes by Trichosporon akiyoshidainum

Textile dyes are engineered to be resistant to environmental conditions. During recent years the treatment of textile dye effluents has been the focus of significant research because of the potentially low cost of the process. Mechanisms of biological textile dye decolorization depend greatly on the chemical structure of the dye and the microorganisms used. While basidiomycetous filamentous fungi are well recognized for dye decolorization through ligninolytic enzymes, reports on textile dye decolorization mechanisms of basidiomycetous yeasts have been scarce. Decolorization of several textile dyes by Trichosporon akiyoshidainum occurs during the first 12 h of cultivation. This fast decolorization process could not be solely related to siderophore production or dye sorption to biomass; it was shown to be a co-metabolic process. T. akiyoshidainum could use glucose, sucrose, and maltose as alternative carbon sources, and urea as an alternative nitrogen source with similar decolorization rates. The activity of two enzymes, manganese peroxidase and tyrosinase, were induced by the presence of dyes in the culture media, pointing to their potential role during the decolorization process. Manganese peroxidase titers reached 666 U l⁻¹ to 10538 U l⁻¹, while tyrosinase titers ranged between 84 U l⁻¹ and 786 U l⁻¹, depending on the dye tested. The present work provides a useful background to propose new eco-friendly alternatives for wastewater treatment in textile dying industries.