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PubMed1975

X-ray crystallographic visualization of drug-nucleic acid intercalative binding: structure of an ethidium-dinucleoside monophosphate crystalline complex, Ethidium: 5-iodouridylyl (3'-5') adenosine.

We have cocrystallized the drug ethidium bromide with the dinucleoside monophosphate 5-iodouridylyl(3'-5')adenosine and have solved the three-dimensional structure to atomic resolution by x-ray crystallography. This has allowed the direct visualization of intercalative binding by this drug to a fragment of a nucleic acid double helix.

Adenine Nucleotides↗
PubMedDate not supplied

[On the quantitative fluorometric determination of cellular DNA by ethidium bromide and the constancy of the quantum yield of the ethidium DNA-complex in the biological environment (author's transl)].

The fluorescent staining of fixed A9 cells (mouse fibroblasts) with ethidium bromide E has been investigated qualitatively and quantitatively. E is bound to DNA, RNA and protein. After enzymatic RNA digestion and staining at pH = 4.0 the dyestuff is bound to DNA specifically. The formed E-DNA-complex is stoichiometric if DNA will be saturated by highdye concentration, CF = 1.0 x 10(-2) M. The stoichiometric factor n = 0.21 was determined from Scatchard binding isotherms and by spectrophotometric titration. The binding of E to DNA and RNA has been investigated by binding isotherms. E is bound to DNA by intercalation and by ionic interaction. It is bound to RNA by ionic interaction only. The ionically bound dyestuff can be replaced by salts like LiCl from DNA and RNA. Only intercalated E remains. The competitive salt effect can be used to avoid the enzymatic RNA digestion in the specific staining of DNA. Within the cell the E-DNA-complex fluoresces strongly. Using a microspectrophotometer we determined the fluorescence intensity J and the extinction E in cell sections of q = 1 mu 2 area. The fluorescence was excited in the minimum of the absorbance of the E-DNA complex at lambda 1 = 365 nm. The extinction E2 was measured in the short wavelength band lambda 2 = 260 nm. Under these conditions we received a linear relation J = J (E2) up to high extinctions E2. The quantum yield Q of the E-DNA-complex is nearly constant and independent of the biological environment. Q is also unaltered by LiCl. Within the limits of error intercalated and ionic bound dye have the same quantum yeild. Under the conditions of stoichiometric staining the amount of E-DNA-complex and therefore DNA in the cell can be determined by J. The extinction coefficient epsilon 2 = 45 200 M-1 cm-1 of the E-DNA-complex at 260 nm was calculated from the concentration of dependence of the absorbance spectra using the law of mass action. By epsilon 2 the amount of DNA in the cell is accessible from J. According to our measurements with A9 cells the superficial density of DNA has the order of magnitude rho N = mN/q = 10(1) nmol cm-2, the amount mN of DNA per section 1 = 1 mu 2, mN = 10(-1) fmol, and the DNA concentration in the cell nucleus CN = 10(-1) M. The ray pass and diagram of electronics of the based microspectrophotometer are described.

Animals↗
PubMed1987

Interaction of noncompetitive inhibitors with the acetylcholine receptor. The site specificity and spectroscopic properties of ethidium binding.

The spectroscopic properties and specificity of binding of a fluorescent quaternary amine, ethidium, with acetylcholine receptor-enriched membranes from Torpedo californica have been examined. Competition binding with [3H]phencyclidine in the presence of carbamylcholine showed that ethidium binds with high affinity to a noncompetitive inhibitor site (KD = 3.6 X 10(-7) M). However, in the presence of alpha-toxin, ethidium's affinity is substantially lower (KD approximately 1 X 10(-3) M). Ethidium was also found to enhance [3H]acetylcholine binding with a KD characteristic of ethidium binding to a high-affinity noncompetitive inhibitor site. These findings indicate that ethidium binds to an allosteric site which is regulated by agonist binding and can convert the agonist sites from low to high affinity. Fluorescence titrations of ethidium in the presence of carbamylcholine yielded a similar KD (2.5 X 10(-7) M) and showed an ethidium stoichiometry of one site/acetylcholine receptor monomer. Ethidium was completely displaced by noncompetitive inhibitors such as phencyclidine, histrionicotoxin, and dibucaine. The enhanced fluorescence lifetime of the bound species showed that the increased fluorescence intensity reflects a 13-fold increase in quantum yield for the complex compared to ethidium in buffer. Fractional dissociation of ethidium with phencyclidine produced a double-exponential fluorescence decay rate with lifetime components characteristic of ethidium free in solution and bound to the receptor. These data argue that the alterations in ethidium fluorescence elicited by other ligands is due to a change in the fraction of specifically bound ethidium rather than a change in quantum yield of a pre-existing ethidium-acetylcholine receptor complex. The extent of polarization indicates that bound ethidium is strongly immobilized. The magnitude of the quantum yield enhancement and the shifts of excitation and emission maxima of bound ethidium suggest that its binding site is within a hydrophobic domain with limited accessibility to the aqueous phase.

Acetylcholine↗
PubMed1980

Control and virus-transformed baby hamster kidney cells resistant to ethidium bromide. I. Characterization and the respiratory enzymes.

Cell lines resistant to ethidium bromide have been developed from cultured mammalian BHK21/C13 cells and these same cells transformed by Rous sarcoma virus (C13/B4). Cells resistant to 2 micrograms ethidium bromide per milliliter have been cloned. One clone of the control and one of the virus-transformed cell lines has been employed for characterization. The resistant cells, in the presence of 2 micrograms ethidium bromide/ml, grow at approximately the same rate as the untreated parental cells. The control cells possess a "normal" karyotype (44 chromosomes), while the corresponding ethidium bromide mutant has a reduced chromosome number of 41 and a number of translocations. The mitochondria displayed morphological alterations compared to the parental lines during the transition phase prior to the isolation of the ethidium bromide-resistant cells. The mitochondria of the ethidium bromide-resistant mutants appear somewhat enlarged with a normal morphology. The effect of ethidium bromide on selected respiratory enzymes in normal and virus-transformed ethidium bromide-resistant baby hamster kidney cells was determined. Ethidium bromide-resistant cells exhibited a depressed level of cytochrome aa3. This depression could not be reversed by growth in ethidium bromide-free media. Ethidium bromide-resistant cells possessed the same cytochrome b, c, and c1 levels per cell as their corresponding parental lines. Purified mitochondria isolated from virus-transformed ethidium bromide-resistant cells exhibited a depression in cytochrome oxidase-specific activity, while the ethidium bromide-resistant control cells did not. All cell lines studied showed a depression in NADH-ferricyanide and NADH-cytochrome c reductase-specific activities relative to their parental BHK21/C13 cells. No increase was observed in virus-transformed ethidium bromide-resistant cells. Ethidium bromide-resistant control cells exhibited a two-fold increase in oligomycin-insensitive adenosine triphosphatase activity relative to their parental cells. All of the cell lines studied possessed equivalent oligomycin-sensitive adenosine triphosphatase-specific activity except for the virus-transformed, dye-resistant mutant, whose activity was increased.

Adenosine Triphosphatases↗
PubMed1984

Effect of mutation, electric membrane potential, and metabolic inhibitors on the accessibility of nucleic acids to ethidium bromide in Escherichia coli cells.

The uptake of ethidium bromide by Escherichia coli K 12 cells has been studied by using 14C-labeled ethidium and spectrofluorometry on three E. coli strains: the first one (AB1157) has an ethidium-resistant phenotype; the second one derives from the first one after a single mutation (at 10 min on the E. coli genetic map) and has an ethidium-sensitive (Ebs) phenotype; the third one is the acrA strain which appeared to have the same phenotype as the Ebs strain. When the cells are in exponential growth, no ethidium enters wild-type cells, and a very limited amount of ethidium enters Ebs and acrA cells. Massive quantities of ethidium enter AB1157, Ebs, and acrA cells treated by uncouplers and respiring Ebs cells treated by the membrane ATPase-inhibitor dicyclohexylcarbodiimide. A small amount of ethidium enters cells treated in M9 succinate medium by metabolic inhibitors such as KCN or cells starved with oxygen in the same M9 medium. The amount of ethidium and ethidium dimer retained at equilibrium by either type of cell, and by cells infected by T5 phage, as well as the kinetics of influx and efflux, has been measured under a variety of situations (membrane energized or not, and/or membrane ATPase inhibited or not). Furthermore, it was shown that ethidium binds to both RNA and DNA when it enters CCCP-treated wild-type E. coli cells, whereas it binds mainly to DNA when it enters Ebs and acrA cells in exponential growth. As it will be discussed, it is difficult to account for the EthBr uptake by invoking only membrane functions and active transport. Therefore, it is proposed that the variations of the nucleic acid accessibility in E. coli cells might play a role in the control of this uptake. Accordingly, in ethidium-sensitive cells, the mutation would have caused a significant part of the chromosomal DNA (10-20%) to become accessible to ethidium. Hansen [Hansen M. T. (1982) Mutat. Res. 106, 209-216], after a study of the photobinding of psoralen to nucleic acids in the acrA mutant, also suggested that DNA environment was modified in acrA cells.

Cell Membrane↗
PubMed1992

Modulation of phencyclidine-sensitive ethidium binding to the Torpedo acetylcholine receptor: interaction of noncompetitive inhibitors with carbamylcholine and cobra alpha-toxin.

Ethidium is one of two fluorescent ligands known to bind to the noncompetitive inhibitor (NCI) site in the central ion channel of the Torpedo acetylcholine receptor with a micromolar dissociation constant. To further characterize heterotropic allosteric regulation of ligand binding in general, and of ethidium binding in particular, to the Torpedo receptor, we measured the effects of three liquid anesthetics (diethyl ether, halothane, and butanol), two barbiturates (secobarbital and thiamylal), and urethane. The phencyclidine-sensitive chromatic shift and the quantum yield increase associated with ethidium binding to the channel NCI site were used as indicators of ethidium binding. In the absence of other ligands, halothane, diethyl ether, and butanol increased the affinity of ethidium toward the channel NCI site to the same extent as carbamylcholine (400-600-fold), whereas the barbiturates and urethane were without effect. Cobra alpha-toxin blocked anesthetic-induced ethidium binding, confirming that cobra alpha-toxin stabilizes the AcChR in the resting-like state. In the presence of carbamylcholine, when ethidium was bound to the channel NCI site, several ligand-dependent effects were observed. 1) Without affecting further the affinity of ethidium for the NCI binding site, diethyl ether and halothane increased and butanol had no effect on the fluorescence emission of channel-bound ethidium. This indicated that there is little relation between the affinity and the quantum yield of the channel-bound ethidium. 2) Addition of secobarbital and thiamylal had no effect, beyond the effect of carbamylcholine, on ethidium binding to the channel NCI site, indicating that the barbiturates did not bind to the channel NCI site. 3) Urethane inhibited carbamylcholine-induced ethidium binding to the channel NCI binding site, suggesting direct interaction of urethane with the channel NCI binding site, at least when the receptor is in a desensitized state. The results confirm the conformational sensitivity of ethidium binding to the channel NCI binding site and demonstrate at least three different modes of action of anesthetics to inhibit the Torpedo receptor noncompetitively.

Anesthetics↗
PubMed1988

Ethidium bromide resistance in a rat liver epithelial cell line: association with enhanced drug efflux.

Ethidium bromide-resistant cell strains were obtained by continuous selection of an adult rat liver-derived cell line (ARL6T) grown in the continuous presence of 200 ng/ml ethidium bromide. Comparison of resistant strains and parental (sensitive) cells was made for uptake and binding of ethidium bromide, visualized as fluorescent ethidium bromide-nucleic acid complexes. Although uptake of ethidium bromide was similar in parental and resistant cells, efflux kinetics were markedly different. Over a three-hour period, parental (sensitive) cells maintained fluorescence following a short ethidium bromide pulse (100 micrograms/ml ethidium bromide). In contrast, ethidium bromide-resistant cell lines eliminated photographically detectable fluorescent complexes within three hours following pulse exposure to ethidium bromide. The rapid elimination of ethidium bromide-fluorescent complexes in all (5) resistant cell strains examined supports an efflux mechanism as contributing to the resistance of ethidium bromide cytotoxicity in these cells.

Animals↗
PubMed1991

Inhibition of the B to Z transition in poly(dGdC).poly(dGdC) by covalent attachment of ethidium: kinetic studies.

The photoaffinity analogue ethidium monoazide was used to prepare samples of poly(dGdC).poly(dGdC) containing covalently attached ethidium. The effects of both noncovalently and covalently bound ethidium on the kinetics of the NaCl-induced B to Z transition in poly(dGdC).poly(dGdC) was examined using absorbance and fluorescence spectroscopy to monitor the reaction. Covalently and noncovalently attached ethidium were equal in the extent to which they reduce the rate of the B to Z transition. By using fluorescence to selectively monitor the fate of noncovalently bound ethidium over the course of the transition, we found that ethidium completely dissociates as the reaction proceeds, but at a rate that lags behind the conversion of the polymer to the Z form. These experiments provide evidence for the redistribution of noncovalently bound ethidium over the course of the B to Z transition, leading to the development of biphasic reaction kinetics. The observed kinetics suggest that the primary effect of both covalently and noncovalently bound ethidium is on the nucleation step of the B to Z transition. The reduction in the rate of the B to Z transition by noncovalently or covalently bound ethidium may be quantitatively explained as resulting from the reduced probability of finding a drug-free length of helix long enough for nucleation to occur. As necessary ancillary experiments, the defined length deoxyoligonucleotides (dGdC)4, (dGdC)5, and (dGdC)6 were synthesized and used in kinetic experiments designed to determine the nucleation length of the B to Z transition, which was found to be 6 bp. The activation energy of the B to Z transition was demonstrated to be independent of the amount of covalently bound ethidium and was found to be 21.2 +/- 1.1 kcal mol-1. Covalent attachment of ethidium was observed to increase the rate of the reverse Z to B transition, presumably by locking regions of the polymer into a right-handed conformation and thereby providing nucleation sites from which the Z to B conversion may propagate.

Affinity Labels↗
PubMed1993

Quinacrine and ethidium bind to different loci on the Torpedo acetylcholine receptor.

Fluorescence spectroscopy was used to determine whether quinacrine and ethidium, two high-affinity noncompetitive inhibitors of the Torpedo acetylcholine receptor (AcChR), bind to the same loci. The ability of three nitroxide spin-labels, 5-doxylstearate (5-SAL), spin-labeled androstane (ASL), and TEMPO, to quench receptor-bound quinacrine and ethidium fluorescence was measured. When bound to a phencyclidine-displaceable site on the AcChR, quinacrine was 16.9 and 19 times more efficiently quenched than ethidium by the highly lipophilic 5-SAL and ASL, respectively. TEMPO, which has a limited ability to partition into Torpedo plasma membranes (< 1%), was only twice as efficient at quenching receptor-bound quinacrine than ethidium fluorescence. The relative sensitivity of quinacrine and ethidium fluorescence to paramagnetic quenching was examined in three solvents, 1-butanol, sodium phosphate buffer, and acetonitrile, with TEMPO as a quencher. The results from the different solvents demonstrate that quinacrine fluorescence is intrinsically 1.4-3.6 times more sensitive than ethidium fluorescence to quenching by nitroxide spin-labels. Examination of the effect of high concentrations of 5-SAL on ethidium and quinacrine dissociation constants showed that quinacrine but not ethidium binding was competitively inhibited. Together, these results indicate that although quinacrine and ethidium bind in a mutually exclusive manner, the two inhibitors interact at different loci on the AcChR. Whereas the ethidium binding site is at a distance from membrane lipids, probably in or near the lumen, the quinacrine binding site appears to be at a lipid-protein interface in the transmembrane domain and at a distance from the lumen.

Animals↗
PubMed1975

The binding of polyamines and of ethidium bromide to tRNA.

The binding of spermidine and ethidium bromide to mixed tRNA and phenylalanine tRNA has been studied under equilibrium conditions. The numbers and classes of binding sites obtained have been compared to those found in complexes isolated by gel filtration a low ionic strength. The latter complexes contain 10-11 moles of either spermidine or ethidium per mole of tRNA; either cation is completely displaceable by the other. In ethidium complexes, the first 2-3 moles are bound in fluorescent binding sites; the remaining 7-8 molecules bind in non-fluorescent form. At least one of the binding sites for spermidine appears similar to a binding site for fluorescent ethidium. Similar results are found with E. coli formylmethionine tRNA. Spermine, in excess of 18-20 moles per mole tRNA, causes precipitation of the complex. Putrescine does not form isolable complexes with yeast tRNA and displaces ethidium less readily from preformed ethidium-tRNA complexes. Under equilibrium conditions, in the absence of Mg++, there are 16-17 moles of spermidine bound per mole of tRNA as determined by equilibrium dialysis. Of these, 2-3 bind with a Ksence of 9 mM Mg++, the total number of binding sites is decreased slightly and there appears to be only one class of sites with a Ka = 600 M(-1). Quantitatively similar results are obtained for the binding of spermidine to yeast phenylalanine tRNA. When the interaction between ethidium bromide and mixed tRNA is studied by equilibrium dialysis or spectrophotometric titration, two classes of binding sites are obtained: 2-3 molecules bind with an average Ka = 6.6 x 10(5) M(-1) and 14-15 molecules bind with an average Ka = 4.1 x 10(4) M(-1). Spermidine, spermine, and Mg++ compete effectively for both classes of ethidium sites and have the effect of reducing the apparent binding constants for ethidium. When the binding of ethidium is studied by fluorometry, there are 3-4 highly fluorescent sites per tRNA. These sites are also affected by spermidine, spermine and Mg++. Putrescine has little effect on any of the classes of binding sites. These data are consistent with those found under non-equilibrium conditions. They suggest that polyamines bind to fairly specific regions of tRNA and may be involved in the maintenance of certain structural features of tRNA.

Binding Sites↗