Mechanism of ethidium bromide inhibition of RNA polymerase

The effect of ethidium bromide on various steps of the reaction catalyzed by Escherichia coli DNA-dependent RNA polymerase is studied. Inhibition caused by low levels (approx. 6 μm) of this DNA-binding drug is a consequence of reducing the rate of RNA chain initiation; the rate of RNA chain growth is unaffected at this concentration. The sensitive step in the initiation process is the formation of stable complexes between RNA polymerase and initiation sites on the DNA. At higher levels (25 μm), ethidium bromide does inhibit the polymerization of those RNA molecules whose initiation has not been blocked.     

Mechanism of ethidium bromide inhibition of RNA polymerase.

2-Oxo-3-phenyl-1,3-oxazetidine was found to thermally undergo a 2,2-cyclo-reversion reaction with an enthalpy of activation of 30.8 Kcal. This suggests that an oxazetidine fused to a flavin could be the labile light producing intermediate in the bacterial luciferase reaction since the reaction would be favored by ring fusion and the lower excited state of flavin.     

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.     

Determination of membrane-bound chloroplast RNA by the ethidium bromide fluorometric method

The method of El-Hamalawi et al. [(1975) Anal. Biochem.67, 384–391] for the fluorometric determination of nucleic acids with ethidium bromide has been adapted for the assay of membrane-associated chloroplast RNA. Membranes are stripped of RNA by incubation in a high-salt buffer lacking Mg²⁺, and the RNA is collected by magnesium phosphate-ethanol coprecipitation. RNA levels are determined by measuring the degree of enhancement of ethidium bromide fluorescence.     

Fluorometric determination of DNA and RNA in Chlamydomonas using ethidium bromide

By using the fluorescence enhancement of ethidium bromide bound to nuclei acid, a very rapid, simple and sensitive assay of DNA in the green alga Chlamydomonas has been devised. Total fluorescence (DNA + RNA) was determined by complex formation with ethidium bromide in a cell lysate made by mixing cell samples with lauroyl sarcosinate, EDTA and NaOH and incubating the mixture for 5 min at room temperature followed by neutralization. For determination of DNA the RNA was digested by incubating the cell sample in te alkaline lysis solution for 45 min at 60 degrees C followed by neutralization, and complex formation with ethidium bromide. Quenching of the fluorescence due to cellular pigments was corrected for using an internal DNA standard.     

Study of complexes of ethidium bromide with DNA by differential pulse voltammetry

The interaction of ethidium bromide with calf thymus DNA was investigated by the method of differential pulse voltammetry. It was found that ethidium bromide binds with DNA in several ways. Corresponding values of the constants and the number of binding sites were determined. The intercalation, semi-intercalation, and electrostatic mechanisms of interaction were shown. The results obtained are in good agreement with the data obtained by spectroscopic (absorption and fluorimetric) methods.     

The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide

Eilatin-containing ruthenium complexes bind to a broad range of different nucleic acids including: calf thymus (CT) DNA, tRNA(Phe), polymeric RNAs and DNAs, and viral RNAs including the HIV-1 RRE and TAR. The nucleic acid specificity of Lambda- and Delta-[Ru(bpy)2eilatin]2+ have been compared to that of the 'free' eilatin ligand, and to the classic intercalating agent ethidium bromide. Interestingly, all four compounds appear to bind to nucleic acids by intercalation, but the trends in nucleic acid binding specificity are highly diverse. Unlike ethidium bromide, both eilatin and the eilatin-containing coordination complexes bind to certain single-stranded RNAs with high affinity (K(d) < or = 1 microM). Eilatin itself is selective for electron-poor polymeric purines, while the eilatin-coordination complexes exhibit preference for the polypyrimidine r(U). These results show how the binding specificity of an intercalating ligand can change upon its incorporation into an octahedral metal complex.     

Location and molecular characteristics of fluorescent complexes of ethidium bromide in the cell

Ethidium bromide is taken up rapidly by bovine kidney cells and yeast. This compound complexes specifically with nucleic acids. Its fluorescence is thereby increased, and characteristic properties of the fluorescence such as polarization, excitation spectrum and decay time depend on the type of nucleic acid and its molecular environment. These characteristics have been measured in ethidium-labeled cells. Polarization values from 0.30 to 0.36 and decay times from 17 to 23 nsec have been found for different cells and conditions. Fluorescence from the cells is characteristic of RNA with intercalated EB. Different fluorescence characteristics are found, depending on the complexing of ethidium with free RNA, RNA in ribosomes or associated with the cell membrane.     

CD of ethidium bromide complexes with normal and electrophoretically anomalous DNA restriction fragments

The equilibrium binding of ethidium bromide (EB) to two small 147 base-pair (bp) DNA restriction fragments, which exhibit different mobilities in polyacrylamide gels, was investigated by CD. Two larger DNA restriction fragments and calf thymus DNA were also studied for comparison. Difference spectra were calculated by subtracting the spectrum of the pure DNA from the spectra of its DNA–EB complexes. The D/P ratios ranged from 0.03 to 1.0. The difference CD spectra of all fragments are characterized by bands with maxima near 310, 275, and 207 nm, and minima near 290, 253, 225, and 190 nm. The band near 310 nm, which has a shoulder at about 335 nm, has zero intensity at D/P ≤ 0.05, and rises to a plateau value, different for each fragment, at D/P ? 0.3 for large fragments (≥ 1400 bp), and D/P ～ 0.7 for the two small 147 bp fragments. The minimum near 290 nm is markedly blue shifted with increasing D/P, the wavelength of the extremum corresponding approximately to the wavelength of the uv absorption maximum of the DNA–EB complex. The negative amplitude of this band at D/P = 1.0 depends on the molecular weight of the DNA. The difference CD maximum near 275 nm is positive at low D/P ratios, increases and goes through a maximum at D/P = 0.06–0.1, and then becomes increasingly negative with increasing D/P. The amplitude of the negative ellipticity per added dye is constant at high D/P ratios, suggesting that the transition can be attributed to outside-bound EB molecules. The ellipticities at 310, 290, and 253 nm increase in absolute magnitude with increasing D/P at approximately the same rate, suggesting that all three bands are associated with the same optical and/or conformational transition. For the two small 147 bp fragments the fractional increases in amplitude of these bands parallel the fractional increase in length of the DNA upon binding EB, determined by electric birefringence measurements. The titration of the restriction fragments with EB was also followed by optical absorption. Two end points are observed, the first at a D/P ratio of ～ 0.1, reflecting the transition between intercalated and outside-bound dye molecules, and the second at D/P ? 1.0, the equivalence point of the titration.     

A synthesis of labeled ethidium bromide

A method is described for the synthesis of labeled ethidium (3,8-diamino-5-ethyl-6-phenyl phenanthridinium) bromide. Based on benzoic acid, the radioactive precursor used, the yield is 15% of a compound that is indistinguishable from authentic ethidium bromide in its absorption spectra (uv, visible, ir), Chromatographie behavior, and mutagenic effectiveness in the induction of respiration-deficient cell lines in baker's yeast.