Binding of ethidium bromide to fractionated chromatin

The binding of ethidium bromide (EB) to different chromatin preparations was tested. Scatchard plots showed that the slowly sedimenting fraction of sheared chromatin is enriched in dye-binding sites. Limited nuclease digestion of rat liver nuclei, which has been shown to preserve the subunit structure of chromatin, reduces the number of binding sites available for intercalation of the dye.     

Interaction of ethidium bromide with synthetic double-stranded polyribonucleotides

The interaction of ethidium bromide (EtBr) with double helical synthetic polyribonucleotides poly(G).poly(C), poly(A).poly(U) and poly(I).poly(C) has been investigated by the method of isothermal microcalorimetry and according to the character of changes on the spectra of circular dichroism, absorption and fluorescence at binding. The calculations showed that at binding of EtBr with poly(A).poly(U) the saturation stechiometry was one EtBr molecule per 2 base pairs with binding constant (2.5 +/- 0.5).10(6) M-1 at 30 degrees C and 0.1 M. NaCl. In the case of binding of EtBr with poly(G).poly(C) and poly(I).poly(C) the saturation stechiometry was not less than 0.2 EtBr molecule per 1 base pair with binding constant (4 +/- 1).10(3) M-1 and (1.5 +/- 0.3).10(4) M-1 respectively, at 25 degrees C and 0.1 M NaCl. The binding enthalpies of EtBr with poly(A).poly(U) and poly(G).poly(C) have been determined to be (-7.5 +/- 0.5) Kcal per 1 mol of bound EtBr in average for both polymers. It has been shown that the observed strong selectivity of EtBr binding with polyribonucleotides is of entropic origin.     

Alteration in the processing of ribosomal ribonucleic acid inSaccharomyces cerevisiae caused by ethidium bromide

Ethidium bromide in a concentration of 200 μg/ml causes a full inhibition of RNA synthesis in aSaccharomyces cerevisiae ρ° strain, while protein synthesis continues at a reduced rate. Under these conditions, processing of rRNA is slowed down and part of the 37S rRNA precursor molecules are cleaved to a 32S RNA fraction (molecular weight 2.15×10⁶). The 32S RNA accumulates in cells treated with ethidium bromide but cannot be processed to mature 25S and 18S rRNA and is degraded. The 32S RNA fraction also appears when processing of rRNA occurs in cells starved for required amino acids. The degradation of 37S precursor molecules through 32S RNA may be a regulatory mechanism of rRNA biosynthesis in yeast, which operates when excess rRNA must be wasted.     

Binding of spermidine to transfer ribonucleic acid

The binding of spermidine to yeast tRNAPhe and Escherichia coli tRNAGlu2 at low and high ionic strength was studied by equilibrium dialysis. Once corrected for the expected Donnan effect, the binding at low ionic strength obeys the simple relationship of equivalent binding sites, and cooperative binding of spermidine to tRNA could not be detected. At low ionic strength (0.013 M Na+ ion), tRNAPhe (yeast) has 13.9 +/- 2.3 strong spermidine binding sites per molecule with Kd = 1.39 X 10(-6) M and a few weak spermidine binding sites which were inaccessible to experimentation; tRNAGlu2 (E. coli) has 14.8 +/- 1.6 strong spermidine binding sites and 4.0 +/- 0.1 weak spermidine binding sites with Kd = 1.4 X 10(-6) M and Kd = 1.23 X 10(-4) M, respectively. At high ionic strength (0.12 M monovalent cation) and 0.01 M Mg2+, tRNAPhe (yeast) has approximately 13 strong spermidine binding sites with an apparent Kd = 3.4 X 10(-3) M while the dimeric complex tRNAPhe X tRNAGlu2 has 10.4 +/- 1.2 strong spermidine binding sites per monomer with an apparent Kd = 2.0 X 10(-3) M. In the presence of increasing Na+ ion or K+ ion concentration, spermidine binding data do not fit a model for competitive binding to tRNA by monovalent cations. Rather, analysis of binding data by the Debye-Hückel approximation results in a good fit of experimental data, indicating that monovalent cations form a counterion atmosphere about tRNA, thus decreasing electrostatic interactions. On the basis of equilibrium binding analyses, it is proposed that the binding of spermidine to tRNA occurs predominantly by electrostatic forces.     

Binding of ethidium bromide to a DNA triple helix. Evidence for intercalation

The interaction of ethidium, a DNA intercalator, with the poly(dA).poly(dT) duplex and the poly (dA).2poly(dT) triplex has been investigated by a variety of spectrophotometric and hydrodynamic techniques. The fluorescence of ethidium is increased when either the duplex or triplex form is present. Binding constants, determined from absorbance measurements, indicate that binding to the triple helical form is substantially stronger than to the duplex, with a larger binding site size (2.8 base triplets compared to 2.4 base pairs). Furthermore, while binding to poly(dA).poly(dT) shows strong positive cooperativity, binding to the triplex is noncooperative. Thermal denaturation experiments demonstrate that ethidium stabilizes the triple helix. Binding to either form induces a weak circular dichroism band in the visible wavelength region, while in the region around 310 nm, there is a band that is strongly dependent on the degree of saturation of the duplex, and which is positive for the duplex but negative for the triplex. Both fluorescence energy transfer and quenching studies provide evidence of intercalation of ethidium in both duplex and triplex complexes. Binding of ethidium leads to an initial decrease in viscosity for both the duplex and triplex structures, followed by an increase, which is greater for the duplex. Taken together, these results strongly suggest that ethidium binds to the poly (dA).2poly(dT) triple helix via an intercalative mechanism.     

Binding of ethidium bromide and quinacrine hydrochloride to nucleic acids and reconstituted nucleohistones

Studies of binding of ethidium bromide and quinacrine hydrochloride to native DNA at low ionic strength indicate that for both compounds the binding is selective, with about one binding site for about four nucleotides. Annealing of unfractionated histones to DNA by a salt-gradient dialysis method slightly decreases the binding of the dyes to DNA. Similar observations made with reconstituted preparations by using individual histone fractions reveal that the arginine-rich histones (histones H3 and H4) are most effective in decreasing the binding. The binding studies with ethidium bromide at high ionic strength and with denatured DNA show that strong dye binding to DNA is strongly dependent on the ionic strength and on the secondary structure of DNA. The histones are not effective in decreasing the dye binding under conditions of high ionic strength. The results are consistent with the observations [Oliver & Chalkley (1974) Biochemistry13, 5093-5098; Axel, Melchoir, Sollner-Web & Felsenfield (1974) Proc. Natl. Acad. Sci. U.S.A.71, 4101-4105] that histones form some kind of surface structures on DNA through non-specific interactions and [Kornberg & Thomas (1974) Science184, 865-868; Kornberg (1974) Science184, 868-871; D'Anna & Isenberg (1974) Biochemistry13, 4992-4997; Vandegrift, Serra, Marve & Wagner (1974) Biochemistry13, 5087-5092] that the tendency of arginine-rich histones to aggregate may be an important factor in determining the structure of chromatin.     

Terbium identifies double-stranded RNA on gels by quenching the fluorescence of intercalated ethidium bromide

We report that the lanthanide cation terbium quenches the fluorescence of ethidium bromide bound to double-stranded RNA by 40-fold, whereas the quenching of double-stranded and single-stranded DNA is under 2.5-fold and the quenching of single-stranded RNA is under 5-fold. This observation was used to develop a convenient method of detecting dsRNA among other nucleic acids in an agarose or polyacrylamide gel. The sensitivity of the method is approximately 4 ng/mm2.     

Yeast mutants resistant to ethidium bromide

Summary Yeast mutants resistant to ethidium bromide have been isolated among sensitive grande cells (⁺) for their ability to grow on glycerol in the presence of the dye. Mutant cells are also resistant to acriflavin and do not yield petites (^-) when grown on galactose with the mutagen. Genetic analysis reveals that resistance to ethidium bromide is controlled by a cytoplasmic factor, carried by, or linked to, the determinant (mitochondrial DNA). The expression of resistance to ethidium bromide seems to be related to the presence in the cell of a product of mitochondrial protein synthesis. It is concluded that some mitochondrial DNA sequence is involved in the resistance to ethidium bromide of yeast mitochondria.     

Yeast killer mutants with altered double-stranded ribonucleic acid

Killer strains of Saccharomyces cerevisiae contain two species of double-stranded ribonucleic acid (dsRNA) with molecular weights estimated at 2.5 x 10(6) (L) and 1.4 x 10(6) (M). The M component appears to have a high adenine content. All mutants of killer which are defective for both the toxin and immunity functions lack the M dsRNA. One of these mutants has a novel dsRNA with a molecular weight of 5 x 10(5). Another class of killer mutants contains strains which are defective for either the toxin or the immunity function. They include temperature-sensitive killers, superkillers, and immunity-minus strains. The dsRNA profile of temperature-sensitive killers resembles that of the standard killer. The superkiller has 2.5 times more of the M dsRNA (1.4 x 10(6) daltons) than does the standard killer. Immunity-minus killers have, in addition to the two dsRNAs species of standard killer, a novel dsRNA with a molecular weight of 2.5 x 10(5). The data are consistent with the hypothesis that the M RNA controls toxin production. In addition, the two RNAs, L and M, seem to be regulated together. When the M RNA is missing, the amount of L is either greatly elevated or greatly reduced.