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

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Abstract
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) Biochemistry 13, 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) Science 184, 865–868; Kornberg (1974) Science 184, 868–871; D'Anna & Isenberg (1974) Biochemistry 13, 4992–4997; Vandegrift, Serra, Marve & Wagner (1974) Biochemistry 13, 5087–5092] that the tendency of arginine-rich histones to aggregate may be an important factor in determining the structure of chromatin.