Interaction of the Dye Ethidium Bromide with DNA Containing Guanine Repeats

DNA containing one or more copies of the motifs repeated in telomere sequences has unusual conformational properties. The isolated sequence from the protozoan Oxytricha, dT₄G₄has the potential to form tetramers in the presence of sodium or potassium ions. We report here that these tetramers bind ethidium tightly, with an interaction that fulfills several criteria for an intercalative mechanism in the G sequence. By contrast, the 4-fold tandem repeat of this subunit, d(T₄G₄)₄, does not interact specifically with ethidium in the presence of Na⁺. This difference might have a simple structural basis: the tetramer of dT₄G₄forms a stack of four G-quartets in the presence of Na⁺or K⁺, whereas the constraint imposed by the T4 “tethers” in the repeat d(T₄G₄)₄ allows only two layers to form in the presence of Na⁺. In the presence of sufficient K⁺, the latter can partially form a four-layer G-quartet structure, which interacts with ethidium. This idea is supported by analysis of a “relaxed” sequence, dT₄G₄(T₇G₄)₃, which allows formation of four G-quartets and binds ethidium in the presence of Na⁺as well as K⁺. Ethidium (and intercalators generally) should thus be able to retard or inhibit the action of telomerase in the presence of K⁺.