Ethidium bromide does not fluoresce when intercalated adjacent to 7-deazaguanine in duplex DNA.

Several synthetic DNAs were prepared containing the unusual bases 7-deazaadenine (c7A) and 7-deazaguanine (c7G). As judged from changes in melting temperatures these modified DNAs bound ethidium to a similar extent as the parent polymers. However, duplexes such as poly d(Tc7G)].polyd(CA)] and polyd-(TC)].polyd(c7GA]) gave no enhancement of ethidium fluorescence in a standard ethidium fluorescence assay. Fluorescence spectra in the range 400-650 nm showed that ethidium bound to polyd(TC)].polyd(Gc7A)] gave 70% of the fluorescence of the parent polymer polyd(TC)].polyd(GA)], whereas the fluorescence of polyd(TC)].polyd(c7GA)] was essentially 0%. Even the intrinsic fluorescence of ethidium in solution was quenched in the presence of polyd(TC)].polyd(c7GA)]. Binding constants were estimated from Scatchard analysis and were 4.8, 3.4, and 2.0 x 10(6) M-1 for polyd(TC)].polyd(GA)], polyd(TC)].polyd(Gc7A)], and polyd(TC)].polyd(c7GA)], respectively. This reduction in binding constant cannot account for the loss of fluorescence. The UV spectrum of ethidium was measured in the presence of these DNAs, and some significant differences were noted. Presumably the presence of 7-deazaguanine alters the electronic structure of bound ethidium so that it can no longer fluoresce.