Quinacrine, a chromosome stain specific for deoxyadenylate-deoxythymidylaterich regions in DNA

Fluorescence of quinacrine in the presence of different polynucleotides was studied to attempt to identify the specific nucleotides responsible for the fluorescence of stained chromosome preparations. A marked enhancement of fluorescence was seen in the presence of bihelical polynucleotides, such as poly(dA-dT), poly(dA).poly(dT), and poly(rA).poly(rU), but not in the presence of single-stranded polynucleotides, such as poly(dA), poly(dT), poly(rA), or poly(rU) alone. The higher was the GC content of natural DNAs, the more they quenched. Quenching was also seen with poly(dG) or poly(rG) alone, but not with poly(dC) or poly(rC) alone. Native and denatured DNA were both effective in quenching fluorescence. Thus, a bihelical conformation is not required for fluorescence quenching. Nearly all of these properties are shared with proflavine. In contrast, acridine orange, which stains most areas of chromosome preparations, shows enhanced fluorescence in the presence of all members of a series of natural DNAs. These data suggest that base-pairs composed of AT (rather than GC) residues are responsible for the observed fluorescence of specific chromosome regions after treatment with quinacrine, and support the proposal of Ellison and Barr (Chromosoma, in press) that the highly localized quinacrine fluorescence in their cytological preparations reflects the presence of DNA that has a high (A + T)/(G + C) ratio.