MECHANISMS OF CHROMOSOME-BANDING .9. ARE VARIATIONS IN DNA-BASE COMPOSITION ADEQUATE TO ACCOUNT FOR QUINACRINE, HOECHST 33258 AND DAUNOMYCIN BANDING

Prior studies on subfractions of mouse and kangaroo rat DNA suggested that variations in base concentration within a given genome may not be great enough to account for Q-banding. Calf DNA was subfractionated by CsCl ultracentrifugation into GC[guanine-cytosine]-rich satellites and the main band DNA was further fractionated into AT[adenine-thymine]-rich, intermediate and GC-rich portions. The effect of varying concentrations of these DNAs on quinacrine and Hoechst 33258 fluorescence was examined. Although with both compounds there was less fluorescence in the presence of the GC-rich satellites than main band fractions, these results did not answer the question of whether the variation in base composition alone was adequate to account for chromosome banding. To answer this, the fluorescence observed in the presence of DNA of a given base composition was related to the fluorescence observed in the presence of DNA of 40% GC content (F/F40). This allowed the derivation of a term B which indicated the relative change in fluorescence per 1% change in base composition of DNA. The percent change in fluorescence observed in Q-banding was determined by photoelectric recordings. Quinacrine is twice as sensitive to changes in base composition as Hoechst 33258. Variation in the base content of DNA along the chromosome is sufficient to account for most Q-banding, except possibly for some of the extremes of quinacrine fluorescence. This was further examined with daunomycin. Even though daunomycin gives good fluorescent banding, DNAs varying in base composition from 100 to 40% GC content all resulted in the same relative fluorescence of 0.03. In the presence of poly (dA-dT) the relative fluorescence was 0.85, indicating a great sensitivity to very AT-rich DNA. With daunomycin and possibly other fluorochromes, stretches of very AT-rich DNA may be more important in fluorescent banding than simple variation in mean base composition.