Figure 7.

Examination of 3′ overhang length by KMnO₄ footprinting. The samples in panel A were run on a 15% sequencing gel while the samples in panel B were run on an 8% gel. (A) Lanes 1–3, denatured DNA from anlagen of aphidicolin-treated cells (lane 1), anlagen of untreated cells (lane 2), or mature macronuclei (lane 3). Lanes 4–6, nondenatured DNA from aphidicolin-treated cells (lane 4), untreated cells (lane 5), or mature macronuclei (lane 6). The heterogeneity in the lower bands of the T₄ repeat pattern was caused by end labeling of molecules ending in both G₂ and G₁ (the macronuclear DNA was slightly degraded). (B) Lane 1, marker lane showing the G-cleavage pattern obtained after DMS treatment of anlagen DNA from untreated cells. Lanes 2 and 3, T-cleavage pattern obtained after KMnO₄ footprinting of denatured anlagen DNA from untreated cells; lane 2, 1 mM KMnO₄; lane 3, 2 mM KMnO₄. Lane 4, T-cleavage pattern obtained with nondenatured anlagen DNA from untreated cells after footprinting with 1 mM KMnO₄.