Fig. 4. P1 nuclease-hypersensitive sites on the G–rich and C–rich DNA strands within the R–loop formed at a 900 bp fragment of the Sμ sequence. (A) Sequencing gel displaying the P1 nuclease-hypersensitive sites on the G–rich (lanes 1–4 and 9–12) and C–rich (lanes 5–8 and 13–16) DNA strands at Sμ within the R–loop and on supercoiled plasmid pGD44. The left panel shows the hypersensitive sites at the 5′ end of Sμ. The right panel shows the sites at the 3′ end. Lanes 1, 5, 9 and 13 are R–loop samples that were probed with P1 nuclease; lanes 3, 7, 11 and 15 are supercoiled pGD44 samples probed with P1 nuclease; lanes 2, 6, 10 and 14 are R–loop samples that were not probed; lanes 4, 8, 12 and 16 are pGD44 samples that were not probed. Ladders of 50 and 250 bp (Pharmacia) were used as standards. The start of Sμ is shown on the left panel. The boundary between the single- and double-stranded regions of the G–rich strand is indicated by the open arrow. (B) Putative model for the R–loop structure formed at a portion of the Sμ sequence as deduced from the P1 nuclease probing data. The hybrid does not extend to the end of the switch sequence for reasons explained in the text.