Figure 3.

Sequence analysis of CL-stimulated DNA cleavage by topoisomerase IV. (A) χ² values of the base distribution at positions ranging from −10 to +10 of the sites of CL stimulation of DNA cleavage. The number −1 indicates the base 5′ of the cleaved phosphodiester bond identified in sequencing gels. (B and C) Probabilities of the observed base frequency deviations from expectation at each position on the forward strand of complementary sites (B) and non-complementary sites (C) (data for the reverse strand are reported in the text). In the ordinate, P is the probability of observing that deviation or more, either as an excess (above base line) or deficit (below base line) relative to the expected frequency of each base. The expected frequencies were calculated using the overall base frequency of SV40 DNA (G = C = 20.4%; A = T = 29.6%).