Bending of the ITR by MOS1. (a) DNA probes used in ITR bending experiments. The nucleotide positions of the 28-bp ITR (gray box) inside the DNA probes are 87 to 113. Six circular permuted fragments were used, which were equal in size (113 bp) and contain either the 3' or the 5'ITR. The arrowhead marks the center of each probe. The corresponding nucleotide positions are indicated. (b) EMSA with MOS1 and the six probes containing the 5'ITR. SEC1 and SEC2 are the lowest and the highest complexes respectively. (c) Mapping the bending center of the 5'ITR containing fragments. The relative mobility (Rf = migration distance of the MOS1-5'ITR complex/mobility distance of free DNA) of each probe was plotted as a function of the position of the center of each probe (shown in A). A sinusoid fit of the data points allowed us to map the center of the MOS1-induced bending. In this representative experiment, the center of the bending core is at position 105 (19th bp in the 5'ITR sequence) for SEC1 (black points), and at position 102 (16th bp in the 5'ITR sequence) for SEC2 (black squares). (d) Localization of the regions bent by MOS1 on the 3' and 5'ITR, for SEC2 (in gray) and SEC1 (underlined). The bending centers are indicated in upper-case letters. The sequence differences between the two ITRs are indicated in lower-case letters in the 5'ITR sequence.