Figure 5.

Changes in 92-bp DNA looping brought about by localized changes in the DNA model. (a) Superimposed images of the optimized DNA pathways found when the sites of pyrimidine-purine steps along the lac operon are softened (blue) and when the helix is overtwisted (green) compared to ideal DNA (gold). Terminal base pairs are constrained to the spatial positions imposed by the V-shaped Lac repressor assembly. The antiparallel loops are rotated ~45° and the parallel loop ~90° about the vertical axis relative to the images in Figure 3a; (b) Changes in the bending Δγ and twisting Δθ between successive base pairs along the depicted loops, with the data color-coded to match the molecular images. The yellow lines denote the locations of the pyrimidine–purine steps, where the softened DNA shows bursts of bending and untwisting. Note the relative insensitivity of the parallel loop and the responses in the antiparallel loops to imposed overtwisting.