Extended Data Fig. 10: The analysis of high-speed atomic force microscopy (HS-AFM) images of interaction processes between CDF1Dof molecules and DNA fragments with no cis elements, single cis element, and four tandem repeats.
The following procedure was applied to each set of the sequential HS-AFM images. A curve was defined along the DNA fragment in each image using Kappa, a plugin of ImageJ software81 (Red dashed curves in the upper HS-AFM images). Here, an initialization curve was created and fitted to the DNA fragment in each image using an iterative minimization algorithm. For HS-AFM images of DNA with CDF1Dof molecules bound around the centre, the curve was adjusted so that it overlaps the highest position of such molecules. Then, the height profiles along the curves were extracted from each AFM image (bottom panels). For DNA fragments without molecules bound in the centre, the height at the centre of each line profile was analysed (indicated by the black arrow in the lower graphs). For DNA fragments with molecules bound around the centre, distinct peaks appear in the height profiles. In this case, the highest point of each peak in the profiles were analysed (indicated by the green, magenta and blue circles in the lower graphs). The analysed heights were plotted against time for each dataset with the lowest height set to 0 nm (Fig. 4e).
