Fig. 4: Higher-order topology of nanosprings revealed by AFM.

a, b High-resolution AFM images of two typical nanosprings in presence of a 100 mM KCl for n = 9 molecules examined over three independent experiments and b 10 µM anti-GQ strands for n = 7 molecules examined over four independent experiments. The yellow arrows mark the bridging regions (slits) between two piers (see Fig. 1a, b). The backbones of the nanosprings are inside out between images in a and b. More images are shown in Supplementary Figs. 11 and 12. c Schematics of two crossing bundles on a 2D surface and section views along two orthogonal planes. A larger slope indicates that the bundle along the sectional plane (A-B) is lying underneath. d High-resolution AFM image of the nanospring in the presence of 100 mM KCl. e, f Slope analyses along the two directions representing two crossing bundles in the presence of 100 mM KCl. g High-resolution AFM image of the nanospring in the presence of 10 µM anti-GQ strands. h, i Slope analyses along the two directions representing two crossing bundles in the presence of 10 µM anti-GQ strands. Note that sectional lines were taken in such a way that the DNA bundle along the line A-B is underneath the other when the structure is right-handed, whereas the DNA bundle along the line C-D is underneath the other when the structure is left-handed. j Box plots of the change in slopes (=slope_AB–slope_CD). A positive value indicates the right-handed structure. The boxes represent Inter Quarter Range (25th–75th percentiles), the center line indicates the median, and the whiskers extend to the maximum and minimum values (n = 9 molecules examined over three independent experiments for +KCl; n = 7 molecules examined over four independent experiments for +anti-GQ). Red dot is an outlier point and excluded from the analysis. Source data are provided as a Source Data file.