Fig. 1

Interaction of the GPC3_3, GPC3_2, and GPC3_9 aptamers with GPC3 protein. A Heatmap and graph of the binding distance between GPC3 amino acids and GPC3_3, GPC3_2 and GPC3_9 aptamers. Dark purple color indicates > 4 Å distance, while the bright color indicates < 4 Å distance or closer. B GPC3 protein–aptamer contact map obtained by COCOMAPS. A significant contact region of GPC3 protein–DNA aptamers (GPC3_3, GPC3_2, and GPC3_9) are shown in light purple, green, and magenta, respectively. Six regions in overlapped area of aptamer (GPC3_3 and GPC3_9) have been highlighted through blue rectangles. C Average distance of hydrogen bond (O–H) length (Å) between GPC3 protein and each DNA aptamer candidate (GPC3_1–GPC3_12). Each value of 12 DNA aptamer candidates was calculated by COCOMAPS/CONSRank and LigPlot+ (see “Materials and methods”). The GPC3 protein is depicted as a ribbon structure with stick structure of D GPC3_3 (green), E GPC3_2 (light purple), and F GPC3_9 (magenta). Each color represents areas in GPC3 protein contacted by nt-paratopes