Figure 3: Analysis of HCV RNA secondary structure. (A) Two representative molecules for Mg2+-containing reactions are shown on the left. In these images, black ˜0 nm, blue ˜0.5 nm, green ˜1.0 nm, red ˜1.5 nm, and white ˜2 nm and larger. The single stranded region of the genome is shown in the dotted box. The arrows point to the kinked region of the genome preceding the appendage-free region of the genome. Bar=80 nm. To the right of each image, a contour plot profile corresponding to each molecule is displayed with the blue line corresponding to the height of features along the length backbone of the molecule and the red line corresponding to the number of appendages protruding out from the molecule along the backbone. Each plot starts at 100 nm along the background of the image. The molecule is then traced starting from the end outlined with the box in the images at the left. A trace of the molecule is shown to the right of each plot. (B) Six representative 0.4×0.4 μm2 images of molecules exhibiting the single stranded ‘tail’ morphology at the end of the molecule. Bar=100 nm (C) A histogram of the length of the tail region of the molecules which exhibited this morphology.