Figure 3. Unpaired nucleotides adjacent to helices are stabilized by the base-phosphate zipper.

Strands forming the bulge, hairpin loop, and stems are shown in cyan, purple, and black, respectively. (A) Base-phosphate zipper and pseudo-continuous helix are in the secondary structure, which is derived from the tertiary structure. Nucleotides at the base-phosphate zipper and pseudo-continuous helix are boxed in green and blue dashed lines, respectively. Strands forming the bulge, hairpin loop, and stems are shown in cyan, purple, and black, respectively. Guanines, adenines, thymines, and cytosines are shown in green, red, yellow, and blue, respectively. (B) Two sequentially consecutive guanine bases interact with phosphate oxygens of the quasi-continuous helix. The pseudo-continuous helix is represented as a transparent sphere. Stick representation of the hairpin-bulge contact indicates the pseudo-continuous helix by coaxial stacking. Strands forming the bulge, hairpin, and stems are shown in cyan, purple, and black, respectively. Guanines, adenines, thymines, and cytosines are shown in green, yellow, pink, and blue, respectively.