FIGURE 2.

(A) The coordinate system for a base pair (U21-A16) in the helix. s and s′ are the pairing strands. The gray and red colors denote the C₄ and the P atom in the helix, respectively. The magenta color denotes the loop region. (B) Helix–bulge loop junction. The deleted bonds (×) show the fixed configuration of the virtual bonds in the A-form helix without the bulge loop. These bonds become flexible in the bulge loop conformation (see the blue bonds). The blue and magenta colors denote the bonds in the bulge loop. The P and C₄ coordinates in the helix are from the crystal structure of r(CGUAC)dG sequences (Biswas et al. 1998).