FIGURE 2.
RNA backbone travels discrete distances that support 2:1 maximum ratios for bulges. (A) A 3-nt fragment with only the atoms in the bases shown in the coordinate system of the 5′ nt. The Z-distance is given as the distance along the z-axis from the first nt to the last nt in the fragment. (B) Histogram of Z-distance for 3-nt fragments in the ribosome (pdb_id=1FFK) such that the first and last nt have Z-axis oriented within 25 degrees. Two distributions of Z-distances account for a compressed and expanded backbone conformation that can account for, at most, a 2:1 ratio of nt in a given bulge.
