Fig. 3. Stem sequence perturbations alter junction angles and influence global symmetry.

a Stereoview of a superposition of the J10 junction structure using the original 4 × 6 sequence motif with P3₂ symmetry (gray), with the scrambled sequence version containing R3 symmetry (teal). The modified sequences were located within the two downstream stem (1 & 2; indicated) regions containing the same GC content as the original 4 × 6 sequence version. The effect of the scrambled sequence on the geometry of the junction is visually apparent when comparing the superimposed Stem 1 & 2 regions. The dramatic difference in junction angle, and its influence on symmetry is evident (Supplementary Fig. 15). b Stereoview of a stick representation of the superimposed J10 structures in (a) with all base modification sites between the original and scrambled sequence version of the 4 × 6 J10 structures are indicated in Stems 1 & 2. Asterisks are included to provide attention towards the sticky end regions that significantly diverge as an apparent result of the angles induced by the modified stem sequences. Atoms are indicated using the following: carbon (teal), nitrogen (blue), oxygen (red), and phosphate (orange). All regions containing identical sequence are left translucent.