Figure 2

Coaxial stacking of helices. A secondary structure illustration of a coaxial stacking between two helices that share the same contiguous single-strand loop, in which unpaired nucleotides may be present. The terminal base pairs from both helices stack each other, resulting in an extra energy reduction calculated as if they were contiguous base pairs (shown in the callout). A, B, C represent the three substructures connected to the two helices, where exactly two substructures can be formed each by one contiguous backbone, and exactly one substructure by two separate backbones. If substructure A or B is formed by two separated backbones, the coaxial stacking is nested; if C is formed by two separated backbones, the stacking is parallel.