FIGURE 6.

Predicted structures and stabilities for the competing two-hairpin and pseudoknot conformations for WT pseudoknot domain constructs. The mutated sequences are indicated by dashed boxes. Predicted stabilities are based on the combination of the nearest-neighbor model and Turner 2004 data set from the Nearest Neighbor Database (NNDB) (Turner and Mathews 2010) and pseudoknot entropic penalties (Gultyaev et al. 1999), as appropriate. The predicted 3° structure between stem 2 and loop 1 triples (Shefer et al. 2007; Qiao and Cech 2008) is indicated on the WT pseudoknot structure with dashed black lines.