FIGURE 6.
The predicted equilibrium unfolding pathways for (A–D) BWYV and (E–H) ΔU177 hTR RNAs. We also show the experimentally observed loop–stem base triples between the loops and stems. The results support the F to PK to hp to U folding pathway (Nixon and Giedroc 2000), where F is the folded state with the tertiary interactions, PK is the pseudoknot structure without the tertiary interactions, hp is a folding intermediate (usually a stem–loop structure), and U is the unfolded state. In the density plots, the x- and y-axes denote the indices of the nucleotides i and j, and the darkness of the points denote the base-pairing probability Pij (from Eq. 4).