How RNA folds to a native conformation : a study using the Tetrahymena ribozyme

The vast conformational space of functional RNAs begs the question of how they achieve structural specificity, stabilizing a native state relative to all other states. Previously, the lab of Rick Russell demonstrated that the P5abc peripheral element of the Tetrahymena thermophila Group I ribozyme stabilized the ribozyme's native conformation (N) relative to a long-lived misfolded intermediate (M) by ~50,000 fold. Here, we employ site-directed mutagenesis to disrupt tertiary interactions outside of P5abc and find that doing so weakens P5abc binding to a great extent in N and a lesser extent in M, showing that both species fold cooperatively but to different degrees. The difference in the degree of cooperativity between N and M rationalizes the structural specificity conferred to N by P5abc. We suggest that physical differences in M result in an energetic penalty upon complete folding, partially countervailing the energy of cooperative folding.