Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics

Folding of the Tetrahymena self-splicing RNA into its active conformation i nvolves a set of discrete intermediate states. The Mg2+-dependent equilibri um transition from the intermediates to the native structure is more cooper ative than the formation of the intermediates from the unfolded states. We show that the degree of cooperativity is linked to the free energy of each transition and that the rate of the slow transition from the intermediates to the native state decreases exponentially with increasing Mg2+ concentrat ion. Monovalent salts, which stabilize the folded RNA nonspecifically, indu ce states that fold in less than 30 s after Mg2+ is added to the RNA. A sim ple model is proposed that predicts the folding kinetics from the Mg2+-depe ndent change in the relative stabilities of the intermediate and native sta tes.