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Recent efforts have been made to unravel the independent roles of monovalent cations in RNA folding, primarily using the Tetrahymena ribozyme as a model. Here we report how monovalent cations impact the folding of the Candida ribozyme. Interestingly, this ribozyme requires an order of magnitude less monovalent cations (Na+ and Tris+) to commit to a new folding starting state in which the J3/4:P6 base triple is partially formed and mispairing in the L2.1 and L6 terminal loops is resolved. When Mg2+-induced ribozyme folding proceeded on the same energy landscape, the altered starting state led to a rapid assembly of the correct ribozyme core and a fivefold to 10-fold increase in the ribozyme activity. Moreover, when the ribozyme folding was started from a misfolding-prone state, high millimolar concentrations of monovalent cations moderately elevated the ribozyme activity by efficiently resolving the misfolding of a peripheral element, P5abc.

Monovalent cations use multiple mechanisms to resolve ribozyme misfolding