Hinge Stiffness Is a Barrier to RNA Folding

Cation-mediated RNA folding from extended to compact, biologically active conformations relies on a temporal balance of forces. The Mg 2 + -mediated folding of the Tetrahymena thermophila ribozyme is characterized by rapid nonspecific collapse followed by tertiary-contact-induced compaction. This article focuses on an autonomously folding portion of the Tetrahymena ribozyme, its P4–P6 domain, in order to probe one facet of the rapid collapse: chain flexibility. The time evolution of P4–P6 folding was followed by global and local measures as a function of Mg 2 + concentration. While all concentrations of Mg 2 + studied are sufficient to screen the charge on the helices, the rates of compaction and tertiary contact formation diverge as the concentration of Mg 2 + increases; collapse is greatly accelerated by Mg 2 + , while tertiary contact formation is not. These studies highlight the importance of chain stiffness to RNA folding; at 10 mM Mg 2 + , a stiff hinge limits the rate of P4–P6 folding. At higher magnesium concentrations, the rate-limiting step shifts from hinge bending to tertiary contact formation.