Role of counterion condensation in folding of the Tetrahymena ribozyme II.Counterion-dependence of folding kinetics

Condensed counterions contribute to the stability of compact structures in RNA, largely by reducing electrostatic repulsion among phosphate groups. Va rieties of cations induce a collapsed state in the Tetrahymena ribozyme tha t is readily transformed to the catalytically active structure in the prese nce of Mg2+. Native gel electrophoresis was used to compare the effects of the valence and size of the counterion on the kinetics of this transition. The rate of folding was found to decrease with the charge of the counterion . Transitions in monovalent ions occur 20- to 40-fold faster than transitio ns induced by multivalent metal ions. These results suggest that multivalen t cations yield stable compact structures, which are slower to reorganize t o the native conformation than those induced by monovalent ions. The foldin g kinetics are 12-fold faster in the presence of spermidine(3+) than [Co(NH 3)(6)](3+), consistent with less effective stabilization of long-range RNA interactions by polyamines. Under most conditions, the observed folding rat e decreases with increasing counterion concentration. In saturating amounts of counterion, folding is accelerated by addition of urea. These observati ons indicate that reorganization of compact intermediates involves partial unfolding of the RNA. We find that folding of the ribozyme is most efficien t in a mixture of monovalent salt and Mg2+. This is attributed to competiti on among counterions for binding to the RNA. The counterion dependence of t he folding kinetics is discussed in terms of the ability of condensed ions to stabilize compact structures in RNA. (C) 2001 Academic Press.