Effects of Preferential Counterion Interactions on the Specificity of RNA Folding

The real-time search for native RNA structure is essential for the operation of regulatory RNAs. We previously reported that a fraction of the Azoarcus ribozyme achieves a compact structure in less than a millisecond. To scrutinize the forces that drive initial folding steps, we used time-resolved SAXS to compare the folding dynamics of this ribozyme in thermodynamically isostable concentrations of different counterions. The results show that the size of the fast-folding population increases with the number of available counterions and correlates with the flexibility of initial RNA structures. Within 1 ms of folding, Mg 2+ exhibits a smaller preferential interaction coefficient per charge, ΔΓ + / Z, than Na + or [Co(NH 3 ) 6 ] 3+ . The lower ΔΓ + / Z corresponds to a smaller yield of folded RNA, although Mg 2+ stabilizes native RNA more efficiently than other ions at equilibrium. These results suggest that strong Mg 2+ -RNA interactions impede the search for globally native structure during early folding stages.