The Role of Counterion Valence and Size in GAAA Tetraloop–Receptor Docking/Undocking Kinetics

For RNA to fold into compact, ordered structures, it must overcome electrostatic repulsion between negatively charged phosphate groups by counterion recruitment. A physical understanding of the counterion-assisted folding process requires addressing how cations kinetically and thermodynamically control the folding equilibrium for each tertiary interaction in a full‐length RNA. In this work, single-molecule FRET (fluorescence resonance energy transfer) techniques are exploited to isolate and explore the cation-concentration‐dependent kinetics for formation of a ubiquitous RNA tertiary interaction, that is, the docking/undocking of a GAAA tetraloop with its 11‐nt receptor. Rate constants for docking (kdock) and undocking (kundock) are obtained as a function of cation concentration, size, and valence, specifically for the series Na+, K+, Mg2 +, Ca2 +, Co(NH3)63 +, and spermidine3 +. Increasing cation concentration accelerates kdock dramatically but achieves only a slight decrease in kundock. These results can be kinetically modeled using parallel cation-dependent and cation‐independent docking pathways, which allows for isolation of the folding kinetics from the interaction energetics of the cations with the undocked and docked states, respectively. This analysis reveals a preferential interaction of the cations with the transition state and docked state as compared to the undocked RNA, with the ion–RNA interaction strength growing with cation valence. However, the corresponding number of cations that are taken up by the RNA upon folding decreases with charge density of the cation. The only exception to these behaviors is spermidine3 +, whose weaker influence on the docking equilibria with respect to Co(NH3)63 + can be ascribed to steric effects preventing complete neutralization of the RNA phosphate groups.