Entropic origin of Mg 2+-facilitated RNA folding

Abstract

Mg 2+ is essential for the proper folding and function of RNA, though the effect of Mg 2+ concentration on the free energy, enthalpy, and entropy landscapes of RNA folding is unknown. This work exploits temperature-controlled single-molecule FRET methods to address the thermodynamics of RNA folding pathways by probing the intramolecular docking/undocking kinetics of the ubiquitous GAAA tetraloop-receptor tertiary interaction as a function of [Mg 2+]. These measurements yield the barrier and standard state enthalpies, entropies, and free energies for an RNA tertiary transition, in particular, revealing the thermodynamic origin of [Mg 2+]-facilitated folding. Surprisingly, these studies reveal that increasing [Mg 2+] promotes tetraloop-receptor interaction by reducing the entropic barrier (-TΔS ‡dock) and the overall entropic penalty (-TΔS° dock) for docking, with essentially negligible effects on both the activation enthalpy (ΔH ‡dock) and overall exothermicity (ΔH° dock). These observations contrast with the conventional notion that increasing [Mg 2+] facilitates folding by minimizing electrostatic repulsion of opposing RNA helices, which would incorrectly predict a decrease in ΔH ‡dock and ΔH° dock with [Mg 2+]. Instead we propose that higher [Mg 2+] can aid RNA folding by decreasing the entropic penalty of counterion uptake and by reducing disorder of the unfolded conformational ensemble.