Thermodynamics of RNA melting, one base pair at a time

Abstract

The melting of base pairs is a ubiquitous feature of RNA structural transitions, which are widely used to sense and respond to cellular stimuli. A recent study employing solution nuclear magnetic resonance (NMR) imino proton exchange spectroscopy provides a rare base-pair-specific view of duplex melting in the Salmonella FourU RNA thermosensor, which regulates gene expression in response to changes in temperature at the translational level by undergoing a melting transition. The authors observe "microscopic" enthalpy-entropy compensation--often seen "macroscopically" across a series of related molecular species--across base pairs within the same RNA. This yields variations in base-pair stabilities that are an order of magnitude smaller than corresponding variations in enthalpy and entropy. A surprising yet convincing link is established between the slopes of enthalpy-entropy correlations and RNA melting points determined by circular dichroism (CD), which argues that unfolding occurs when base-pair stabilities are equalized. A single AG-to-CG mutation, which enhances the macroscopic hairpin thermostability and folding cooperativity and renders the RNA thermometer inactive in vivo, spreads its effect microscopically throughout all base pairs in the RNA, including ones far removed from the site of mutation. The authors suggest that an extended network of hydration underlies this long-range communication. This study suggests that the deconstruction of macroscopic RNA unfolding in terms of microscopic unfolding events will require careful consideration of water interactions.

FIGURE 1.

RNA imino proton exchange by NMR. (A) Schematic of a two-step direct (or water-mediated) imino proton exchange reaction for a GC base pair with a base catalyst, which is followed by reversible base-pair formation (data not shown). Secondary structure and base-pair thermodynamic parameters for the wild-type (wt) Salmonella FourU RNA thermometer (B) and the A8C mutant RNA (C) showing color-coded free energy (ΔG_diss) values relative to the open state (left) and a plot of free energy (ΔG_diss), enthalpy (ΔH_diss), and entropy (T ΔS_diss) at 20°C versus nucleobase examined (right). Temperature dependence of ΔG_diss values derived from ΔH_diss and ΔS_diss using the Gibbs-Helmholtz equation for the wt RNA (D) and A8C mutant RNA (E). Corresponding T_m values obtained from CD are indicated (inset) to show coincidence with the intersection point of linear curves ([B,C,D,E]; adapted from the original article [Rinnenthal et al. 2010] with permission from the authors and Oxford University Press © 2010).