Thermodynamic correlation analysis: hydration and perturbation sensitivity of RNA secondary structures

The thermodynamic parameters DeltaH, DeltaS, T(m), and DeltaG of a total of 36 RNA strands, 22 tetralooped 22mers, and 14 heptalooped 25mers (same stem sequence) were analyzed with respect to enthalpy-entropy compensation (EEC). The EEC plots [DeltaH, DeltaS] were compared with collected literature data from protein and nucleic acid unfolding studies (3224 and 241 datapoints, respectively) which all proved to be remarkably linear. The similarity of the compensation slopes and intercepts for all compounds indicate that, irrespective of the chemical nature and stability of the folding solutes, the exothermicity DeltaH and entropic penalty T x DeltaS of folding are strongly dominated by the rearrangement and formation of hydration layers around the solutes, while it is well-known that the stability of folding results only from the difference (DeltaG) and ratio (T(m)) of both parameters. EEC plots [DeltaH, DeltaS] are presented in an extended context, as 3D plots [DeltaH, DeltaS, T(m)] allowing for a correct analytical description of the enthalpy-entropy relationship and for more practical interpretations of large amounts of thermodynamic data when replotted as [DeltaH, T(m)] or [DeltaG(T), T(m)]. The introduction of a variety of mismatches into nucleic acids, or limited irreguliarities into any supramolecular complex, and the analysis of the involved thermodynamics as shown in this study-i.e., scanning the "enthalpy-entropy space" of whole macromolecular subgroups-should permit to extract and quantify more "hidden information", such as hydration extent and sensitivity of macromolecular frameworks toward desolvation and structural perturbation, from thermodynamic analyses of large sample sizes.