Thermodynamic comparison of the salt dependence of natural RNA hairpins and RNA hairpins with non-nucleotide spacers.

RNA hairpins with loops of either ten or eight nucleotides, or seven nucleotides with (ethylene glycol)n spacers, have been compared in experiments that measure the NaCl dependence of their thermodynamic properties. In 1 M NaCl, the eight-nucleotide RNA hairpin/loop has the most favorable folding free energy (delta G degree = -8.6 kcal/mol), while the RNAs containing the spacers are considerably more unstable (delta G degree = -5.2 to -5.7 kcal/mol); for these RNA/linker species, there are compensating reductions in favorable entropy and unfavorable enthalpy of the helix-coil transition. Preferential interaction coefficients (delta IN) determined from analyses of melting transitions as a function of NaCl concentration are compared to determine the effect of the ethylene glycol on differential ion association. While the difference in ion association to the helix and coil states of the fully RNA molecules follows prediction, the RNAs with linkers do not, indicating that the description of their native and/or denatured state has changed.