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 n ucleotides with (ethylene glycol), spacers, have been compared in expe riments that measure the NaCl dependence of their thermodynamic proper ties. In 1 M NaCl, the eight-nucleotide RNA hairpin/loop has the most favorable folding free energy (Delta D degrees = -8.6 kcal/mol), while the RNAs containing the spacers are considerably more unstable (Delta D degrees = -5.2 to -5.7 kcal/mol); for these RNA/linker species, the re are compensating reductions in favorable entropy and unfavorable en thalpy of the helix-coil transition. Preferential interaction coeffici ents (Delta Gamma(N)) determined from analyses of melting transitions as a function of NaCl concentration are compared to determine the effe ct of the ethylene glycol on differential ion association. While the d ifference in ion association to the helix and coil states of the fully RNA molecules follows prediction, the RNAs with linkers do not, indic ating that the description of their native and/or denatured state has changed.