Table 2. Measured and Predicted Thermodynamic Parameters for RNA Internal Loop Formation in 1 M NaCl.

^aCalculated from eq 3a and data in Table 1 unless noted otherwise. Experimental errors for ΔG°₃₇, ΔH°, and ΔS° for the canonical stems are estimated as 4, 12, and 13.5%, respectively, according to ref (25). These errors were propagated to estimate errors in loop thermodynamics. For each duplex, the values from the bottom to the top are measured at pH 5.5, 7, and 8, respectively. Sequences are ordered from the most negative to the most positive values of ΔΔG°_37,pH = ΔG°_37,pH5.5 − ΔG°_37,pH7, except for (GCCCGAGCG)₂ and those noted in footnote , where ΔΔG°_37,pH is divided by 2. ΔG°_predicted values are calculated according to eq 4. Loops smaller than 3 × 3 nucleotides are predicted according to refs (16, 29, and 31).

^bImino proton NMR spectra were measured (Figure 2).

^cΔG°_{5′CR/3′AA bonus} is applied twice to predict the free energy for loop formation.

^dLoop sequence from a J4/5 loop of a group I intron (36).

^eData at pH 7 are from ref (19).

^fLoop sequence from the substrate loop of a VS ribozyme (8,9).

^gLoop sequence derived from the loop A of hairpin ribozyme (8).

^hLoop sequence from a leadzyme (1,65−67).

ⁱLoop sequence from the Alu domain of human SRP RNA (71).

^jThe pH-independent thermodynamics is consistent with the NMR structure without the formation of the C⁺U pair (61).

^kThe pH-independent thermodynamics is consistent with the NMR structure without the formation of the UC⁺ pair (62).