Table 3.
Calculated and predicted thermodynamic parameters for the unfolding of the unpaired adenosine and loop 2 mutants at 50 mM K+, pH 7.0
| RNA | Stem | ΔHstema | ΔHpredb | ΔG° | ΔG°predc | ΔΔG°wt-mutant |
|---|---|---|---|---|---|---|
| mIAP | 2 | 75.4 (68.2) | 77.3 | 1.9 (2.7) | 5.3 | - |
| 1 | 66.9 (68.6) | 68.4 | 10.1 (10.7) | 12.3 | - | |
| Δ A15 | 2 | 66.1 (68.4) | 77.3 | 1.5 (1.9) | 5.3 | 0.4 (0.8) |
| 1 | 62.3 (68.3) | 68.4 | 9.5 (10.5) | 12.3 | 0.6 (0.2) | |
| Δ A35 | 2 | 66.6 (64.7) | 81.0 | 5.1 (5.0) | 9.0 | −3.2(-2.3) |
| 1 | 64.6 (73.4) | 68.4 | 9.8 (11.3) | 12.3 | 0.3 (−0.6) | |
| Δ A35A15 | 2 | 57.3 (52.8) | 81.0 | 3.8 (3.9) | 9.0 | −1.9 (−1.2) |
| 1 | 58.8 (62.3) | 68.4 | 8.7 (9.3) | 12.3 | 1.4 (1.4) | |
| L2U | 2 | 70.8 (64.4) | 77.3 | 1.4 (0.9) | 5.3 | 0.5 (1.8) |
| 1 | 64.5 (63.3) | 68.4 | 9.4 (9.5) | 12.3 | 0.7 (1.2) | |
| AA-HP | 1 | 61.6 | 68.4 | 9.4 | 12.3 | 0.6 |
Enthalpy and free energy are reported in kcal mol−1 for the sum of unfolding transitions 1, 2 and 4. ΔG° values are calculated at 37 °C. Parameters determined from calorimetry data are shown in parentheses.
The two stem 2 transition enthalpies are summed for mIAP, ΔA15, and L2U.
Does not include a contribution from the helical junction (ΔH=10.6 kcal mol−1) but does include a contribution from the 3′ stack.
Calculated at 1.0 M Na+. Incorporates a fixed value of 9 kcal mol−1 for the pseudoknot loop closing entropy estimated from the unfolding of H-type pseudoknots previously studied Theimer et al 1998, Nixon and Giedroc 1998. Previous studies show that the free energy calculated for a simple hairpin at 100 mM KCl is 2-4 kcal mol−1 smaller than that observed at high Mg2+ (equivalent stabilization to high monovalent concentrations) (Theimer et al., 1998); thus, the experimental ΔG° values are in good agreement with predicted ΔG° values.