TABLE 2.
The thermodynamic parameters for nucleic acid hairpins used in the calculations
| Label* | Ref. | Helix length (bp) | Loop size | −ΔH° (kcal/mol)† | −ΔS° (cal/mol K)† | ΔG°loop (kBT)‡ | −ΔG°37 (kcal/mol)§ |
|---|---|---|---|---|---|---|---|
| RH1 | (49) | 6 | 10 | 63.6 | 161.7 | 8.4 | 8.3 |
| RH2 | (49) | 6 | 8 | 63.6 | 161.7 | 7.9 | 8.6 |
| RH3 | (20,95) | 5 | 6 | 60.0 | 150.3 | 7.2 | 8.9 |
| RH4 | (96) | 7 | 9 | 68.8 | 179.3 | 8.2 | 8.1 |
| RH5 | (97) | 7 | 12 | 77.9 | 203.8 | 8.7 | 9.3 |
| RH6 | (93) | 5 | j+2 | 50.2 | 131.0 | ¶ | ¶ |
| DH1 | (93) | 7 | i | 53‖ | 143‖ | ¶ | ¶ |
In our calculations for salt-dependent nucleic acid hairpin thermodynamics, we use the values listed in the table at 1 M NaCl.
The sequences of the hairpins are shown in Fig. 1.
The listed thermodynamic parameters are calculated for helix stem at standard salt (1 M NaCl), through the nearest-neighbor model. The parameters for base stacking are taken from Xia et al. (31), and the parameters for terminal mismatches are taken from Serra et al. (27).
The loop free energy is obtained from our calculations for loops (Eq. 15), rather than the experimentally derived values.
Calculated for the whole RNA hairpin at standard salt (1 M NaCl).
The loop and hairpin free energies depend on the loop sizes j+2 and i.