TABLE 1.
Thermodynamic parameters obtained at 1 M NaCl
| Observed | Predicteda | |||
|---|---|---|---|---|
| RNA | −ΔHtotal | −ΔGtotal | −ΔHtotal | −ΔGtotal |
| ΔH is model-dependent van’t Hoff enthalpy. ΔH and ΔG are reported in kcal/mole. ΔG is calculated at 37°C and compared to nearest-neighbor predictions for stacking (Xia et al. 1998), loop free energies, and tetraloop stabilization (Mathews et al. 1999). Parameters are the average of five independent measurements, and errors are standard deviations from repeated experiments. | ||||
| aPrediction is based on the nearest-neighbor rules for stacking of the Watson-Crick bp in the stem and a +5.6 kcal/mole loop free-energy penalty for capping a helix with a 4- or 5-nt hairpin loop (Mathews et al. 1999). | ||||
| HPdc | 100.4 ± 1.1 | 10.8 ± 0.1 | 75.0 | 10.9 |
| DCloop | 53.4 ± 1.0 | 7.4 ± 0.3 | 51.2 | 5.5 |
| UCAG | 51.6 ± 1.5 | 7.2 ± 0.2 | 51.2 | 5.5 |
