Table 1:
Melting temperatures (in K) and binding free energy contributions (in kcal/mol, calculated for T = 295 K) derived from UV-monitored melting experiments and MD simulations.
| Observable | PNA1-PNA2 | PNA1-RNA2 | RNA1-RNA2 |
|---|---|---|---|
| from thermal melting experiments | |||
| Tm [K] | 347.0 (0.6) | 332.8 (0.3) | 314.6 (0.6) |
| ΔGUV [kcal/mol] | −21.8 (1.0) | −17.1 (0.9) | −13.3 (0.5) |
| ΔHUV [kcal/mol] | −92.6 (5.7) | −80.8 (7.7) | −86.3 (4.2) |
| TΔSUV [kcal/mol] | −70.8 (4.8) | −63.7 (6.9) | −73.0 (3.8) |
| experimental data extrapolated to MD simulation concentrations | |||
| csim [mM] | 5 | 6 | 7 |
| Tm (Eq. 3) [K] | 368.4 | 356.2 | 334.3 |
| ΔG (Eq. 4) [kcal/mol] | −26.0 | −21.4 | −17.7 |
| from MD simulations | |||
| Tm (ΔG = 0) [K] | 418.4 (2.0) | 365.4 (10.0) | 331.1 (3.7) |
| ΔGcalc [kcal/mol] | −44.8 (1.1) | −32.0 (5.6) | −17.1 (2.0) |
| ΔGGB +ΔGSASA + ΔGelec [kcal/mol] | −28.6 (0.6) | −19.0 (1.6) | 17.6 (2.8) |
| ΔGvdW [kcal/mol] | −56.7 (0.1) | −56.9 (0.7) | −58.2 (1.9) |
| TΔS [kcal/mol] | −40.7 (1.5) | −44.7 (4.3) | −24.4 (2.5) |
Values in parentheses represent standard errors of the mean. For ΔGcalc calculations and its contributions see Methods. ΔGvdW reflects the Lennard-Jones energy term. Energy errors from MD simulations were calculated at 295 K. Errors in the Tm estimates from simulation were obtained by applying the uncertainty in ΔGcalc when estimating Tm from the exponential fit.