TABLE 2.
Parameters in the energy function 
for duplexes in the secondary structure
| Pair energies, Ebp | Duplex stacking energies (5′ on 3′), Esk | ||||||
|---|---|---|---|---|---|---|---|
| AU or UA | −0.0275 | A (3′) | C (3′) | G (3′) | U (3′) | ||
| CG or GC | −1.0425 | A (5′) | −3.03125 | −2.99 | −3.12167 | −3.10125 | |
| GU or UG | 0.82 | C (5′) | −3.44 | −3.89875 | −3.22375 | −3.59667 | |
| Penalties for palindromic GU doublets | G (5′) | −3.88833 | −3.73375 | −3.47875 | −3.795 | ||
| GU|UG | 2.95 | U (5′) | −3.21125 | −3.06333 | −3.245 | −2.96125 | |
| UG|GU | 0.85 | Coaxial stacking,  −1.50
|
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All values are in kcal/mol.
