TABLE 2.

Parameters in the energy function $E_{\mathrm{dp}}$ 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, $E_{cx}$ −1.50

All values are in kcal/mol.