Table 3. Free-Energy Parameters (kcal/mol) at 37 °C for Predicting 3 × 3 Nucleotide and Larger RNA Internal Loops.

^aThese parameters are used to predict the free energy of the 3 × 3 nucleotide and larger internal loops in 1 M NaCl according to eq 4. Except for the new parameters, ΔG°_{5′CR/3′AA bonus} and ΔG°_{5′CR/3′AA, pH bonus}, the parameters derived here are similar to those in ref (16). YR is a canonical pair of CG, UA, or UG, with the pyrimidine Y on the 5′ side of the internal loop. In general, Y and R are defined, respectively, as U or C and A or G in the UG, UA, or CG pair.