Table 2.
Free energies for loop formation
| Secondary structure of the loop a |
Source of structural model | ΔG°37 LOOP (kcal/mol) |
|---|---|---|
| C UAA G G AAG C |
NMR b | −1.78 c |
| CUAAG GAAGC |
Predicted | −1.06 d |
| C UAAG G AA GC |
Crystal structure of D. radiodurans | 3.53d 1.09 e |
a
Non-Watson–Crick pairs are in bold.
b
UA forms a single hydrogen bonded base pair in the NMR structure.
c
Measured ΔG°37LOOP as calculated from eq. 2
d
Value for ΔG°LOOP as predicted from updated nearest neighbor parameters that incorporate previous data (1, 2, 96) and assuming a single Watson–Crick UA pair.
e
Value for ΔG°LOOP was predicted assuming a 3 × 3 nucleotide internal loop (73) with the non-Watson–Crick UA pair treated as part of the loop.