Table 1.
Pseudoknot loop entropies parameters defined in Equation 3.
| Stem size (bp) | Loop size (nt) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | |
| (S2) | L1 (across the deep groove of S2) | |||||||||||
| 2 | — | — | — | 6.2 | 6.4 | 6.4 | 6.6 | 6.8 | 6.9 | 7.1 | 7.2 | |
| 3 | — | 6.4* | 6.4* | 6.4 | 6.6 | 6.6 | 6.8 | 6.9 | 7.1 | 7.3 | 7.5 | |
| 4 | 4.4* | 4.4* | 4.5 | 5.4 | 5.6 | 6.0 | 6.3 | 6.6 | 6.9 | 7.1 | 7.3 | |
| 5 | 2.3 | 4.4 | 4.6 | 5.7 | 6.0 | 6.5 | 6.9 | 7.2 | 7.5 | 7.8 | 8.0 | |
| 6 | 2.3 | 4.4 | 4.8 | 5.8 | 6.0 | 6.5 | 6.8 | 7.1 | 7.4 | 7.6 | 7.8 | |
| 7 | 2.3 | 4.4 | 5.0 | 5.9 | 6.2 | 6.8 | 7.0 | 7.3 | 7.6 | 7.8 | 8.0 | |
| 8 | — | 4.4 | 5.2 | 5.7 | 6.4 | 6.7 | 7.1 | 7.3 | 7.5 | 7.7 | 7.9 | |
| 9 | — | 5.5* | 5.5 | 6.4 | 6.7 | 7.2 | 7.5 | 7.9 | 8.1 | 8.3 | 8.5 | |
| 10 | — | 6.9* | 6.9* | 6.9 | 7.5 | 7.7 | 8.1 | 8.3 | 8.6 | 8.8 | 8.9 | |
| 11 | — | — | — | — | 8.7 | 8.8 | 8.9 | 9.1 | 9.2 | 9.3 | 9.3 | |
| 12 | — | — | — | — | 9.8 | 9.2 | 9.5 | 9.6 | 9.7 | 9.8 | 9.8 | |
| (S1) | L2 (across the shallow groove of S1) | |||||||||||
| 2 | — | — | — | 7.6 | 7.0 | 7.0 | 7.1 | 7.2 | 7.3 | 7.4 | 7.5 | 7.7 |
| 3 | — | 6.5* | 6.5* | 6.5 | 6.6 | 6.7 | 6.9 | 7.1 | 7.2 | 7.4 | 7.6 | 7.7 |
| 4 | — | — | 9.2* | 9.2* | 9.2 | 8.9 | 8.9 | 8.9 | 9.0 | 9.0 | 9.1 | 9.2 |
| 5 | — | — | — | 9.8* | 9.8* | 9.8 | 9.1 | 8.9 | 8.8 | 8.8 | 8.8 | 8.8 |
| 6 | — | — | — | 11.9* | 11.9* | 11.9* | 11.9 | 11.0 | 10.4 | 10.1 | 9.9 | 9.8 |
| 7 | — | — | — | — | 12.4* | 12.4* | 12.4* | 12.4 | 11.4 | 11.0 | 10.7 | 10.5 |
| 8 | — | — | — | — | 12.1* | 12.1* | 12.1* | 12.1 | 11.6 | 11.4 | 11.2 | 11.1 |
| 9 | — | — | — | — | — | 13.7* | 13.7* | 13.7* | 13.7 | 12.6 | 12.0 | 11.5 |
| 10 | — | — | — | — | — | 13.7* | 13.7* | 13.7 | 12.7 | 12.2 | 11.8 | 11.5 |
| 11 | — | — | — | — | — | — | — | — | 15.9 | 14.1 | 13.0 | 12.4 |
| 12 | — | — | — | — | — | — | — | — | 18.7 | 15.8 | 14.2 | 13.2 |
The upper half of the Table gives (−Δ SL1/kB) for loop L1 as a function of the S2 helix stem length and the L1 loop length. The lower half of the Table gives (−Δ SL2/kB) for loop L2 as a function of the S1 helix stem length and the L2 loop length. See Figure 1 for the stem–loop construct of a pseudoknot. The * entries in the Table indicate the long stem and short loop structures that cannot be realized in the diamond lattice but may be viable for a realistic pseudoknot. For these restricted loops, we use the entropies of the minimal loop lengths for the same helix length.