Table 2.
Table of Free-Energy Cost of Forming a Three-Way Junction in kcal/mol as a Function of the 5′ and 3′ Junction Length in Nucleotide ( and , Respectively) with the Center Junction Length () Kept at 1 nt as a Parameter
| Center Loop Length b = 1 nt | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| 5′Loop Length (nt), a | 3′ Loop Length (nt), c | ||||||||
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | ||
| 0 | 6.54 (0.10) | 6.97 (0.15) | 7.21 (0.18) | 6.84 (0.13) | 7.03 (0.16) | 7.09 (0.17) | 7.34 (0.21) | 7.00 (0.15) | |
| 1 | 6.94 (0.14) | 7.06 (0.16) | 7.25 (0.19) | 7.06 (0.16) | 7.25 (0.19) | 7.59 (0.27) | 7.09 (0.17) | 7.30 (0.20) | |
| 2 | 6.87 (0.13) | 6.82 (0.13) | 7.03 (0.16) | 7.30 (0.20) | 7.46 (0.23) | 7.30 (0.20) | 7.17 (0.18) | 7.40 (0.22) | |
| 3 | 7.25 (0.19) | 7.21 (0.18) | 7.25 (0.19) | 7.34 (0.21) | 7.25 (0.19) | 7.46 (0.23) | 7.40 (0.22) | 7.13 (0.17) | |
| 4 | 7.30 (0.20) | 7.30 (0.20) | 6.97 (0.15) | 7.88 (0.37) | 7.46 (0.23) | 7.46 (0.23) | 7.46 (0.23) | 7.59 (0.27) | |
| 5 | 7.09 (0.17) | 7.30 (0.20) | 7.59 (0.27) | 7.52 (0.25) | 7.46 (0.23) | 7.34 (0.21) | 7.25 (0.19) | 7.00 (0.15) | |
| 6 | 7.34 (0.21) | 7.40 (0.22) | 7.25 (0.19) | 7.40 (0.22) | 7.34 (0.21) | 7.34 (0.21) | 7.30 (0.20) | 7.21 (0.18) | |
| 7 | 6.97 (0.15) | 7.09 (0.17) | 6.94 (0.14) | 7.17 (0.18) | 7.06 (0.16) | 7.25 (0.19) | 7.46 (0.23) | 7.13 (0.17) | |
For and , see Tables S1–S3. Error estimates from the simulation are given in parentheses. Entries that have “inf” errors were too infrequently observed during the simulation for errors to be accurately calculated.