Table 3.
Table of Free-Energy Cost of Forming a Four-Way Junction in kcal/mol as a Function of the 5′ and 3′ Junction Length in Nucleotide ( and , Respectively) with the Middle Junction Lengths Fixed (nt)
| Four-Way Junctions with Center Loops with Lengths b = c = 4 nt | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| 5′ Loop Length (nt), a | 3′ Loop Length (nt), d | ||||||||
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | ||
| 0 | 7.85 (0.43) | 7.85 (0.43) | 7.60 (0.32) | 8.03 (0.53) | 8.27 (0.76) | 8.03 (0.53) | – | 7.42 (0.27) | |
| 1 | 7.71 (0.37) | 8.03 (0.53) | 8.27 (0.76) | 8.03 (0.53) | 8.27 (0.76) | 8.03 (0.53) | – | 7.85 (0.43) | |
| 2 | 8.03 (0.53) | 8.03 (0.53) | 7.85 (0.43) | 8.27 (0.76) | 7.71 (0.37) | 8.27 (0.76) | 7.71 (0.37) | 7.60 (0.32) | |
| 3 | 8.03 (0.53) | 7.85 (0.43) | 7.85 (0.43) | 7.85 (0.43) | – | 8.03 (0.53) | 7.71 (0.37) | 7.85 (0.43) | |
| 4 | 7.85 (0.43) | 7.71 (0.37) | 7.85 (0.43) | 8.27 (0.76) | 7.85 (0.43) | 8.27 (0.76) | 8.03 (0.53) | 7.85 (0.43) | |
| 5 | 7.71 (0.37) | 8.03 (0.53) | 7.85 (0.43) | – | 7.71 (0.37) | 8.03 (0.53) | 7.71 (0.37) | 7.42 (0.27) | |
| 6 | 7.71 (0.37) | 7.71 (0.37) | 8.27 (0.76) | – | 7.71 (0.37) | 7.60 (0.32) | 7.50 (0.29) | 7.60 (0.32) | |
| 7 | 7.50 (0.29) | 7.85 (0.43) | 7.60 (0.32) | 7.42 (0.27) | 7.71 (0.37) | 8.03 (0.53) | 7.85 (0.43) | 7.85 (0.43) | |
Error estimates from the simulation are given in parentheses. Blank entries correspond to events that were not observed during the simulation despite the large size of the ensemble generated.