Table 2. (Top row) Hybridization (k+) and melting (k−) rate constants for P3T3 and P4T4 duplexes, all measured relative to P0T0, for the experiment (1) (k+ only) and oxDNA. In the case of P4T4, Gao et al. claimed to measure a fast (f) and a slow (s) regime (1) (Bottom row). Listed are the measured rates, r+, relative to P0T0 that a state starting from the unbound state goes to a state with one inter-strand base pair (second column), and the measured probabilities, P+, relative to P0T0 that a state starting from one inter-strand base pair goes to a full duplex with 25 base pairs (third column). Listed are the ratios of the calculated equilibrium constants measured relative to P0T0.
| Duplex | Experiment  /k+
|
oxDNA  /k+
|
oxDNA k−/
|
|---|---|---|---|
| P0T0 | 1 | 1 | 1 |
| P3T3 | 1.8 ± 0.2 | 2.1 ± 0.3 | 100 ± 25 |
| P4T4 | 6.0 ± 0.3 (f) | 10.6 ± 3.4 | 1934 ± 712 |
| 25.0 ± 1.3 (s) | |||
 / (0 → 1) |
 / (1 → 25) |
 /
|
|
| P0T0 | 1 | 1 | 1 |
| P3T3 | 1.85 ± 0.17 | 1.14 ± 0.19 | 204 ± 45 |
| P4T4 | 2.11 ± 0.11 | 4.93 ± 0.33 | 20539 ± 4096 |