Table 2.
Trends in thermal stability using experimental and predicted melting temperatures and overview of experimental pKa values in singly, doubly and triply modified model duplex systems
| Duplex | Motif | T m a | ΔTmb | pKa | pKa | 0 ≤ fi ≤ 1c | ΔmaxTmp d | ΔTmp e | (ΔTmp – ΔTm) |
|---|---|---|---|---|---|---|---|---|---|
| (°C) | (°C) | Ti | Tj>i | (°C) | (°C) | (°C) | |||
| Model | n.a. | 58.9 ± 0.2 | ref | ||||||
| T21-model | n.a. | 57.2 ± 0.2 | ref* | ||||||
| T8 ImH+ | in | 64.1 ± 0.6 | 5.2 ± 0.6 | 8.72 ± 0.02 | n.a. | ∼1 | 5.2 | ref | ref |
| T18 ImH+ | in | 64.2 ± 0.6 | 5.3 ± 0.6 | 8.57 ± 0.03 | n.a. | ∼1 | 5.2 | 5.2 | -0.1 |
| T21ImH+ | non | 59.3 ± 0.5 | 2.1 ± 0.5* | 7.62 ± 0.03 | n.a. | 0.81 | 2.6 | ref | n.a. |
| (T6T8)ImH+ | non/in | 65.0 ± 0.2 | 6.1 ± 0.3 | 7.82 ± 0.05 | 8.90 ± 0.05 | 0.87 | 7.8 | 7.6 | 1.5 |
| (T7T8)ImH+ | non/in | 63.9 ± 0.4 | 5.0 ± 0.4 | 6.96 ± 0.08 | 8.70 ± 0.07 | 0.48 | 7.8 | 6.5 | 1.5 |
| (T6T18)ImH+ | non/in | 64.7 ± 0.3 | 5.8 ± 0.4 | 8.01 ± 0.04 | 8.53 ± 0.03 | 0.91 | 7.8 | 7.7 | 1.9 |
| (T6T7)ImH+ | non/non | 59.6 ± 0.1 | 0.7 ± 0.2 | 7.50 ± 0.05 | 7.64 ± 0.04 | 0.76/0.82 | 5.2 | 4.1 | 3.4 |
| T7T8T23-model | n.a. | 62.5 ± 1.5 | 3.6 ± 1.7 | ||||||
| (T7T8T23)ImH+ | non/in/in | 71.8 ± 0.9 | 9.3 ± 1.8∧ | 7.40 ± 0.08 | 8.59 ± 0.08 | 0.72 | 13.0 | 12.3 | 3.0 |
| 9.03 ± 0.02 |
a1 μM strand concentration, 100 mM NaCl, 10 mM sodium phosphate, pH 7.0 The reported errors are one standard deviation as described in the materials section.
bThe reference system used for calculations is always the model except when T21-model is used as indicated by an * or when the triply modified system is used indicated by ∧.
cProtonation degree calculated using the experimental pKa; underlined pKa values are those for in-motif imidazolium moieties.
dMaximum predicted increase in Tm and [e] predicted increase taking protonation in c into account.