Table 1.
Dissociation constant (Kd in µM) of RNA aptamers with theophylline or 3MX ligands a
| Aptamer Constructs |
Ligand | Steady-State Fluorescence | ITC |
|---|---|---|---|
| Theophylline-binding Aptamer | |||
| WT | theophylline | — | 0.86 ± 0.12 |
| 3MX | — | 1.6 ± 0.5 | |
| P27 | theophylline | 0.72 ± 0.01 | 1.4 ± 0.12 |
| 3MX | 1.9 ± 0.7 | 2.6 ± 0.6 | |
| P27Z26 | theophylline | 220 ± 120 | 281 ± 38 |
| P27X28 | theophylline | ND | 1050 ± 280 |
| P10 | theophylline | ~ 4 b | 9.4 ± 0.8 |
| P10Z11 | theophylline | ~ 12 b | 9.4 ± 0.7 |
| P10Z25 | theophylline | > 100 b | ND |
| P10Z11Z25 | theophylline | > 100 b | ND |
| 3MX-binding Aptamer | |||
| WT | 3MX | — | 2.7 ± 2.0 |
| P27 | 3MX | 3.6 ± 0.3 | 3 ± 0.5 |
| theophylline | >1000 | ND | |
| P10 | 3MX | ND | 24 ± 5 |
a
Uncertainties in parameters were estimated from multiple measurements. All measurements were performed in a buffer of 100 mM HEPES, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, pH 7.5, and at 25 °C.
b
Kd was only estimated due to extremely small change of the fluorescence intensity upon ligand binding. ND = not determined due to weak binding or lack of fluorescence change upon binding.