Table 1.
Binding affinities of analogs measured for the ydaO riboswitch
| Modification | Analog | Kd (nM) | Fold Loss | ΔΔGbind (kcal/mol) |
|---|---|---|---|---|
| c-di-AMP | 0.43 ± 0.02 | |||
| Base | c-AMP-GMP | > 2.3 × 106a | > 4.2 × 106 | > 9.0 |
| c-di-GMP | > 1.1 × 107 | > 2.0 × 107 | > 10 | |
| c-AMP-IMP | 750 ± 43 | 1400 | 4.3 | |
| c-di-IMP | 2000 ± 460 | 3600 | 4.9 | |
| c-AMP-Purine | 18 ± 1.6 | 33 | 2.1 | |
| c-di-Purine | 2900 ± 270 | 5300 | 5.1 | |
| c-di-N6m,N6mAMP | > 5 × 105 | > 9.1 × 105 | > 8.1 | |
| c-AMP-DAP | 360 ± 38 | 650 | 3.8 | |
| c-di-DAP | > 1.5 × 106 | > 2.7 × 106 | > 8.8 | |
| c-di-2AP | > 2.5 × 106 | > 4.5 × 106 | > 9.1 | |
| c-di-c7AMP | 6.4 ± 0.6 | 12 | 1.5 | |
| Ribose | c-dA-AMP | 11 ± 1.6 | 20 | 1.8 |
| c-di-dAMP | 160 ± 13 | 290 | 3.4 | |
| c-2’F-A-AMP | 26 ± 2.4 | 47 | 2.3 | |
| c-di-2’F-AMP | 2800 ± 330 | 5100 | 5.1 | |
| c-dA-2’F-A | 290 ± 23 | 530 | 3.7 | |
| c-2’OMe-A-AMP | 340 ± 41 | 620 | 3.8 | |
| c-di-2’OMe-AMP | > 1.6 × 106 | > 2.9 × 106 | > 8.8 | |
| Phosphate | c-(RpRp)-di-Aps | 1.0 ± 0.1 | 1.8 | 0.4 |
| c-(RpSp)-di-Aps | 1.6 ± 0.4 | 2.9 | 0.6 |
a
No detectable binding at the highest ligand concentration tested (≥200 µM). Kd values were estimated based on a 5% detection limit.