Table 3. Binding Constants of Neomycin Dimers with TAR RNA.
| Ligand | Linker Length | K (M-1) | ||||
|---|---|---|---|---|---|---|
|
| ||||||
| Wildtype | Bulgeless | Tetraloop | Bulgeless Tetraloop | U3 Bulge | ||
| DPA51 | 7 | 1.2×108 | 7.5×107 | 2.7×107 | 2.3×108 | 1.6×107 |
| DPA52 | 7 | 7.1×107 | 8.9×107 | 1.4×107 | 7.5×107 | 6.9×106 |
| DPA65 | 7 | 1.4×108 | 1.0×108 | 1.3×107 | 6.9×107 | - |
| DPA53 | 8 | 1.5×108 | - | - | - | - |
| DPA54 | 8 | 2.6×107 | 2.2×107 | - | 1.2×107 | 2.1×106 |
| DPA55 | 10 | 1.1×107 | 3.6×107 | 3.5×106 | 2.8×107 | 2.6×106 |
| DPA56 | 10 | 6.6×107 | 6.3×107 | 5.0×106 | 5.9×107 | 3.8×106 |
| DPA58 | 16 | 7.6×106 | 6.8×107 | 1.4×107 | 7.2×107 | 4.8×106 |
| DPA60 | 20 | 2.5×107 | 4.4×107 | 2.0×106 | 2.7×107 | 1.5×106 |
| Neo | N/A | - | 3.0×107 | - | 1.6×107 | - |
Table representing the binding constants derived from Scatchard analysis from the ethidium bromide displacement assay using the neomycin dimers and neomycin with wildtype and mutant TAR RNA. Buffer conditions: 100 mM KCl, 10 mM SC, 0.5 mM EDTA, pH 6.8. [TAR RNA] = 200 nM/strand. [EtBr] = 5 μM.