Table 1.
Binding affinities (M−1) for parent polyamides on plasmid pMFST2 (1–2) and plasmid pMFST (3–6). Equilibrium association constants reported are mean values from three DNase I footprinting titration experiments. Standard deviations are shown in parentheses. Bolded numbers in brackets indicate fold decrease in match site binding affinity for α-DABA-linked versus γ-DABA-linked polyamides. Mismatch base pairs are indicated in bold.
| Polyamide | Match Site | Ka (M−1) | Mismatch Site | Ka (M−1) | Mismatch Site | Ka(M−1) | |||
|---|---|---|---|---|---|---|---|---|---|
| 1 | 5′-TAGGTGT-3′ | 3.0(±1.3)x108 | [147] | 5′-TAGGTCT-3′ | 8.5(±3.1)x107 | [129] | 5′-TAGCTGT-3′ | – | |
| 2 | 5′-TAGGTGT-3′ | 4.4(±0.4)x1010 | 5′-TAGGTCT-3′ | 1.1 (±0.8)x1010 | 5′-TAGCTGT-3′ | 1.1 (±0.3)x109 | |||
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| 3 | 5′-ATGGTCA-3′ | 4.4(±0.6)x109 | [11] | 5′-AACGACT-3′ | 1.5(±0.3)x108 | [120] | 5′-TAGCACA-3′ | – | |
| 4 | 5′-ATGGTCA-3′ | 4.9(±0.7)x1010 | 5′-AACGACT-3′ | 1.8(±0.3)x1010 | 5′-TAGCACA-3′ | 3.9(±1.0)x108 | |||
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| 5 | 5′-TAGTGGT-3′ | 8.0(±0.6)x108 | [54] | 5′-ATATGGT-3′ | – | 5′-TAGTCGT-3′ | 6.2(±3.0)x107 | [100] | |
| 6 | 5′-TAGTGGT-3′ | 4.3(±0.3)x1010 | 5′-ATATGGT-3′ | 9.9(±0.3)x108 | 5′-TAGTCGT-3′ | 6.2(±0.2)x109 | |||