Table 1.
The affinity of XPA DBD for ss-ds junction DNA substrates
Dissociation constants were extracted from the MST data plotted in Fig. 2. The 8/12 HP splayed-arm substrate is composed of a Y-shaped ss-dsDNA junction with 8-nt duplex and 12-nt ssDNA overhangs on both 5′ and 3′ ends and a 4-nt HP on the opposite end. The nomenclature for other substrates follows the same system. The numbers in parentheses identify each substrate as shown in Fig. 1, which also includes the chemical structures. The errors are standard deviations from at least three measurements. The less than 3-fold difference between the Kd values indicates that the protein does not have substantial junction substrate specificity.
| Substrate | Kd |
|---|---|
| μm | |
| 8/12 HP splayed arm (3) | 3.0 ± 0.1 |
| 8/12 HP 5′ overhang (5) | 5.2 ± 0.2 |
| 8/12 HP 3′ overhang (4) | 8.2 ± 0.5 |
| 8/10 HP 5′ overhang (6) | 5.9 ± 0.2 |
| 8/8 HP 5′ overhang (7) | 4.6 ± 0.1 |
| 8/6 HP 5′ overhang (8) | 4.2 ± 0.2 |
| 8/4 HP 5′ overhang (9) | 3.5 ± 0.2 |