TABLE 1.
Effect of probe length and ionic strength on the DNA binding affinities of the OBD and N260 proteinsa
| Probe or buffer constituent | Probe length or ionic strength |
KD (nM) for:
|
|
|---|---|---|---|
| OBD | N260 | ||
| 5′-F-CCGAGGCC-3′ | 8 bp | >2,500 | >2,500 |
| 5′-F-CCGAGGCCATTC-3′ | 12 bp | 41 ± 3 | 121 ± 5 |
| 5′-F-CCGAGGCCATTCTGAG-3′ | 16 bp | 26 ± 2 | 60 ± 3 |
| 5′-F-CCGAGGCCATTCTGAGAATT-3′ | 20 bp | 21 ± 2 | 52 ± 3 |
| 5′-F-CCGAGGCCATTCTGAGAATTGAGC-3′ | 24 bp | 29 ± 2 | 61 ± 3 |
| NaCl | 50 nM | 22 ± 2 | 46 ± 2 |
| 100 nM | 269 ± 39 | 828 ± 99 | |
| 150 nM | >2,500 | >2,500 | |
| 200 nM | >2,500 | >2,500 | |
a
The KD values for the OBD and N260 proteins for the indicated probes (with TBS underlined and in boldface) at 50 mM NaCl (top) and for a 24-bp probe at the indicated concentrations of salt (NaCl; bottom) were calculated from binding isotherms performed as described for Fig. 4. Standard deviations were calculated from two independent binding isotherms, with each data point performed in triplicate.