Figure 4.
Relative affinity of RepB for different DNA sequences. The indicated fragments were mixed and incubated in the absence of RepB (-) or in the presence of increasing concentrations of the protein. The relative equilibrium binding constant (Krel) was calculated from Eq. 2. Relative affinities of RepB for the bind locus compared to the nic locus (A) and for the nic locus compared to a non-specific (nsp) DNA (B). A 3-fold molar excess of either the fragment containing the nic locus relative to the fragment harbouring the DDR (A), or of the nsp DNA relative to the nic fragment (B) was used. (C) Relative affinity of RepB for DNAs containing 1, 2 or 3 repeats of the DDR. The three duplex oligonucleotides were used at the same molar ratio. Note that the complexes corresponding to the three different DNAs could not be solved.