Figure 4.

Relationship between relative fluorescence intensity and DNA-binding affinity. (A) SybrGreen I-stained microarray; (B) low laser-power scan of wild-type Zif268 bound to a microarray; (C) high laser-power scan of wild-type Zif268 bound to a microarray. Red pixels indicate saturated signal intensity. (D) Plot showing the relationship between relative signal intensity and K. Error bars indicate 1 SD of the SybrGreen I normalized binding data. These sequences were chosen because they span a range of relative fluorescence intensities. For this evaluation, a separate set of microarrays was spotted with these DNA sequences. Because some of these sequences contain mutations in the binding sites for fingers 1 and 3 of Zif268, they were not printed on the microarrays containing all different 3-bp binding sites for finger 2.