Figure 6.

Model to explain gel mobility anomalies of Fos–Jun–DNA complexes. The two rectangular shaped boxes represent the heterodimer Fos–Jun, bound to the AP-1 site in DNA containing a curved A-tract region. (A) Fos–Jun bound to oppositely phased DNA isomers with short (11–19 bp) phasing linkers. Y-shaped, slower moving complexes are formed between Fos–Jun and hcgDNA11 and hcgDNA19; however F-shaped, faster moving complexes are formed between Fos–Jun and hcgDNA15. The gel-phasing amplitude observed is significant. (B) The effect of Mg²⁺, incorporated into the gel and running buffer, on the gel mobilities of Fos–Jun–DNA complexes. We propose that Mg²⁺ competes with stabilizing electrostatic interactions between Fos–Jun and DNA, which results in an increase in the flexibility of the orientation of the leucine zipper arm with respect to the DNA helix and a decrease in the gel-phasing amplitude. (C) Fos–Jun bound to oppositely phased DNA isomers with long (35–43 bp) phasing linkers. The local structure at the Fos–Jun–DNA junction is T-shaped for oppositely phased isomers, which is reflected in their similar gel mobilities and lack of gel-phasing amplitude.