The preparation of a heterogeneous non-histone protein extract from wheat germ utilizing Br-poly(dG-dC)-poly(dG-dC) (Z-DNA) affinity chromatography is described. The binding characteristics of antibodies against Z-DNA are used as a model system to define important criteria that the DNA binding behavior of a Z-DNA binding protein should display. We show that the wheat germ extract contains DNA binding proteins specific for left-handed Z-DNA by these criteria. The affinity of the proteins measured by competition experiments was approximately 105 greater for Br-poly(dG-dC)-poly(dG-dC) (Z-DNA) than for poly(dG-dC)-poly(dG-dC) (B-DNA). The affinity of the proteins for plasmid DNA increases with increasing negative superhelicity which is known to stabilize Z-DNA. The proteins are shown to compete with Z-DNA antibodies for binding to supercoiled plasmids. Finally, the affinity for two plasmids at a given superhelical density is greater for the plasmid containing an insert known to form Z-DNA than for a plasmid without the insert. The proteins exhibit a 2-3-fold greater affinity for stretches of (dC-dA)n-(dT-dG)n over stretches of (dG-dC)n-(dG-dC)n when both sequences are induced to form Z-DNA by supercoiling.
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