The function of individual zinc fingers in sequence-specific DNA recognition by transcription factor IIIA

Mutations in Zn(2+)-coordinating histidine residues have been used to generate forms of transcription factor IIIA containing structural disruptions in single zinc fingers. These mutant proteins have been analyzed with respect to the structural and functional independence of individual zinc fingers in TFIIIA. They have also been used to assess the energetic contributions to binding and the sites of interaction of each of the nine zinc fingers of TFIIIA with the 5 S rRNA gene. The results are surprising and suggest a complex mode of binding in which the interactions of structurally independent zinc fingers with the DNA substrate are non-uniform and functionally interdependent in a way that may help to explain some of the unusual properties of TFIIIA.