Dissection of the DNA-binding domain of Xenopus laevis TFIIIA. Quantitative DNase I footprinting analysis of specific complexes between a 5 S RNA gene fragment and N-terminal fragments of TFIIIA containing three, four or five zinc-finger domains.

Recombinant zinc finger proteins corresponding to N-terminal fragments of Xenopus laevis transcription factor IIIA (TFIIIA) comprising three, four and five fingers produced in Escherichia coli as cleavable hybrid proteins were shown to form specific stoichiometric complexes with DNA fragments containing the internal control region (ICR) of a 5 S RNA gene. The ordered set of DNase I footprints of each of the three proteins on the ICR comprise a nested set of footprints extending upstream from its 3' end (position +96 relative to start of the mature transcript) 20 bp, 20 bp or 34 bp into the ICR, respectively. Quantitative analysis of the footprinting data provided firm evidence that the DNase I footprint, and hence the structure, of the authentic TFIIIA:ICR complex in this region is fully and precisely accounted for by the N-terminal three fingers binding within the +77 to +96 region plus the pair of fingers 4 and 5, both required to extend the footprint upwards from the +77 to the +63 position. A structural interpretation of this set of new footprinting data in view of previous results and data is presented and discussed in terms of a refined model in which the protein-DNA interaction between the ICR and the three N-terminal fingers corresponds closely to that observed in the homologous three-finger zif268:DNA complex, whereas the basic mode of protein-DNA interaction, in which the pair of fingers 4 and 5 is engaged in forming the TFIIIA:ICR complex is of an entirely different, albeit not yet understood nature. To allow assessment of our model in terms of potential specificity-determining H-bonding patterns, a molecular model of the complex between the three-finger TFIIIA fragment and the ICR was constructed, using the zif268:DNA co-ordinates. Eight out of the nine amino acid residues, which according to our model are suitably located for forming hydrogen bonds with the bases, are potential H-bond acceptors or donors.