Sequence-specific binding of the N-terminal three-finger fragment of Xenopus transcription factor IIIA to the internal control region of a 5S RNA gene.

An N-terminal fragment of Xenopus TFIIIA, containing domains 1-3, (TF 3), was expressed in E. coli. High yields of recombinant zinc finger protein was isolated, and its DNA binding activity for the internal control region (ICR) of the Xenopus 5S RNA gene, was demonstrated by band-shift experiments and DNase I footprinting analysis. TF 3 protects 20 bp of ICR against DNase I digestion. The limits of protection are from +77 to +96 on both coding and noncoding strand. This protection pattern is identical to the protection pattern obtained with TFIIIA in the overlapping region, showing that the 3-finger fragment accounts fully for the protein-DNA interactions in TFIIIA-5S RNA gene over this region.