The 5S gene internal control region is B-form both free in solution and in a complex with TFIIIA.

Rhodes and Klug have recently proposed that the internal control region of the Xenopus 5S RNA gene adopts an A-type DNA structure in solution. This suggestion was based on a Fourier analysis of both the spacing of DNase I cutting sites and on the distribution of G residues in the DNA sequence. Both revealed a approximately 5.6-5.7-base periodicity which the authors interpreted as a structural repeat every half helical turn of A-type DNA. This contention was strengthened by the finding that a 9-base-pair (bp) double-stranded deoxyoligonucleotide corresponding to residues +81 to +89 of the 5S gene exhibits an A' RNA-like crystal structure. This region of DNA is of special interest as it forms the binding site for the 5S gene-specific transcription factor IIIA (TFIIIA). TFIIIA is a Zn2+-binding protein which interacts with both the internal control region of the gene and the 5S transcript. As base-paired regions of RNA are of the A type, it was reasonable to postulate that 5S DNA might also adopt this conformation. We report here that the circular dichroism (CD) spectrum of a synthetic 54-bp deoxyoligonucleotide corresponding to the TFIIIA binding site is similar to the CD spectrum of B-form DNA in solution. Further, DNA-TFIIIA complexes show an unaltered DNA CD component indicating no gross alteration in DNA structure on protein binding.