The position and magnitude of the Zn induced bend within the 5s RNA gene of Xenopus has been determined. The center of the bend is located at about bp +65 within the gene. The bend magnitude is at least 50-60 degrees, comparable to naturally occuring bends from phased A tracts, until now the only other sequence known to bend DNA. These values were obtained by quantitative analysis of changes in rotational diffusion coefficients with and without added Zn for a series of overlapping DNA fragments spanning the 5s RNA gene. Given the specificity of Zn binding for purines, the most probable cause of the bending is due to junction angles between oligopurines tracts with a Zn induced altered conformation and adjacent canonical B-form structures. Both the oocyte and somatic sequences have four of these oligopurine tracts within a 60 bp region. They are symmetrically located about a bp +70 center and have an underlying 10 bp phasing. This bend is found within the binding domain of TF IIIA, a zinc finger protein that plays a key role in regulating 5s RNA gene activity. There is evidence in the literature, as well as our own preliminary results, that TF IIIA binding also bends DNA. The binding strength of TF IIIA to sequence variants of the binding domains seems to correlate with the symmetry and phasing of the oligopurine tracts. The bending of DNA by TF IIIA binding is likely accomplished by stabilizing the same alternate DNA conformation as Zn binding.
