Alternative non-B DNA structures may play a role in gene function by modulating interactions with regulatory proteins. We are using two related physical techniques to analyze possible conformations of DNA and DNA- protein complexes. A. Birefringence. We have analyzed the persistence length of a 250bp fragment of DNA containing the 5s RNA gene of Xenopus borealis. In the presence of Zinc (+2) or spermidine this fragment has an altered structure not assumed by a control piece of DNA. This altered structure is a bend centered at +50 to +60, which is the 5' end of the internal control region. We are currently analyzing this 5S RNA gene complexed to TFIIIA, a protein which binds in the middle of the gene and is essential for transcription. B. Photochemical Electric Dichroism. We have developed a new technique for analyzing DNA structure and DNA-protein interaction. It involves combination of photochemical techniques (generation of UV pyrimidine dimer crosslinks by laser illumination) with electric dichroism (orientation of DNA in a high electric field). We have analyzed the 5S RNA gene of sea urchins and have found an alternate DNA structure associated with oligopurine tracts within the TFIIIA-binding domain of this gene.
