I. Definition of binding site interactions upstream of the Epstein Barr Nuclear Antigen Wp promoter: This study resulted in a further definition of a previously reported binding site in the Epstein Barr virus Wp latent promoter. The sequence of the undefined binding site was analyzed by a standard analysis using the TFD SITES table. The existence of proposed binding activities resulting from this sequence analysis was tested by mobility shift competition and high resolution copper-phenanthrolinefoot printing assays. The study indicates that at least one of the proposed interactions occurs under standard experimental in vitro binding conditions.The testing of the functional relevance of a YY1 site far upstream of this promoter,as well as a possible E-box site within the previously identified binding site,would be an area of additional investigation . II. A common motif found in potential DNA-binding domains of NF-kB binding site proteins: This study identified a region of similarity between two families of DNA binding domains that recognize NF-kB sites. Amino terminal residues in NF-kB polypeptides, identified as being required for sequence-specific binding by a number of laboratories, were analyzed by sequence analysis tools aimed at uncovering evolutionarily distant relationships, using the TFD DOMAINS table as well as the NCBI nonredundant protein database. The analyses identified a seven-residue motif that is shared between the NF-kB subunit residues shown to be required for DNA binding, and the amino terminal beta-turn of the zinc finger of PRDII-BF1. Experiments to test the role of the corresponding residues in the binding efficiency of the PRDII-BF1 zinc finger are in progress.
