Immunoassay for sequence-specific DNA-protein interaction.

An immunoassay that allows a quantitative measure of the interaction of DNA and specific DNA binding proteins has been described here. A detailed quantitative description of the assay has previously been published. In this chapter the assay has been used to determine the size and location of the SV40 sequences that bind the viral protein, T antigen, by new DNase protection and footprinting procedures. These results are consistent with the observations of Tjian, who used purified protein to establish the sizes and locations of T-antigen binding sites. In addition, the assay is shown to be capable of detecting specific binding even in crude protein extracts of SV40 virus-transformed cell lines that carry only one copy of the viral genome. These results suggest that this procedure may be useful in the identification and purification of specific DNA binding proteins in eukaryotic cells.