Mechanistic studies on the DNA linking activity of Epstein-Barr nuclear antigen 1. Nucleic Acids Res

The DNA replication, plasmid segregation and trans-activation functions of Epstein–Barr nuclear antigen 1 (EBNA1) require the binding of EBNA1 to specific DNA recognition sites in the two non-contiguous functional elements of the Epstein–Barr virus latent origin of replication, oriP. EBNA1 molecules bound to these elements interact with each other resulting in the formation of looped individual DNA molecules and multiply linked DNA molecules. We have developed a glycerol gradient sedimentation assay suitable for quantitative analysis of the DNA linking activity of EBNA1 and used it to investigate the contribution of EBNA1 residues to the linking interaction and the mechanism of the interaction. Using overlapping internal deletion mutants, we found that two regions of EBNA1 can cause DNA linking, amino acids 40–100 and 327–377, but that the stabilities of the linked complexes formed by the two regions differ dramatically; only complexes formed through the latter region are stable to glycerol gradient sedimentation analysis. Mechanistic studies using EBNA1 in combination with GAL4–EBNA1 fusion proteins showed that linking inter-actions mediated by residues 327–377 are homotypic. Our results also suggest that only the DNA-bound form of EBNA1 participates in the protein–protein interactions seen in DNA linking