E1 initiator DNA binding specificity is unmasked by selective inhibition of non‐specific DNA binding

Initiator proteins are critical components of the DNA replication machinery and mark the site of initiation. This activity probably requires highly selective DNA binding; however, many initiators display modest specificity in vitro. We demonstrate that low specificity of the papillomavirus E1 initiator results from the presence of a non‐specific DNA‐binding activity, involved in melting, which masks the specificity intrinsic to the E1 DNA‐binding domain. The viral factor E2 restores specificity through a physical interaction with E1 that suppresses non‐specific binding. We propose that this arrangement, where one DNA‐binding activity tethers the initiator to ori while another alters DNA structure, is a characteristic of other viral and cellular initiator proteins. This arrangement would provide an explanation for the low selectivity observed for DNA binding by initiator proteins.