Characterization of the ColE1 primer-RNA1 complex: analysis of a domain of ColE1 RNA1 necessary for its interaction with primer RNA.

RNA1 is a small, plasmid-encoded transcript involved in the replication control of the plasmid ColE1. RNA1 blocks replication by preventing processing of the primer RNA necessary for the initiation of replication. It has been proposed that inhibition by RNA1 involves a direct interaction between RNA1 and primer RNA. Here we describe an in vitro system that allows the detection and characterization of the RNA1-primer complex. Using this system, we have demonstrated that the association between ColE1 RNA1 and primer results in the formation of an RNA X RNA hybrid between RNA1 and the 5' end of primer RNA. Furthermore, analysis of mutant RNA1 molecules containing sequence alterations in the 5' single-stranded region of the molecule has revealed that this portion of RNA1 is necessary for the formation of the RNA1-primer complex. These experiments indicate that, in addition to the three single-stranded loops of RNA1, the 5' single-stranded region is a functional domain of the molecule.