FIGURE 7.

T7 helicase·polymerase encountering a nick. A, T7 helicase and/or gp5·trx cannot initiate DNA unwinding or polymerization of nucleotides at a nick. The helicase needs an ssDNA tail to load while polymerase needs ssDNA as template. B, a polymerizing DNA polymerase cannot bypass a nick in the presence of exogenous helicase. The pre-assembly of helicase·polymerase in the leading-strand synthesis mode is necessary for nick bypass. C, an ongoing helicase·polymerase complex cannot bypass a nick on the template strand. When polymerase reaches the nick, the helicase that encountered the nick earlier has already stopped or has started translocation on the dsDNA. In either condition the polymerase loses the opportunity to contact the DNA terminus on the other side of the nick. D, an ongoing helicase·polymerase complex can bypass a nick on the non-template strand. Helicase unwinding might at first be terminated at the nick, but when polymerase reaches the nick it may attempt to continue DNA synthesis, because the template is continuous and the polymerase is capable of at least destabilizing the dsDNA downstream of the nick. These events would favor the loading of the helicase onto the non-template strand downstream of the nick to re-establish the replication fork. The tight association of helicase with polymerase increases the chance of helicase contacting the DNA terminus downstream of the nick. gp2.5 may facilitate the binding.