Two mechanisms have been proposed to describe how and when these multiple events of Okazaki fragment initiation occur to maintain the coordinated replication of the leading and lagging DNA strands within a replisome, and evidence suggests that both mechanisms operate in the replisomes studied thus far. The initiation of each new Okazaki fragment involves the release of the current Okazaki fragment by the lagging-strand holoenzyme, the synthesis of a primer by primase, and the handoff of the primer to the recycled lagging-strand polymerase. The results reproduce experimental data, providing insights into events related to Okazaki fragment initiation and the overall functioning of DNA replisomes.ĭuring DNA replication, the opposite polarity of the two DNA strands necessitates that the leading DNA strand is copied continuously whereas the lagging DNA strand is copied in discrete segments known as Okazaki fragments. We have modeled repeated cycles of Okazaki fragment initiation using a collision with a completed Okazaki fragment or primer–primase complexes as the recycling mechanism. The collision with primer–primase complexes triggering the early termination of Okazaki fragment synthesis has distinct advantages over those previously proposed because this signal requires no transmission to the lagging-strand polymerase through protein or DNA interactions, the mechanism for rapid dissociation of the holoenzyme is always collision, and no unique characteristics need to be assigned to either identical polymerase in the replisome. We show for the T4 bacteriophage DNA replication system that primer–primase complexes have a residence time similar to the timescale of Okazaki fragment synthesis and the ability to block a holoenzyme synthesizing DNA and stimulate the dissociation of the holoenzyme to trigger polymerase recycling. We examined the role of RNA primer–primase complexes left on the lagging ssDNA from primer synthesis in initiating early lagging-strand polymerase recycling. The mechanism and signal that initiate this behavior-that is, the signaling mechanism-have not been definitively identified. The lagging-strand polymerase sometimes recycles to begin the synthesis of a new Okazaki fragment before finishing the previous fragment, creating a gap between the Okazaki fragments. The opposite strand polarity of duplex DNA necessitates that the leading strand is replicated continuously whereas the lagging strand is replicated in discrete segments known as Okazaki fragments.
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