Three reports in Nature address some pertinent questions regarding prokaryotic DNA replication — how the DNA-synthesis machinery replicates past DNA damage, how continuous DNA synthesis on the leading strand is coordinated with the discontinuous replication of the lagging strand, and how RNA polymerases can produce RNA primers for DNA replication.

How the cell ensures accurate DNA replication when one or both of the strands are damaged has puzzled scientists for decades. It has been shown that ultraviolet irradiation can lead to single-stranded gaps on both leading and lagging strands, which indicates that leading-strand synthesis is not continuous. Heller and Marians now provide mechanistic insights into how leading-strand synthesis can restart downstream of an unrepaired strand, leaving a gap that is presumably filled after the damage has been repaired.

The authors showed that in the presence of a blocking lesion on the leading strand, replication-protein PriC-dependent loading of the replication fork helicase, DnaB, was sufficient to allow the reassembly of the replication machinery, to unwind the replication-fork duplex and to coordinate the repriming of both the leading and lagging strands. In fact, a single DnaB hexamer on the lagging-strand template coordinated the priming of both strands, thereby coupling the 'unzipping' and priming activities.

In a second report, Lee, van Oijen and colleagues studied the kinetics of leading- and lagging-strand synthesis at the single-molecule level by monitoring the length of individual DNA molecules during DNA replication. They noticed short pauses in the synthesis of the leading strand, which were primase dependent and preceded the formation and release of a replication loop on the lagging strand. Primases synthesize RNA primers on the lagging strand at a much slower rate than the rate of DNA synthesis on the leading strand. The authors propose that, as a way of coordinating the two events, the primase activity on the lagging strand temporarily halts the progression of the replication fork, thereby preventing the synthesis of the leading strand from progressing too far ahead of that of the lagging strand.

Several viral and plasmid DNA-replication systems use bacterial RNA polymerase to synthesize a replication primer, but how the primer's 3′ end anneals to the DNA template was unknown. Reporting in a third paper, Zenkin, Severinov and co-workers carried out an in vitro primer RNA synthesis reaction on DNA from bacteriophage M13. The replication primer co-eluted with Escherichia coli RNA polymerase as part of the so-called priming complex.

The authors noted that the properties of the replication-priming complex differed from that of known transcription-elongation complexes. The complex contained an overextended RNA–DNA hybrid, which caused the termination of transcription, and the topology of the complex left the 3′ end of the RNA available for interaction with the DNA polymerase to initiate DNA synthesis. Transcription complexes with similar topologies in other bacterial systems might use the same replication-priming mechanism.