primase

Primase is an RNA polymerase that synthesizes short RNA primers required to initiate DNA synthesis during DNA replication. These primers provide a 3′-OH end for DNA polymerases to begin extending DNA. At replication forks, primase is recruited to the unwinding DNA by interactions with helicase and other replisome components and then generates a short RNA primer on the template strand.

Two main evolutionary families exist. In bacteria, primase is DnaG, which works with the helicase DnaB. In archaea and eukaryotes, primase is part of the heterotetrameric Pol alpha-primase complex (PriS/PriL in archaea; PRIM1/PRIM2 in eukaryotes). The primase subunits synthesize the RNA primer, which is then extended by the associated DNA polymerase alpha. In this system, primer synthesis and a short DNA stretch are produced in a two-step action within the same complex, after which replication proceeds with higher-processivity polymerases.

Primers on the leading vs lagging strand: On the lagging strand, primers are laid repeatedly to initiate Okazaki fragment synthesis; on the leading strand, a primer primes continuous synthesis at the start of a new stretch, after which the polymerase extends without further primers under normal fork progression.

Primer removal and replacement: After extension, primers are removed and replaced with DNA. In bacteria, DNA polymerase I performs 5′-to-3′ exonuclease–mediated primer removal and gap filling. In eukaryotes, RNase H and FEN1 remove RNA primers, and DNA polymerase delta fills the gaps, followed by ligation.