PrimaseEdit
Primase is a specialized RNA polymerase that catalyzes the synthesis of short RNA primers required to start DNA synthesis during genome replication. By laying down these primers, primase provides a free 3'-hydroxyl group that DNA polymerases can extend, enabling the rapid duplication of genetic material. The enzyme’s activity is essential in all domains of life that use RNA-primed mechanisms to initiate replication, and it operates within larger protein assemblies that coordinate unwinding, primer placement, and DNA synthesis.
Across organisms, primase exists in different organizational forms but maintains a common role: to generate primers that initiate the synthesis of new DNA strands. In bacteria, the enzyme is known as DnaG and functions as part of the primosome together with the DnaB helicase. In archaea and eukaryotes, primase is a heterodimer composed of a catalytic subunit and a regulatory subunit (often referred to as PriS and PriL in prokaryotic-like notation, with the human equivalents named PRIM1 and PRIM2). In eukaryotes, primase works in concert with DNA polymerase α to form an initiation complex that first creates an RNA primer and then extends it with a short stretch of DNA.
Structure and function
Bacterial primase and the primosome
In bacteria, primase is a single polypeptide known as DnaG that collaborates closely with the DnaB helicase during replication. DnaG possesses an RNA polymerase–like active site and interacts with DnaB through its C-terminal region. This partnership is central to the coordinated progression of the replication fork: helicase unwinds the duplex, exposing single-stranded DNA, and primase synthesizes the RNA primer on the exposed template. The primers are typically short, on the order of a dozen nucleotides, and are subsequently extended by DNA polymerases and processed to produce a continuous new strand. See also the concept of the Okazaki fragment as the discrete RNA-primed segments synthesized on the lagging strand.
Archaeal and eukaryotic primase
In archaea and eukaryotes, primase is a heterodimer comprising a catalytic subunit (often referred to as PriS or PRIM1) and a regulatory subunit (PriL or PRIM2). This complex is part of a larger replication apparatus that, in many systems, includes the DNA polymerase α–primase complex in eukaryotes. The PriS subunit carries the RNA polymerase active site, while PriL modulates primer synthesis and interacts with other replication factors. The resulting RNA primer is then handed off to DNA polymerase α, which begins primer extension with a short DNA segment; subsequently, processive polymerases such as DNA polymerase δ or ε take over for bulk DNA synthesis. See DNA polymerase α, DNA polymerase δ, and DNA polymerase ε for related enzymes in replication.
Primer synthesis and primer handling
Primase typically initiates primer synthesis de novo, without a preexisting primer, using the DNA template to start a new RNA chain. The primer length is constrained by the polymerase’s initiation mechanism and the need to complete primer handoff to the next synthesis stage. After primer synthesis, the RNA segment is removed and replaced with DNA during maturation steps that involve ribonucleases (such as RNase H) and structure-specific nucleases (for example, FEN1 in certain systems), followed by gap filling by DNA polymerases and ligation. See also the concept of the RNA primer and the mechanics of ribonucleotide removal during lagging-strand maturation.
Role in DNA replication
Primase’s core function is to initialize the synthesis of new DNA strands at replication origins or at the discontinuities of the lagging strand. On the lagging strand, the replication machinery repeatedly synthesizes short RNA primers to start each Okazaki fragment; these fragments are later converted into continuous DNA as primers are removed and replaced with DNA. On the leading strand, primers are generally required only at the initial origin firing, after which continuous replication proceeds with a single, long primer typically supplanted by DNA polymerases as needed. The activity of primase is tightly coordinated with the helicase, clamp, and polymerases to ensure accurate and timely replication; see the roles of DnaB, PCNA, and RFC for related coordination mechanisms.
Regulation and interactions
Primase does not act in isolation. In bacteria, the DnaG–DnaB interaction is a central regulatory node that links unwinding with primer synthesis. In eukaryotes, the PriS–PriL complex is regulated in the context of the cell cycle and genome maintenance pathways, with its activity integrated into the larger [ DNA polymerase α–primase complex ] and coordinated with the RFC clamp loader and the sliding clamp PCNA. Postsynthetic processing of primers involves nucleases such as RNase H and other processing factors that facilitate the replacement of RNA with DNA and final ligation of nicks. The primer-hand-off step is a focal point for maintaining replication speed and genome stability, making primase a target for studies of replication stress and cellular responses to DNA damage.
Evolution and diversity
Primases show evolutionary diversity that reflects the split between bacterial and archaeal/eukaryotic replication strategies. Bacterial primases (DnaG) operate within the bacterial primosome with helicase partners, while archaeal and eukaryotic primases form part of a more elaborate initiation complex that couples RNA primer synthesis to de novo DNA synthesis by DNA polymerase α and beyond. The fundamental concept—synthesizing a short RNA primer to enable DNA polymerases to begin synthesis—remains conserved, but the protein architecture and regulatory interactions differ across life’s major lineages. See primosome for the bacterial assembly that coordinates these activities and DNA replication for the overarching process in which primase participates.