Replicative DNA Polymerases

Abstract

In 1959, Arthur Kornberg was awarded the Nobel Prize for his work on the principles by which DNA is duplicated by DNA polymerases. Since then, it has been confirmed in all branches of life that replicative DNA polymerases require a single-stranded template to build a complementary strand, but they cannot start a new DNA strand de novo. Thus, they also depend on a primase, which generally assembles a short RNA primer to provide a 3 0 -OH that can be extended by the replicative DNA polymerase. The general principles that (1) a helicase unwinds the double-stranded DNA, (2) single-stranded DNA-binding proteins stabilize the single-stranded DNA, (3) a primase builds a short RNA primer, and (4) a clamp loader loads a clamp to (5) facilitate the loading and processivity of the replicative polymerase, are well conserved among all species. Replication of the genome is remarkably robust and is performed with high fidelity even in extreme environments. Work over the last decade or so has confirmed (6) that a common two-metal ion-promoted mechanism exists for the nucleotidyltransferase reaction that builds DNA strands, and (7) that the replicative DNA polymerases always act as a key component of larger multiprotein assemblies, termed replisomes. Furthermore (8), the integrity of replisomes is maintained by multiple protein-protein and protein -DNA interactions, many of which are inherently weak. This enables large conformational changes to occur without dissociation of replisome components, and also means that in general replisomes cannot be isolated intact.

The C-terminal Domain of the DNA Polymerase Catalytic Subunit Regulates the Primase and Polymerase Activities of the Human DNA Polymerase α-Primase Complex

“…pol⑀ is indispensable for the assembly of the replisomes at origins (7), pol␣-primase (pol␣-prim) generates primers for the synthesis (8), pol␦ (9) and pol⑀ (10) participate in elongation and bulk DNA synthesis (11)(12)(13), and pol is a key player in the synthesis on templates that are difficult to replicate (14,15). The critical essential step of the replication is the initial primer synthesis by pol␣-prim, because pol␦, pol⑀, or pol cannot start DNA synthesis without a primer with a free 3Ј-OH end.…”

DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity

“…protein-primed DNA polymerase | Bam35 | abasic sites | translesion synthesis | isothermal DNA amplification R eplicative DNA polymerases (DNAPs) from A and B families, collectively termed replicases, exhibit a "tight fit" for their DNA and dNTP substrates and are wondrously adapted to form correct Watson-Crick base pairs, resulting in very pronounced fidelity (1,2). This strict preference to produce A:T and G:C base pairs is also the Achilles heel of faithful DNA polymerases, however, because they are strongly inhibited by modified nucleotides present at sites of DNA damage, leading to the stalling of replication fork and eventually to replicative stress and cell death (3).…”

Regulating DNA Replication in Plants

“…Eukaryotic DNA polymerases have been grouped in five different families, of which family B contains the replicative polymerases (Johansson and Dixon 2013). Like in animals, plant replicative DNA polymerases have been classified in three-major types: DNA polymerase a (POLA), DNA polymerase d (POLD), and DNA polymerase 1 (POLE).…”