Eukaryotic DNA Polymerases

Sue Cotterill, St George's Hospital Medical School, London, UK
Stephen Kearsey, University of Oxford, Oxford, UK

Published online: December 2009

DOI: 10.1002/9780470015902.a0001045.pub2

Deoxyribonucleic acid (DNA) is replicated and repaired by a family of enzymes called DNA polymerases. Eukaryotic cells have a diversity of these enzymes that, while sharing a common biochemical activity, are specialized for particular roles. Three polymerases are required for the replication of the nuclear genome, with pol involved in priming and initial synthesis and pols and involved in bulk DNA replication. These polymerases are dependent on a large number of other proteins which unwind the DNA and perform other functions essential for efficient DNA synthesis. Polymerases are also involved in DNA repair and many repair-specific enzymes have been identified. Some repair polymerases can refill a gap generated by removal of damaged DNA, or copy a damaged template, allowing DNA synthesis to proceed across a damaged template. Repair polymerases can also have tissue-specific functions in lymphoid cells, where they contribute to somatic hypermutation of immunoglobulin genes.

Key concepts:

  • Catalytic function of DNA polymerases.
  • Concepts of ‘proofreading’ and ‘processivity’.
  • Roles of replicative DNA polymerases needed for chromosome replication and organization at the replication fork.
  • Function of accessory proteins needed for polymerase function in chromosome replication.
  • Different modes of action of specialized polymerases involved in DNA repair.
  • Catalytic mechanism of polymerases.
  • Assays used to detect polymerase function in vitro.

Keywords: replication; DNA repair; DNA synthesis; cell cycle

Figure 1. (a) Basic mechanism catalysed by DNA polymerases. Polymerization of nucleotides on the single-stranded template requires a primer (RNA or DNA) which provides a 3¢-OH group to which the incoming nucleotide is joined and the direction of synthesis is thus 5¢ to 3¢. Only nucleotides that correctly base pair with the templates strand (according to A • T, G • C rules) are incorporated. One molecule of pyrophosphate (PPi) is produced per nucleotide incorporated. (b) Steps in the polymerization reaction. The order of the reaction is binding to the template–primer, followed by binding of the dNTP. dNTP is cleaved at the / bond to give dNMP that is added onto the chain, PPi is released, and the polymerase translocates along to the next 3¢ terminus or dissociates.
Figure 2. Structure of RB69 polymerase. RB69 is a prokaryotic family B polymerase, and is therefore likely to have a structure representative of eukaryotic replicative polymerases (, , ; Franklin et al., 2001). (a) Polymerization mode. DNA template–primer (pink-orange) first binds to the polymerase thumb domain, followed by binding of a nucleotide triphosphate (blue), complementary to the template base immediately adjacent to the 3¢-OH of the primer. On binding the dNTP, the finger domain (shown here in the open conformation) rotates (black arrow) towards the palm domain to form a closed ternary complex. This facilitates phosphodiester bond formation between primer 3¢-OH and the -phosphate of the incoming dNTP. (b) In the exonuclease (proof-reading) mode, the thumb tip rotates to partition the DNA to the exonuclease site (shown in yellow), allowing removal of a noncomplementary base. Reproduced with permission from Patel and Loeb (2001).
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    Stillman B (1994) Smart machines at the DNA replication fork. Cell 78: 725–728.
    book Vengrova S and Dalgaard JZ (eds) (2009) DNA Replication, Methods and Protocols. New York, NY: Humana Press.

Related Sub-Topics:

Replication and Recombination | DNA Damage and Repair | Enzymes: Structure and Action Mechanism | Nucleic Acids: Structure, Function, Metabolism
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Article Title: Eukaryotic DNA Polymerases
 
How to Cite close
Cotterill, Sue, and Kearsey, Stephen(Dec 2009) Eukaryotic DNA Polymerases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001045.pub2]