There are several families of prokaryotic and eukaryotic DNA polymerases, classified based on sequence homology and crystal structure. They are all associated with three main activities:

    • 5’–3’ polymerase activity—the addition of a new nucleotide at the 3’ end of a strand, which would primarily determine the speed of an enzyme
    • 5’–3’ exonuclease activity—the removal of nucleotides at the 5’ end of a molecule, which is physiologically responsible for the removal of ribonucleotide primers used for the replication of the lagging strand of DNA
    • 3’–5’ exonuclease activity—the removal of nucleotides at the 3’ end of a molecule, which would determine the accuracy (or proofreading activity) of an enzyme

Family A polymerases are either replicative or repair DNA enzymes. The replicative polymerases (e.g., T7 DNA polymerase, mitochondrial polymerase gamma, Taq polymerase) match free nucleotides to a template DNA sequence, while the repair polymerases (e.g., E. coli DNA polymerase I, Bst polymerase) rectify any mistakes in base pairing while amplifying. The replicative enzymes have a high speed of reaction but lack proofreading activity. They also have a 5’ to 3’ exonuclease activity, particularly useful if a fluorescent probe is used for the detection of amplification, as it would allow the probe to hydrolyze and emit fluorescence. Modified repair enzymes of family A (e.g., Klenow fragment from E. coli DNA polymerase I or Bst pol large fragment, which are lacking 5’ to 3’ exonuclease activity) are particularly useful for special reactions due to their strand displacement activity.

Family B includes replicative polymerases (e.g., Pfu polymerase, phi29 DNA polymerase, E. coli DNA polymerase II) involved in the biosynthesis of both the leading and lagging DNA strands during cellular replication. They are highly accurate, performing 3’–5’ proofreading of the newly synthesized DNA, but at the cost of the reaction speed.

Family C includes prokaryotic replicative polymerases (e.g., E. coli DNA polymerase III) involved in the replication of bacterial genome. They too have a 3’–5’ proofreading activity.

Family D includes some eukaryotic replicative polymerase (e.g., Pyrococcus furious DNA polymerase II) and is functionally close related to family B.

Family X includes eukaryotic enzymes (e.g., pol β, pol μ, pol λ) mostly involved in repairing DNA after chemical, oxidative, or radiation-dependent damages.

Family Y (e.g., E. coli pol IV and pol V) includes prokaryotic or eukaryotic enzymes with a low fidelity for intact DNA strands that are capable of replicating damaged DNA.

Family RT includes eukaryotic telomerases and the reverse transcriptases found in viruses, which work using RNA as a template to synthesize a DNA strand. Members of family RT are required when a RNA template is used to generate DNA (reverse transcription).

The vast majority of enzymes used in in vitro experiments belong to family A, B, or RT.

Information source: Matteo Beretta, Molecular Biologist, PCR Biosystems

For more information on DNA Polymerases check out this related article: Tips on Choosing the Right DNA Polymerase