DNA POLYMERASE

CLASSIFICATION OF DNA POLYMERASES

Based on sequence homology and the comparison of the features of their primary sequence,
DNA polymerases are classified into seven families. A, B, C, D, X, Y, and RT.

Family Types of DNA Species Examples

polymerase

A Replicative and Eukaryotic and T7 DNA polymerase,

Repair Polymerases Prokaryotic Pol I, and DNA
Polymerase γ

B Replicative and Eukaryotic and Pol II, Pol B, Pol ζ,

Repair Polymerases Prokaryotic Pol α, δ, and ε

C Replicative Prokaryotic Pol III

Polymerases

D Replicative Euryarchaeota Not well-

Polymerases characterized

X Replicative and Eukaryotic Pol β, Pol σ, Pol λ,

Repair Polymerases Pol μ, and Terminal
deoxynucleotidyl
transferase

Y Replicative and Eukaryotic and Pol ι (iota), Pol κ

Repair Polymerases Prokaryotic (kappa), Pol IV, and
Pol V

RT Replicative and Viruses, Retroviruses Telomerase, Hepatitis

Repair Polymerases and Eukaryotic B virus
Prokaryotic DNA polymerase

a) Pol I
Polymerase I is a DNA repair enzyme from the family A polymerases that has a 5’ to 3’ and 3’
to 5’ activity (DNA synthesis).
Pol I accounts for more than 95% of polymerase activity in coli, although cells that lack this
polymerase have been found and its activity can be replaced by the other four types of
polymerase.
This DNA polymerase has a poor processivity rate, adding around 15 to 20 nucleotides per
second.
This repair polymerase is involved in excision repair with 3'-5' and 5'-3' exonuclease activity
and processing of Okazaki fragments generated during lagging strand synthesis.

*KLENOW fragment

b) Pol II
DNA polymerase II, a Family B polymerase. Polymerase II is a DNA repair enzyme with a 3’ to
5’ exonuclease activity.
When DNA acquires damage in the form of short gaps, which block Pol III activity, Pol II helps to
remedy this problem by restarting DNA synthesis downstream of these gaps.
Pol II has 3'-5' exonuclease activity and participates in DNA repair, replication restart to bypass
lesions, and its cell presence can jump from ~30-50 copies per cell
to ~200-300 during SOS (response to DNA damage in which the cell cycle is arrested and DNA
repair and mutagenesis is induced. The system involves the RecA protein (Rad51 in
eukaryotes)) induction.

c) Pol III
This holoenzyme is the main polymerase in E. coli DNA replication and is one of the family C
polymerases.
Polymerase III has the 3’ to 5’ exonucleolytic proofreading activity, and can process both
the leading and lagging DNA strands.

d) Pol IV
This enzyme belongs to the Y family of DNA polymerases.
In E. coli, DNA polymerase IV is involved in non-targeted mutagenesis
Pol IV is an error-prone polymerase that has NO 3’ to 5’ proofreading activity and is involved
in mutagenesis or the altering of DNA to give rise to a mutation.

e) Pol V
Pol V also belongs to the Y family of polymerases and allows DNA damage to be bypassed in
order for replication to continue.
It is involved in SOS response (response to DNA damage in which the cell cycle is arrested and
DNA repair and mutagenesis is induced. The system involves the RecA protein (Rad51 in
eukaryotes)) and translesion synthesis DNA repair mechanisms.
Eukaryotic DNA Polymerase

f) Bacteriophage T4 DNA polymerase

Bacteriophage (phage) T4 encodes a DNA polymerase that catalyzes DNA synthesis in a 5’ to

3’ direction.
The phage polymerase also has an exonuclease activity that acts in a 3’ to 5’ direction, and
this activity is employed in the proofreading and editing of newly inserted bases.
A phage mutant with a temperature sensitive DNA polymerase, when grown at permissive
temperatures, was observed to undergo recombination at frequencies that are about two-fold
higher than that of wild-type phage.

It was proposed that a mutational alteration in the phage DNA polymerase can stimulate
template strand switching (copy choice recombination) during replication.

g) T7 DNA Polymerase
T7 DNA polymerase catalyzes the phosphoryl transfer during DNA replication of the T7 phage.
During this process, the DNA polymerase “reads” existing DNA strands and creates two new
strands that match the existing ones. The T7 DNA polymerase requires a host factor, E. coli
thioredoxin,[1] in order to carry out its function.
It LACKS the 5′–3′ exonuclease activity found in E. coli DNA polymerase I but does possess
a strong 3′–5′ single and double stranded DNA exonuclease activity
 h) POL α
POL α is a member of Family B Polymerases and are the main polymerases involved with
nuclear DNA replication.
This unique enzyme has two distinct polymerase activities: a 5’- 3’ DNA-dependent DNA
polymerase, and a 5’- 3’ DNA-dependent RNA polymerase.
The RNA polymerase activity is a primase. Because of this, the enzyme is often referred to as
Pol α primase. It is the only enzyme known to have both DNA polymerase and primase
activities, and the only one capable of self-primed DNA synthesis on a previously
unprimed ssDNA.
Pol α does NOT have an intrinsic 3'- 5' exonuclease activity and also LACKS a 5'- 3'
exonuclease activity.
In vivo, the primary function of Pol α primase is to make short RNA/DNA primers for replicative
DNA synthesis.

i) DNA polymerase δ (delta)

DNA polymerase δ has 5’- 3’ DNA polymerase activity and an intrinsic 3'- 5' exonuclease
activity.
Pol δ requires an associated 30 kDa protein, called proliferating cell nuclear antigen (PCNA), for
full polymerase activity and processivity. In the presence of PCNA, Pol δ is highly processive,
and it is PCNA that acts as a processivity factor. Biochemical and genetic studies in yeast and
mammalian cells suggest that Pol δ is also involved in some types of DNA repair synthesis.
Due to its high processivity, Pol δ takes over the leading and lagging strand synthesis from
Polα.

j) DNA polymerase ε (epsilon)

Belongs to Family B Polymerases and are the main polymerases involved with nuclear DNA
replication. Pol ε has 3'-5' exonuclease activity.
Pol ε is a reasonably processive enzyme that also associates with PCNA at a primer terminus.
This suggests that it is a replicative polymerase.
Because of its high processivity and proofreading activity, it has been further suggested that Pol
ε is involved in primer elongation.
Pol ε participates in repairing errors made in the leading strand during Pol δ replication in
conjunction with DNA mismatch repair machinery.

k) DNA polymerase β
Belongs to family X polymerases are found mainly in vertebrates, and a few are found in plants
and fungi
Pol β is required for short-patch base excision repair, a DNA repair pathway that is essential for
repairing alkylated or oxidized bases as well as abasic sites.
This is the smallest and simplest of the classical eukaryotic polymerases; it is composed of a
single ~40-48 kDa protein.
Pol β is not highly active and is not very processive. It has NO intrinsic exonuclease
activities.
Its preferred template is duplex DNA with short gaps, although it can bind a nicked duplex and is
capable of some limited displacement synthesis. Pol β is primarily involved in DNA repair.

l) Polymerases λ, σ and μ (lambda, sigma, and mu)

Family X polymerases also contain the well-known eukaryotic polymerase such as Pol σ
(sigma), Pol λ (lambda), Pol μ (mu), and Terminal deoxynucleotidyl transferase (TdT).
Pol λ and Pol μ, are involved in non-homologous end-joining, a mechanism for rejoining DNA
double strand breaks due to hydrogen peroxide and ionizing radiation, respectively.

m) Polymerases η, ι and κ (eta, iota, and kappa)

Pol η (eta), Pol ι (iota), and Pol κ (kappa), are Family Y DNA polymerases involved in the DNA
repair by translesion synthesis.
Polymerases in Family Y are low-fidelity polymerases, but have been proven to do more good
than harm as mutations that affect the polymerase can cause various diseases, such as skin
cancer and Xeroderma Pigmentosum Variant (XPS).
Pol η is particularly important for allowing accurate translesion synthesis of DNA damage
resulting from ultraviolet radiation.
Pol κ is thought to act as an extender or an inserter of a specific base at certain DNA lesions.

n) Polymerases ζ (zeta)
Pol ζ, another B family polymerase, is involved in translesion synthesis.
Pol ζ LACKS 3' to 5' exonuclease activity and is unique in that it can extend primers with
terminal mismatches.

o) Polymerases γ and θ (gamma and theta)

Pol γ (gamma) and Pol θ (theta) are Family A polymerases.
Pol γ, is the only mtDNA polymerase and therefore replicates, repairs, and has proofreading
3'-5' exonuclease.
Any mutation that leads to limited or non-functioning Pol γ has a significant effect on mtDNA and
is the most common cause of autosomal inherited mitochondrial disorders.
Pol θ, found in eukaryotes, its function is not clearly understood. Pol θ belongs to Family A
polymerase.
Pol θ extends mismatched primer termini and can bypass abasic sites by adding a nucleotide.

p) Reverse transcriptase
Retrovirus reverse transcriptase
Retroviruses package their genomes as ssRNA but replicate this RNA through a dsDNA
intermediate. To do this, they employ an RNA dependent DNA polymerase (reverse
transcriptase).
RT is a typical DNA polymerase in the 5'- 3' direction of synthesis, requirement for a
template primer with a 3'-OH terminus, and requirements for dNTPs and Mg2+.
RT does NOT have a detectable DNA specific exonuclease activity, and therefore has no
proofreading function. As a result, its error rate is relatively high. This is reflected in a high
mutation rate; virus variants are generated at high frequency. This is an important aspect of
pathogenesis: retroviruses are adept at evading host immuno-surveillance because of high
mutation frequency.
RT is unique among DNA polymerases in at least two respects:
• It can use primed, natural ssRNAs as a template. It can also use a primed ssDNA as a
template.
• It has intrinsic RNase H activity. RNase H is a processive exonuclease that specifically
degrades the RNA strand of a DNA-RNA hybrid beginning from either the 5' or 3' end. It
can also act as an endonuclease. RNase H hydrolyzes phosphodiester bonds to leave
products with 3' hydroxyl and 5' phosphate ends.
The enzyme is relatively processive and can replicate the 8 kb retrovirus genome without a
processivity factor.

q) Telomerase
Telomerase is a ribonucleoprotein recruited to replicate ends of linear chromosomes because
normal DNA polymerase cannot replicate the ends, or telomere.
Telomerase acts like other DNA polymerases by extending in 3’ to 5’ direction, but, unlike
other DNA polymerases, telomerase does NOT require a template.
The protein and RNA components make up an active enzyme of ~200 kDa. The RNA
component (~1.3 kb in yeast) contains the template sequence that is used for DNA synthesis.
(So telomerase carries its own template.)
In vitro, telomerase from a given species synthesizes the G-rich strand sequence characteristic
of the species.
However, telomerase activity is present in actively dividing cells, including immortalized
(transformed) cells in culture, and in most cancer cells. So telomerase may be useful for cancer
diagnostics, and is a possible target for therapeutics.
Thermostable DNA polymerase

r) Taq DNA Polymerase

It is highly thermostable DNA polymerase from the thermophilic bacterium Thermus
aquaticus.
The enzyme catalyzes 5'→3' synthesis of DNA, has NO detectable 3'→5' exonuclease
(proofreading) activity and possesses LOW 5'→3' exonuclease activity.
In addition, Taq DNA Polymerase exhibits deoxynucleotidyl transferase activity, which
frequently results in the addition of extra adenines at the 3'-end of PCR products.
Recombinant Taq DNA Polymerase is the ideal tool for standard PCR of templates 5 kb
or shorter.

s) Pfu
3' to 5' Exonuclease
From Pyrococcus furiosus
Appears to have the lowest error rate of known thermophilic DNA polymerases

t) Vent (also known as Tli polymerase)

3' to 5' Exonuclease
From Thermococcus litoralis
Half Life at 95 C is approximately 7 hours