Definition of DNA polymerase
DNA polymerases are a group of enzymes used to make copies of DNA templates, which are essentially used in DNA replication mechanisms. These enzymes make new copies of DNA from existing templates and also function by repairing the synthesised DNA to prevent mutations. DNA polymerase catalyses the formation of the phosphodiester bond which constitutes the backbone of DNA molecules. It uses an ion magnesium in catalytic activity to balance the charge of the phosphate group.
What are DNA polymerases?
- DNA polymerase was first identified by Arthur Kornberg in lysates of Escherichia coliin 1956.
- The enzyme is found and used in the DNA replication of prokaryotic cells and eukaryotes.
- Several types of DNA polymerase enzymes have been discovered and the first one to be discovered is called DNA polymerase I.
- Each of these types plays an important role in the mechanisms of DNA replication and repair.
- However, DNA polymerases are not used to initiate the synthesis of new strands, but in the extension of existing DNA or RNA strands that are paired with a template strand.
- DNA polymerase starts its mechanism after a short fragment of RNA is created as a primer and paired with a template DNA strand.
- DNA polymerase acts by synthesising the new DNA strand by adding new nucleotides that match those in the template, extending the 3′ end of the template strand. Each nucleotide is linked to a phosphodiester bond.
- DNA polymerase uses energy from the hydrolysis of the phosphoanhydride bond between the three phosphates (nucleoside triphosphates) attached to each free base (nucleotides).
- Addition of a nucleotide to a growing DNA strand forms a phosphodiester bond between the nucleotide phosphate and the growing strand using the high-energy phosphate bond of hydrolysis, releasing two distal phosphates known as pyrophosphate.
- DNA polymerases are very precise in their mechanism with minimal errors of less than one error for each 107 nucleotides.
- Some types of DNA polymerase have the ability to correct and remove mismatched nucleotide bases and correct them.
- They also correct post-replication mismatches by controlling and repairing errors, distinguishing mismatches in the new strand from the template strand sequences.
- The cell eukaryotic contains five DNA polymerases α, β, γ, δ and ε. Polymerase γ is found in the mitochondria of the cell and actively replicates mitochondrial DNA, while polymerase α, β, δ are found in the nucleus cellularand is thus involved in nuclear DNA replication.
- Polymerase α and δ are mainly applied and active in diving cells, thus involved in replication, while polymerase β is active in both diving and non-dividing cells, thus involved in DNA damage repair.

Structure of DNA polymerase
- DNA polymerases generally have a conserved structure and thus define their vital role in cellular function that cannot be replaced.
- DNA polymerases are made up of subdomains that resemble an open right hand like the palm, fingers and thumb.
- The palm contains the amino acids essential catalytic at their active sites.
- Fingers play an important role in nucleotide recognition and binding.
- The thumb is for the binding of substrate of DNA.
- There is a domain located between the finger and thumb known as the pocket, which is composed of two regions, i.e. the insertion site and the post-insertion site.
- The incoming nucleotides bind to the insertion site, while the new base pair binds at the site downstream of the insertion.
- Other subdomains along with these domains are family-specific and each has essential functions in DNA replication.
- However, these subdomains are different for each polymerase.
Structure of the A family
- In addition to the subdomains already discussed, family A polymerase also has a 5′ to 3′ exonuclease that is used to remove RNA primers from Okazaki fragments.
- Some A family groups also have a 3 ′ to 5 ′ exonuclease activity that functions to correct DNA.
Structure of the B family
- They also possess the basic subdomains with 3′ to 5 extremely active; exonuclease to correct DNA replication errors.
Structure of the X family
- These family groups have thumb, palm and finger subdomains that are structurally part of the N-terminus or in the 31 kDA polymerase fragment.
- The palm of this family contains three aspartic acid motifs, the fingers have M and N helices containing amino acid residues.
- The N-terminus is connected to an 8 kDa amino-terminal domain which contains a 5 ‘deoxyribose phosphate lyase, which is essential in base excision repair.
Structure of the Y family
- The N-terminus of this group contains the catalytic core of the palm, fingers and thumb.
- They also have a C-terminus which has a tertiary structure preserved from a sheet A four-stranded beta-sheet supported on one side by two alpha helices, which are also known as the little finger domain. They play a role in DNA binding and are essential for the completion of polymerase activity.
- However, this family lacks flexibility, unlike the other families.
Types of DNA polymerase
Basically, the types of DNA polymerase are also divided depending on the organism which possess them, i.e. eukaryotic and prokaryotic DNA polymerases. These types of DNA polymerase are classified according to their characteristics, including structural sequences and functions.
Eukaryotic DNA polymerase types
Polymerase γ
- Polymerase γ is a type A polymerase, whose main function is to replicate and repair mitochondrial DNA.
- It also functions by revising 3′ to 5′ exonuclease activity.
- Mutations in Poly γ significantly affect mitochondrial DNA causing autosomal mitochondrial disorders.
Polymerase α, polymerase δ and polymerase ε.
- These are the B-type polymerase enzymes and are the main polymerases applied in DNA replication.
- Pol α acts by binding to the primase enzyme, forming a complex, where both play a role in initiating replication. The primase enzyme creates and positions a short RNA primer that allows Pol α to initiate the replication process.
- Pol δ initiates the synthesis of the delayed strand of Pol α, while Pol ε is thought to synthesise the leading strand during replication.
- Studies indicate that Pol δ replicates both the leading and lagging strand.
- Pol δ and ε also have 3′ to 5′ exonuclease activity.
Polymerase β, polymerase μ and polymerase λ.
- These are the type 3 or X family of polymerase enzymes.
- Pol β has a short-patch base excision repair mechanism in which it repairs alkylated or oxidised bases.
- Pol λ and Pol μ are important for rejoining DNA double-strand breaks due to DNA peroxide. hydrogen peroxide and the ionising radiationrespectively.
Polymerases η, polymerase ι and polymerase κ
- These are type 4 or Y-family polymerases that are mainly used in DNA repair by a mechanism known as translesion synthesis.
- They are error-prone during DNA synthesis.
- Pol η works by accurately securing the synthesis by translesion of DNA damage caused by ultraviolet radiation.
- Pol κ is still a student, but one of its known functions is to extend or insert specific bases into certain DNA lesions.
- Translesion synthesis polymerases are activated by stalled replicative DNA polymerase.
Terminal deoxynucleotidyl transferase (TdT).
- TdT functions by catalysing the polymerisation of deoxynucleoside triphosphate at the 3′-hydroxyl group of a preformed polynucleotide chain.
- TdT is a non-template-directed DNA polymerase.
- It was first detected in the gland thymus gland.
Types of DNA polymerase prokaryote
DNA polymerase I
- This is a type A or family A polymerase enzyme that was initially isolated from E. coli and was found most abundantly in E. coli.
- Its main function is DNA strand excision repair from the 3′-5 ′ direction to the 5′-3 direction, as an exonuclease.
- It also helps with the maturation of Okazaki fragments, which are short strands of DNA that form the lagging strand during DNA replication.
- Its function during replication is the addition of nucleotides into the RNA primer and moves along the 5′-3 ′ direction.
- The DNA polymerase I binding site is known as an octylglycoside.
DNA polymerase II
- It belongs to Type B or Family B of polymerases.
- Its main function is 3′ – 5′ exonuclease activity and also to restart replication after replication stops due to DNA strand damage.
- DNA polymerase II is located at the replication fork, to help direct the activities of other polymerases.
DNA polymerase III
- This is the main enzyme used in DNA replication, belonging to Family C or Type C.
- It is responsible for the synthesis of new strands by the addition of nucleotides to the 3′-OH group of the primer.
- It has a 3′-5 ′ exonuclease activity, so it can also correct errors that may arise during DNA strand replication.
DNA polymerase IV
- Belongs to Family Y and is involved in non-directed mutagenesis.
- Its activation is based on the stalling activity of the replication fork.
- When activated, it creates a checkpoint, stops replication and allows time for proper repair of lesions in the new DNA strand.
- It is also involved in the repair mechanism of translesion synthesis.
- It has no nuclease activity, so it is prone to errors in DNA replication.
DNA polymerase V
- Belongs to Family Y, with high regulatory activity.
- It is produced only when DNA is damaged and requires translesion synthesis.
- It also lacks exonuclease functions and therefore cannot correct DNA replication synthesis, making it less efficient.
Taq DNA polymerase
- The polymerase Taq is a thermostable type of DNA polymerase 1 that was initially isolated from a thermophilic eubacterium known as Thermus aquaticus.
- Abbreviated as Taq or Taq pol.
- It is commonly used in the polymerase chain reaction to amplify short strands of DNA.
- Due to its thermophilic nature, it is capable of resisting the denaturation which is required during PCR, so it replaced the DNA polymerase from E. coli.
Mechanism of DNA polymerase
The mechanism of DNA polymerase is called the two-metal ion mechanism, i.e. two metal ions act as active sites to stabilise replication transmission. The first metal ion acts by activating the hydroxyl group which attacks the phosphate group of the dNTP and the second metal ion stabilises the negative charges and accumulates on the oxygen and the chelating phosphate groups.
DNA polymerase vs. RNA polymerase
SN | Features | DNA polymerase | RNA polymerase |
1. | Definition | An enzyme that synthesises DNA. | It is an enzyme that synthesises RNA. |
2. | Mechanism | The mechanism of DNA polymerase is during replication by which it synthesises new strands of DNA. | RNA polymerase functions during the transcriptionwhich is the synthesis of RNA. |
3. | Strands | Synthesizes a molecule double-stranded DNA molecule. | Synthesise a single-stranded RNA molecule. |
4. | Presence or absence of Primer | Its replication mechanism is initiated by a short RNA primer. | It does not need a primer to initiate transcription. |
5. | Nucleotide insertion | Inserts nucleotides after finding the free 3’OH end with the help of the primer-synthesiser, the primase enzyme. | Adds nucleotides directly. |
6. | Amino acid bases | Adds dATP (adenine-thymine), dGTP, dCTP and dTTP to the newly growing DNA strand. | Inserts dATP, dGTP, dCTP and dUTP into the growing RNA strand. |
7. | Functionality | It has polymerisation and proofreading activity. | RNA polymerase has only polymerisation activity. |
8. | Polymerisation rate | The rate of polymerisation by DNA polymerase is approximately 1000 nucleotides per second in prokaryotes. | The rate of RNA polymerase is 40 to 80 nucleotides per second. |
9. | Efficiency | The DNA polymerase enzyme is faster, more efficient and more accurate considering its proofreading activity. | RNA polymerase is slower, inefficient and inaccurate. |
10. | Subtypes | DNA polymerase has three different subtypes: Type 1, 2 and 3. | RNA polymerase has five different subtypes in eukaryotes |
11. | Termination | DNA synthesis continues to the end when the strand is terminated, i.e. when polymerisation stops, so that all chromosomal DNA is synthesised. | Polymerisation ends when RNA polymerase encounters the termination codon or the termination codon on the strand of nucleic acid. |