DNA Polymerases

In 1956, Arthur Kornberg identified DNA polymerase for the first time in E. coli lysates. The enzyme is used in the replication of DNA by both prokaryotic and eukaryotic cells. DNA polymerase enzymes come in a variety of forms, with DNA polymerase I being the first to be discovered. Each of these types is essential in the replication and repair of DNA activities. DNA polymerases, on the other hand, are used to expand existing DNA or RNA strands that have been mated with a template strand rather than to commence strand synthesis. DNA polymerase begins its work when a tiny RNA fragment known as a primer is created and attached to a template DNA strand.

DNA Polymerase

DNA polymerase extends the template chain’s 3′ end by synthesising a new DNA strand with extra nucleotides that match those in the template. Each nucleotide is joined together by a phosphodiester link.

The DNA polymerase obtains energy from the hydrolysis of the phosphoanhydride link between the three phosphates (nucleoside triphosphates) attached to each free base (nucleotides).

When a nucleotide is added to a developing DNA strand, the high-energy phosphate link of hydrolysis forms a phosphodiester bond between the phosphate of the nucleotide and the expanding chain, releasing two distal phosphates known as pyrophosphates. DNA polymerases have an incredibly exact mechanism, with errors of less than one per 107 nucleotides. Some DNA polymerases have the ability to proofread, delete, and repair mismatched nucleotide bases.

Structure of DNA Double Helix

The structure of DNA polymerases is conserved, indicating that they play a fundamental role in cell activity that cannot be substituted.

Subdomains of DNA polymerases resemble the palm, fingers, and thumb of an open right hand. The catalytic essential amino acids are present in the palm’s active sites. The fingers play an important role in nucleotide recognition and binding. The DNA substrate is held in situ with the thumb.

A pocket exists between the finger and the thumb and is separated into two regions: the insertion site and the post-insertion site. The inbound nucleotides bind in the insertion site, while the fresh base pair binds in the post-insertion site. In addition to these domains, each family has its own set of subdomains that play key roles in DNA replication. Each polymerase, on the other hand, has its own collection of subdomains.

• The Organization of a Family

In addition to the previously listed subdomains, Family A polymerase contains a 5′ to 3′ exonuclease that removes the RNA primers from Okazaki fragments.

Several Family A groups exhibit 3′ to 5′ exonuclease activity, which aids in DNA proofreading.

• The Organization of Family B

They also have basic subdomains, which contain a highly active 3′ to 5′ exonuclease that corrects DNA replication errors.

• The Organization of Family X

In these family groups, the thumb, palm, and finger subdomains are structurally part of the N-terminal or on the 31-kDA polymerase segment.

This family’s palm contains three aspartic acid motifs, whereas the fingers include amino acid residues in helices M and N.

The N-terminus is connected to an 8-kilo amino-terminal region containing a 5′ deoxyribose phosphate lyase necessary for base excision repair.

This family’s N-terminus contains the catalytic core of the palm, fingers, and thumb.

They also have a C-terminal domain known as the little finger domain, which has a conserved tertiary structure consisting of a four-stranded beta-sheet supported on one side by two-alpha helices. They are necessary for appropriate polymerase activity and help in DNA binding.

This family, however, is less versatile than the others.

DNA polymerases of various types

DNA polymerases are classed as eukaryotic or prokaryotic depending on the organism that has them. These DNA polymerases are classified based on their features, such as structural sequences and functions.

• Polymerase I (DNA Polymerase I) is a type of DNA polymerase.

This is a type A or Family A polymerase enzyme that was discovered in E. coli and is abundant in that organism.

Its principal function as an exonuclease is excision repair of DNA strands from the 3′-5′ to the 5′-3′ direction.

It also aids in the maturation of Okazaki fragments, which are short DNA strands that make up the lagging strand during DNA replication.

During replication, it adds nucleotides to the RNA primer and moves in the 5′-3′ direction.

The binding site for DNA polymerase I is octylglucoside.

• DNA Polymerase II is a type of DNA polymerase that is employed in genetic research.

It belongs to the Type B or Family B polymerases.

Its primary function is to act as a 3′–5′ exonuclease and restart replication once it has been halted due to DNA strand damage.

DNA polymerase II is found in the replication fork and helps to coordinate the activity of other polymerases.

• DNA Polymerase III is a specific type of DNA polymerase

This enzyme belongs to the Family C or Type C enzyme family and is involved in DNA replication.

It is in charge of constructing new strands by attaching nucleotides to the 3′-OH group of the primer.

It contains 3′-5′ exonuclease activity, which means it can detect errors during DNA strand replication.

• DNA Polymerase IV

It belongs to the Y family and is involved in non-targeted mutagenesis.

Its activation is dependent on the stalling activity of the replication fork.

When triggered, it sets a checkpoint, stops replication, and allows time for correct repair of lesions in the new DNA strand.

It is also involved in the repair of translesion synthesis.

It is prone to DNA replication errors because it lacks nuclease function.

• DNA Polymerase V is a specific type of DNA polymerase

It belongs to the Y family and has a lot of regulatory action.

It is only generated when DNA is damaged, which demands translesion synthesis.

It also lacks exonuclease functions, which makes it inefficient because it cannot proofread DNA replica creation.

• DNA polymerase Taq Taq polymerase is a thermostable DNA polymerase 1 that was discovered in the thermophilic bacterium Thermus aquaticus

The abbreviation is Taq or Taq pol.

It is frequently employed in Polymerase Chain Reaction to amplify short strands of DNA.

It replaced E. coli DNA polymerase due to its thermophilic nature, which allows it to resist denaturation during PCR.

Conclusion 

DNA polymerase also rectifies post-replication mismatches by monitoring and correcting errors and distinguishing between new and template strand sequence mismatches. Eukaryotic cells have five DNA polymerase enzymes. Polymerase is found in the cell mitochondria and is engaged in mitochondrial DNA replication, whereas polymerase is found in the cell nucleus and is involved in nuclear DNA replication. Polymerase is largely used and active in dividing cells, indicating that they are involved in replication, whereas polymerase is active in both dividing and nondividing cells, indicating that it is involved in DNA damage repair.