Introduction to DNA Polymerase
What is the DNA polymerase?
Figure 1. DNA polymerase
DNA polymerase, also known as DNA dependent DNA polymerase (DNA pol), is an important enzyme in cell DNA replication. DNA polymerase is an enzyme that replicates DNA from the 5' end to the 3' end using DNA as a template. The main activity of DNA polymerase is to catalyze the synthesis of DNA and its auxiliary activity.
Characteristics of DNA polymerase
- Polymerization:dNTP is used as the substrate at the RNA-OH end of the primer. And according to the instructions on the template DNA, i.e. the pairing principle of a and T, C and G, dNTP is added to the 3'- OH end of the extended DNA molecule one by one, and the extended sub chain DNA is synthesized step by step. This is the main function of DNA polymerase.
- 3'→5' exonuclease activity (proofreading):The main function of 3'→5' exonuclease activity is to recognize and remove the nucleotides at the end of the growth chain of mismatched DNA from the direction of 3'→5', that is, When the added nucleotides are not complementary with the template and free from the template, they will be removed by 3'→5' exonuclease, thereby polymerizing into pairs at this position again. It can be seen that the activity of 3'→5' exonuclease is very important to maintain the authenticity and accuracy of DNA replication.
- 5'→3' exonuclease activity (removal and repair):5'→3' exonuclease activity is to hydrolyze the DNA chain in front of the DNA extension chain from the direction of 5'→3' to produce 5'- deoxynucleotides. This activity may play an important role in the repair of DNA damage.
Types of DNA polymerases
- Five DNA polymerases found in prokaryotes and bacteria
①DNA polymerase I (Pol Ⅰ)
The DNA polymerase of prokaryote has a molecular weight of 109kd and is composed of single peptide chain. It was first named DNA polymerase I. Pol I is an important molecular motor, which can walk along the DNA template chain, absorb DNA nucleotides, synthesize and extend new DNA sub chains. Its structure is composed of core region, 5'nuclease region and a protein polypeptide chain linker. Pol I plays an important role in DNA replication and repair. Pol I plays an even more important role in the process of synthesizing Okazaki fragment. Pol I is a folded polypeptide chain consisting of about 930 amino acids. The structure of Pol I consists of three parts: a main heart region, a 5'nuclease region, and a polypeptide chain composed of 16 amino acid residues connecting these two regions. The main heart region consists of a polymerase region and a 3'-5'exonuclease region. The polymerase region resembles the palm of the hand and is divided into the thumb, finger, and palm.
②DNA polymerase II (Pol II):
Pol II plays a role in repairing damage during DNA stabilization.
③DNA polymerase III (Pol III):
Pol III has both 5'3' directional polymerase activity and 3'5' exonuclease activity. The activity of this enzyme is strong, 15 times that of DNA polymerase I and 300 times that of DNA polymerase II. It can elongate new DNA strands at a rate of about 50,000 nucleotides per minute on the 3'-OH of primers, and is the dominant polymerase in the chain elongation reaction of E. coli DNA replication.
④DNA polymerase IV (Pol IV):
Together with Pol II, it is responsible for damage repair in the stable phase.
⑤DNA polymerase V (Pol V):
It is involved in SOS repair.
- SixDNA polymerases found in eukaryotes
①DNA polymerase ɑ (Pol ɑ):
Pol ɑ is the earliest eukaryotic DNA polymerase discovered, and its research is more thorough at present. Pol ɑ is a macromolecular protein consisting of four subunits, of which the large subunit 165-180 kD has catalytic activity, the function of the subunit 70 kD is unknown, the subunits 55-60 kD and 48-49 kD are related to primer enzyme activity.
②DNA polymerase β (Pol β):
It is the smallest DNA polymerase in eukaryotic cells and its DNA sequence is highly conserved. It has no 5'-3'exonuclease activity. Pol β is the DNA polymerase with lowest replication fidelity and its single base incorporation rate is 1/1000-1/6600 in the in vitro DNA polymerization reaction. It is mainly involved in DNA repair.
③DNA polymerase γ (Pol γ):
It is localized in mitochondria and participates in DNA replication in mitochondria. It does not have 5'-3' exonuclease activity, but has 3'-5' exo-activity.
④DNA polymerase δ (Pol δ):
Pol δ participates in DNA replication and has 3'-5' exo-activity but not 5'-3' exo-activity. It is the major DNA polymerase in eukaryotes. It catalyzes the synthesis of new chains templated by previous leads and also catalyzes the synthesis of some or most of the new chains templated by lagging chains. Recombination experiments of the in vitro replication system shows that it is the core enzyme in the process of DNA replication. When Pol ɑ completes primer synthesis, Pol δ can synthesize new chains using both the previous lead and the lagging chain as templates. Pol δ also has a 3'-5' exonuclease activity, which can proofread DNA mismatches and add nucleotides at the 3' end of the primer. Mismatch repair can correct the errors caused by base pairing during replication. In addition, Pol δ can maintain gene integrity because it can regulate telomere length together with Pol ɑ.
⑤DNA polymerase ε (Pol ε):
It has 3'-5' exo-activity but not 5'-3' exo-activity. Pol ɑ synthesizes RNA-DNA primers during DNA replication, and Pol δ and Pol ε are able to utilize these primers for large amounts of DNA synthesis. In addition, Pol ε plays an important role in nucleotide excision repair, base excision repair and recombination.
⑥DNA polymerase ζ (Pol ζ):
Its main role in cell metabolism is to participate in the translesion repair, and it also has an important relationship with genetic instability.
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