DNA-dependent DNA polymerases are enzymes that direct the synthesis of new DNA from deoxyribonucleotide triphosphates (dNTPs) in the opposite direction of an existing DNA template, which holds the genetic information necessary for an organism’s survival. A polymerase must choose and catalyse the insertion of a complementary nucleotide (dNTP) substrate into a nascent DNA strand from a pool of four structurally identical molecules during each cycle of catalysis to properly maintain this information. Polymerases are required and diversely used throughout DNA replication, recombination, repair, and translesion synthesis across all three domains of life, including Archaea, Bacteria, and Eukaryota (TLS).
DNA Polymerase Functions
- In DNA replication, fidelity is crucial. Mismatches in DNA base pairing can lead to defective proteins and, in the worst-case scenario, cancer.
- Many DNA polymerases have an exonuclease domain that detects base pair mismatches and then removes the erroneous nucleotide, which is then replaced with the correct one.
- The form and interactions of the Watson and Crick base pair are the most important factors in determining whether or not an error has occurred. Hydrogen bonds are important in the binding and interaction of base pairs.
- A shift in the balance for the binding of the template-primer from the polymerase to the exonuclease domain is stated to occur when an interaction is lost due to a mismatch.
- Incorporation of the incorrect nucleotide also causes a delay in DNA polymerization. This allows the DNA enough time to transition from the polymerase to the exonuclease site.
- At certain mismatches, distinct structural changes and loss of interaction occur.
- The pyrimidine is displaced towards the major groove while the purine is displaced towards the minor groove in a purine:pyrimidine mismatch.
- The purine and residues in the minor groove have steric conflicts, and the pyrimidine loses crucial van der Waals and electrostatic contacts due to the structure of DNA polymerase’s binding pocket. Because the bases are moved towards the main groove and there is less steric hindrance, pyrimidine:pyrimidine and purine:purine mismatches show less noticeable alterations.
- Despite the fact that distinct mismatches have varying steric characteristics, DNA polymerase is nonetheless able to detect and distinguish them consistently and preserve DNA replication fidelity.
- Many mutagenesis methods rely on DNA polymerization, which is frequently used in biotechnologies.
DNA replication in prokaryotes
In prokaryotic cells, there may be only one element of foundation, whereas replication takes place in the mobile cytoplasm. Prokaryotic cells have one or two types of polymerases, and replication occurs in two opposing directions at the same time. In comparison to eukaryotes, prokaryotes replicate at a far higher rate. In a few microbes, it’s completed in 40 minutes, and because they have circular chromosomes, they don’t have any ends to manufacture like telomeres in eukaryotes.
When replication occurs in the cytoplasm of prokaryotic cells, there is only one point of origin. Prokaryotic cells have one or two types of polymerases, and replication occurs in two opposing directions at the same time.
DNA replication in eukaryotes
A prokaryotic cell’s DNA is 25 times larger than that of a normal eukaryotic cell. Eukaryotic cells use unidirectional replication inside the cellular nucleus and have a few factors of genesis. These include four or more polymerase enzymes to help with DNA replication. Eukaryotes can take up to 400 hours to replicate their chromosomes, and they have a unique way for replicating the telomeres at the ends of their chromosomes. For the duration of the S-segment of the cell cycle, the cell replicates its DNA here.
The DNA of an average eukaryotic cell is 25 times larger than that of a prokaryotic cell. Eukaryotic cells undergo unidirectional replication within the cell nucleus and have numerous sources of origin.
DNA dependent DNA Polymerase is associated with
DNA-dependent DNA polymerases are in charge of directing the synthesis of new DNA from deoxyribonucleotide triphosphates (dNTPs) on the opposite side of an existing DNA template, which holds vital genetic information for an organism’s existence. A polymerase must reliably choose and catalyse the insertion of a complementary nucleotide (dNTP) substrate into a nascent DNA strand from a pool of four structurally identical molecules during each cycle of catalysis to properly maintain this information. Polymerases are essential and diversely used during DNA replication, recombination, repair, and translesion synthesis in all three domains of life, including Archaea, Bacteria, and Eukaryota (TLS).
Conclusion
DNA polymerase’s main job is to make DNA from deoxyribonucleotides, which are the building blocks of DNA. The nucleotides are paired with the bases on each strand of the original DNA molecule to make DNA copies. This pairing always occurs in certain combinations, with cytosine and guanine creating two separate pairs, and thymine and adenine forming two separate pairs. RNA polymerases, on the other hand, make RNA from ribonucleotides derived from either RNA or DNA.
DNA polymerase’s function is far from perfect, with the enzyme making around one error for every billion base pairs replicated. Some DNA polymerases, but not all, have the ability to fix errors. This procedure corrects errors in DNA that has just been produced. When DNA polymerase recognises an erroneous base pair, it transfers one base pair of DNA backwards. The enzyme’s 3’–5′ exonuclease activity allows the erroneous base pair to be removed (this activity is known as proofreading). Following base excision, the polymerase can re-insert the proper base and continue replication. The integrity of the original DNA strand that is passed on to the daughter cells is preserved as a result.