Proofreading

DNA polymerase employs three proofreading mechanisms. First, it binds more strongly to correctly paired nucleotides, reducing incorrect pairings. Second, it undergoes a conformational change that causes incorrectly paired nucleotides to detach. Third, if an incorrect nucleotide reaches the three-prime end, the mismatch distorts DNA structure and pauses polymerase movement, allowing correction.

DNA polymerase possesses three-prime-to-five-prime exonuclease activity, enabling it to reverse direction and remove incorrectly added nucleotides from the growing DNA chain. After removing the wrong nucleotide, the polymerase inserts the correct one. This exonucleolytic proofreading process separates nucleotide selection from error correction, maintaining replication accuracy.

When mutations alter the exonuclease domain, DNA polymerase loses its ability to remove incorrect nucleotides. This causes mutations to accumulate rapidly throughout the genome. These uncorrected errors can disrupt normal gene function and cellular regulation, leading to uncontrolled cell growth and various types of cancer.

When adenine incorrectly pairs with cytosine instead of thymine, a mispairing error occurs. DNA polymerase detects this incorrect pairing through its proofreading mechanisms. If not corrected, these errors can persist as mutations and potentially cause disease by altering the genetic code in newly synthesized DNA.

High-fidelity polymerases maintain strong proofreading ability and are used when accurate DNA copies are essential. Error-prone polymerases have compromised proofreading ability and are intentionally used in techniques like error-prone PCR to generate mutations in DNA sequences on purpose for research applications.

DNA polymerase delta and epsilon are the primary eukaryotic polymerases that possess proofreading ability during nuclear DNA replication. These polymerases read each base after it is added to the new strand and use their exonucleolytic domains to correct errors, ensuring high-fidelity replication in eukaryotic cells.

DNA polymerase has higher affinity for correct base pairs, where adenine pairs with thymine and cytosine pairs with guanine. This selective binding preference ensures fidelity during replication by favoring correct nucleotide incorporation. Combined with proofreading mechanisms, this dual-level control significantly reduces replication errors and mutation rates.