6 public questions tagged with this topic.
DNA polymerase has proofreading ability to correct errors during DNA replication. This follows from NCERT principle where the relation explains the outcome clearly for students in simple steps.
Ref: NCERT Biology Textbook for Class XI and XII (Botany section), Chapter: Morphology and Anatomy of Flowering Plants, Topic: Plant structure and tissue systems.
DNA replication fidelity arises from sequential error control. Base selection by polymerase active site contributes 10^4 to 10^5 discrimination, but misincorporation still 10^-4 to 10^-5. Intrinsic 3' to 5' exonuclease proofreading removes ~90-99% of misinserted nucleotides, increasing accuracy additional hundredfold, dropping error rate to about 10^-7. Subsequent mismatch repair scanning newly replicated strand improves further thousandfold to 10^-10. Thus proofreading accounts for approximately two orders magnitude improvement. Without exonuclease, mutator phenotype observed, leading to increased spontaneous mutations and cancer predisposition, illustrating quantitative importance of editing.
Ref: Watson et al., Molecular Biology of the Gene, 7th ed., Chapter 10: Quantitative Contribution of Proofreading 100-fold
Replicative DNA polymerases such as Pol delta and Pol epsilon possess intrinsic 3' to 5' exonuclease domain distinct from polymerase active site. When incorrect nucleotide incorporated, duplex fraying moves primer terminus from polymerase to exonuclease site, hydrolyzing mispaired nucleotide before next incorporation. This proofreading activity is intrinsic exonuclease not 5' to 3' activity associated with removal of primers like Pol I. Endonuclease cleavage at internal sites and ligase activity sealing nicks are different repair steps unrelated to immediate correction during chain elongation, providing immediate fidelity check during replication.
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 5: Proofreading 3' to 5' Exonuclease Activity
DNA polymerases universally synthesize only 5' to 3' direction adding nucleotides to free 3' hydroxyl of growing primer chain. Proofreading exonuclease activity scans most recently added nucleotide because misincorporation creates mismatch at growing tip distorting duplex geometry and slowing next polymerization step dramatically. Polymerase then reverses one step moving branched 3' terminus from polymerase site to distinct exonuclease site that specifically hydrolyzes phosphodiester bond from 3' end preferentially. Excision cannot occur internally or at 5' terminus restricting surveillance efficiently to active 3' terminus where errors arise during elongation.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 11: Proofreading at the 3' terminus during replication
Even highly selective polymerases occasionally incorporate non-complementary nucleotides at rates near 10^-5 during rapid synthesis. Immediate correction relies heavily on intrinsic 3' to 5' exonuclease proofreading activity located in separate domain. When misincorporation distorts primer-template duplex geometry, polymerase stalls and transfers frayed 3' end from polymerase active site to exonuclease site that hydrolyzes phosphodiester bond and excises incorrect base. Strand then repositions into polymerase site for continued accurate synthesis. This kinetic proofreading step improves fidelity about 100-fold reducing errors to 10^-7 before mismatch repair.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 11: DNA replication fidelity and proofreading exonuclease
DNA polymerases achieve high fidelity through kinetic discrimination at active site and separate proofreading exonuclease function. When misincorporated nucleotide distorts primer-template duplex, synthesis stalls, transferring strand to exonuclease site located 30 Å distant, catalyzing hydrolysis in 3' to 5' direction removing unpaired base. This 3'->5' exonuclease activity is intrinsic to replicative polymerases Pol III ε subunit, Pol δ and Pol ε and Klenow fragment, distinct from 5'->3' exonuclease of Pol I involved in primer removal. Proofreading increases accuracy ~100-fold, complementing mismatch repair for overall error rate 10^-9.
Ref: Kunkel TA, Annu Rev Biochem 1988: DNA Polymerase Proofreading Activity is 3' to 5' Exonuclease
