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Related Concept Videos

Proofreading01:31

Proofreading

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Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore,  it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...
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Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Overview of DNA Repair02:25

Overview of DNA Repair

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In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
Chemically...
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Base Excision Repair01:54

Base Excision Repair

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
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Genome Copying Errors02:46

Genome Copying Errors

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DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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Base-pairing and DNA Repair02:27

Base-pairing and DNA Repair

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Related Experiment Video

Updated: Jul 7, 2025

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
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Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

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Structural basis for DNA proofreading.

Gina Buchel1, Ashok R Nayak1, Karl Herbine1

  • 1Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.

Nature Communications
|December 27, 2023
PubMed
Summary
This summary is machine-generated.

Human mitochondrial DNA polymerase Gamma (Polγ) proofreading involves a conserved "bolt-action" mechanism. This process iteratively translocates the polymerase along DNA without dissociation, enabling error correction crucial for cell viability.

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • DNA polymerase (DNAP) proofreading is essential for maintaining genomic integrity and cell viability.
  • The precise mechanism of error translocation and DNA repositioning during DNAP proofreading remains incompletely understood.

Purpose of the Study:

  • To elucidate the step-by-step mechanism of DNA proofreading by human mitochondrial DNA polymerase Gamma (Polγ).
  • To reveal the structural dynamics involved in translocating mismatched bases from the polymerase to the exonuclease site.

Main Methods:

  • High-resolution structural analysis of nine distinct states of human Polγ during proofreading.
  • Functional assays and mutagenesis studies to validate the proposed mechanism.

Main Results:

  • Detailed structures capture key events: mismatched base recognition, dissociation from the polymerase site, DNAP translocation, DNA trajectory changes, and primer repositioning.
  • Evidence for a 'bolt-action' mechanism involving iterative DNAP translocation without dissociation, facilitating primer transfer.
  • Pathogenic mutations were linked to critical structural elements involved in proofreading steps.

Conclusions:

  • A conserved 'bolt-action' mechanism governs DNA proofreading by human Polγ, involving continuous polymerase translocation.
  • This mechanism ensures efficient error correction and highlights the functional importance of specific structural elements.
  • Understanding this process provides insights into DNA replication fidelity and associated genetic disorders.