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Related Concept Videos

Proofreading01:43

Proofreading

Overview
Proofreading01:31

Proofreading

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 Enzyme
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

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Related Experiment Video

Updated: May 13, 2026

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
07:27

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Published on: April 29, 2010

A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode.

Slobodan Jergic1, Nicholas P Horan, Mohamed M Elshenawy

  • 1School of Chemistry, University of Wollongong, Wollongong, New South Wales, Australia.

The EMBO Journal
|February 26, 2013
PubMed
Summary

The epsilon subunit of E. coli Pol III replicase has a novel DNA binding site that helps maintain replicase stability. This interaction, alongside the alpha subunit, is crucial for processive DNA synthesis.

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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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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • Processive DNA synthesis by Escherichia coli Pol III replicase relies on the αεθ core bound to the β2 clamp.
  • The role of the ε proofreading exonuclease subunit in DNA synthesis by the α subunit was previously unclear.

Purpose of the Study:

  • To investigate the influence of the ε subunit on DNA synthesis by the α subunit.
  • To uncover novel functions of the ε subunit beyond its proofreading activity.

Main Methods:

  • Bulk DNA replication assays.
  • Mutagenesis studies.
  • Biophysical analyses.
  • Single-molecule leading-strand replication assays.

Main Results:

  • A non-proofreading activity of the ε subunit was identified.
  • A novel β-binding site in the ε subunit was discovered.
  • This ε-β interaction, along with the α subunit's binding site, stabilizes the αεθ-β2 replicase in a closed state during DNA polymerization.

Conclusions:

  • The ε subunit contributes to DNA replication stability through a novel interaction with the β2 clamp.
  • This weak, transient ε-β interaction is evolutionarily selected to allow access for other proteins.
  • The ε-β interaction is a key component in regulating replicase stability and function.