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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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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.
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The Replisome03:01

The Replisome

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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.
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Restarting Stalled Replication Forks02:37

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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,...
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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.
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Related Experiment Video

Updated: Sep 11, 2025

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

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

Published on: April 4, 2025

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DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.

Longfu Xu1, Shikai Jin2,3, Mia Urem4

  • 1Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.

Nature Communications
|August 11, 2025
PubMed
Summary
This summary is machine-generated.

DNA polymerase (DNAp) displaces single-stranded DNA-binding proteins (SSBs) by lowering their dissociation barrier, ensuring efficient DNA replication and genomic integrity.

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Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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Last Updated: Sep 11, 2025

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

Published on: April 4, 2025

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

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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

Published on: May 2, 2025

482

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genomics

Background:

  • Single-stranded DNA-binding proteins (SSBs) are crucial for protecting exposed single-stranded DNA (ssDNA) during replication.
  • The mechanism by which DNA polymerases (DNAp) displace SSBs to facilitate replication is not fully understood.

Purpose of the Study:

  • To investigate the molecular mechanisms of SSB displacement by DNAp during replication.
  • To elucidate the spatiotemporal coordination between DNAp and SSB.

Main Methods:

  • Single-molecule force spectroscopy
  • Dual-color imaging
  • Molecular dynamics simulations
  • Förster Resonance Energy Transfer (FRET)

Main Results:

  • T7 SSB's effect on replication is force-dependent, enhancing it at low tension and impeding it at high tension.
  • SSBs remain stationary as DNAp advances, supporting a sequential displacement model.
  • DNAp actively reduces the SSB dissociation energy barrier via interactions with the SSB C-terminal tail.

Conclusions:

  • The spatiotemporal coordination between DNAp and SSB is vital for resolving molecular collisions during replication.
  • This coordination ensures both DNA replication processivity and genomic integrity.
  • A balance between SSB protection and replication efficiency is critical for optimal DNA synthesis.