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Related Concept Videos

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...
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...
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
Homologous Recombination02:31

Homologous Recombination

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...
Homologous Recombination02:31

Homologous Recombination

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: May 29, 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

Distinct repair outcomes from single and convergent replication fork collapse.

Sara C Conwell1, Khushi V N Patel1, Savannah J Weeks-Pollenz1

  • 1Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.

Nature Structural & Molecular Biology
|May 27, 2026
PubMed
Summary

Replication fork collapse at DNA breaks can be repaired differently. Single forks undergo recombination or degradation, while converging forks use annealing-dependent repair, leading to distinct outcomes for genome stability.

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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

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Detection of Post-Replicative Gaps Accumulation and Repair in Human Cells Using the DNA Fiber Assay
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Detection of Post-Replicative Gaps Accumulation and Repair in Human Cells Using the DNA Fiber Assay

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Last Updated: May 29, 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

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
07:55

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Detection of Post-Replicative Gaps Accumulation and Repair in Human Cells Using the DNA Fiber Assay
10:32

Detection of Post-Replicative Gaps Accumulation and Repair in Human Cells Using the DNA Fiber Assay

Published on: February 3, 2022

Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Replication fork collapse at DNA breaks poses a threat to genome stability.
  • Mechanisms for repairing and resolving collapsed replication forks remain poorly understood.

Purpose of the Study:

  • To investigate the distinct repair pathways of single versus converging replication fork collapse.
  • To elucidate the resolution mechanisms of single-ended and double-ended double-strand breaks (DSBs) arising from fork collapse.

Main Methods:

  • Replication of site-specific nicks using single or converging replication forks in Xenopus laevis egg extracts.
  • Analysis of DNA repair outcomes, including homologous recombination, nucleolytic degradation, and annealing-dependent DSB repair.

Main Results:

  • Single fork collapse results in single-ended DSBs repaired by homologous recombination or nucleolytic degradation, without DNA synthesis restart.
  • Converging fork collapse generates double-ended DSBs repaired by annealing-dependent mechanisms, leading to precise deletions and templated insertions.
  • Distinct repair pathways were observed for single and converging collapsed forks.

Conclusions:

  • The study reveals context-dependent repair outcomes for collapsed replication forks.
  • Understanding these pathways is crucial for maintaining genome stability and preventing mutations.