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Related Concept Videos

The DNA Replication Fork01:02

The DNA Replication Fork

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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...
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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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Replication in Prokaryotes01:32

Replication in Prokaryotes

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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
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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.
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...
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Homologous Recombination02:31

Homologous Recombination

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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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Replication in Eukaryotes01:29

Replication in Eukaryotes

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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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Related Experiment Video

Updated: Jun 18, 2025

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System
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Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

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Replication fork barriers to study site-specific DNA replication perturbation.

Jenevieve D'Souza1, Ian D Hickson1

  • 1Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark.

DNA Repair
|July 30, 2024
PubMed
Summary
This summary is machine-generated.

This review compares protein-based systems that create site-specific DNA replication fork barriers. These systems offer a precise method to study cellular responses to replication stress, complementing traditional chemical inhibitor approaches.

Keywords:
Cell cycle checkpointsDNA damage responseDNA-protein interactionsFork protection complexReplication stress

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Visualization of DNA Replication in the Vertebrate Model System DT40 using the DNA Fiber Technique
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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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Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • DNA replication is essential for accurate genome duplication.
  • Traditional methods use chemical inhibitors (e.g., hydroxyurea) to study replication fork progression.
  • These inhibitors affect the entire genome, limiting detailed analysis of cellular responses.

Purpose of the Study:

  • To review and compare protein-based replication fork barrier systems.
  • To highlight an alternative to chemical inhibitors for studying DNA replication perturbation.
  • To emphasize the utility of site-specific replication fork stalling for detailed cellular response investigation.

Main Methods:

  • Comparison of various protein-mediated replication fork blocking systems across different organisms.
  • Analysis of systems utilizing high-affinity protein-DNA binding at specific genomic loci.
  • Review of methodologies for generating site-specific replication fork perturbation.

Main Results:

  • Protein-based systems enable precise, site-specific replication fork stalling.
  • These systems facilitate a more forensic investigation of cellular responses to replication stress.
  • Different organisms employ diverse protein-based strategies for replication fork control.

Conclusions:

  • Protein-based replication fork barriers are valuable tools for understanding DNA replication.
  • Site-specific perturbation allows for detailed study of cellular coping mechanisms.
  • This approach complements traditional methods by offering greater precision.