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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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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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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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Updated: Jun 27, 2025

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Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the

Phuong Pham1, Elizabeth A Wood2, Emma L Dunbar2

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Nucleic Acids Research
|April 27, 2024
PubMed
Summary
This summary is machine-generated.

Novel DNA sequences called Replication Risk Sequences (RRS) in Escherichia coli create temporary gaps during DNA replication. These essential elements impact genome structure and may act as topological relief valves.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Microbial Genetics

Background:

  • The Escherichia coli chromosome harbors unique GC-rich genomic structures.
  • Replication fork progression can be impeded by specific DNA sequences.
  • Understanding DNA replication challenges is crucial for genome stability.

Purpose of the Study:

  • To identify and characterize novel genomic structural elements in E. coli.
  • To investigate the role of these elements in DNA replication and genome topology.
  • To explore the potential conserved function of these elements in other organisms.

Main Methods:

  • Bioinformatic analysis to identify conserved DNA sequences.
  • Genetic manipulation (deletion studies) to assess functional impact.
  • DNA replication assays to detect post-replication gaps and DNA polymerase extension impediments.

Main Results:

  • Discovery of two novel, conserved 222 bp repeats named Replication Risk Sequences (RRS).
  • RRS are located near the dif and Ter macrodomain, flanking the terminus.
  • RRS impede DNA polymerase extension on the lagging strand, forming single-stranded DNA gaps up to 2000 bp.
  • Deletion of RRS significantly alters global genome structure and topology.
  • At least one RRS is essential for viability unless a specific genomic region is amplified.

Conclusions:

  • RRS are essential genomic elements that induce transient post-replication gaps in E. coli.
  • These sequences contain G-quadruplexes that likely cause replication stress.
  • RRS may function as topological relief valves during chromosome replication and segregation.
  • Functional analogs of RRS might be widespread, potentially including eukaryotic G-quadruplexes.