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Related Concept Videos

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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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...
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Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

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Single-Molecule Förster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1
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Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a

Hisashi Ishida1

  • 1Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan. ishida.hisashi@jaea.go.jp

Journal of Computational Chemistry
|June 25, 2010
PubMed
Summary

RuvA tetramer facilitates Holliday junction branch migration. Simulations reveal acidic pins stabilize interactions with unpaired bases during DNA repair, guiding the migration pathway.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • Holliday junctions are crucial intermediates in DNA recombination and repair.
  • The RuvA tetramer protein complex is essential for resolving Holliday junctions.
  • Understanding the mechanism of branch migration is key to DNA repair comprehension.

Purpose of the Study:

  • To elucidate the molecular mechanism of Holliday junction branch migration mediated by the RuvA tetramer.
  • To investigate the role of RuvA's acidic pins in the branch migration process.
  • To determine the free-energy landscape of branch migration.

Main Methods:

  • Umbrella sampling molecular dynamics simulations were employed.
  • Simulations focused on complexes of the RuvA tetramer and Holliday junction DNA.
  • A novel, step-by-step approach was used to set sampling points, enabling realistic path searching.

Main Results:

  • Branch migration initiates with the unforming of hydrogen bonds in base pairs.
  • Intermediate stages show unpaired bases interacting with RuvA's acidic pins.
  • The free-energy profile indicates a meta-stable intermediate state between energy barriers.

Conclusions:

  • RuvA tetramer's acidic pins play a critical role in stabilizing interactions with unpaired bases during branch migration.
  • The simulations provide a detailed, step-by-step view of the branch migration pathway.
  • This study offers insights into the structural dynamics governing DNA repair mechanisms.