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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...
Hybridoma Technology01:31

Hybridoma Technology

Hybridoma technology is used for the large-scale production of monoclonal antibodies. Monoclonal antibodies bind to only a single antigenic determinant or epitope. Such antibodies are used in research, diagnostics, and disease therapy. The hybridoma technology established in 1975 by Georges Köhler and Cesar Milstein was awarded the Nobel Prize in Medicine in 1984 for revolutionizing research and therapy.
Hybridoma Selection
Commonly used fusion techniques — electroporation, polyethylene glycol...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
Antigen Processing Pathways01:31

Antigen Processing Pathways

MHC molecules are key players in the immune response, enabling T cells to recognize and respond to specific antigens. They are present on the surface of all nucleated cells in the body and are instrumental in presenting antigens to T cells and activating them. T cells recognize the MHC-antigen complex and initiate an immune response. MHC class I and MHC class II are two main types of MHC molecules, each associated with a distinct antigen processing pathway.
MHC Class I: Presenting Endogenous...
Labeling DNA Probes03:31

Labeling DNA Probes

DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...

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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

Published on: September 11, 2022

Homology recognition funnel.

Dominic Lee1, Alexei A Kornyshev

  • 1Max Planck Institute for the Physics of Complex Systems, D-01187 Dresden, Germany. domolee@hotmail.com

The Journal of Chemical Physics
|June 24, 2010
PubMed
Summary
This summary is machine-generated.

Investigating DNA

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Computational Chemistry

Background:

  • Homologous recombination is crucial for DNA repair and genetic diversity.
  • The initial recognition of homologous DNA sequences before strand exchange remains poorly understood.
  • Previous models explored DNA recognition mechanisms and torsional elasticity effects.

Purpose of the Study:

  • To investigate the impact of torsional flexibility on the DNA recognition funnel.
  • To analyze how molecular flexibility influences the interaction energy between homologous DNA duplexes.
  • To understand the role of counterion adsorption in DNA-DNA recognition.

Main Methods:

  • Variational approach to model DNA-DNA interactions.
  • Numerical solution of a transcendental equation derived from the model.
  • Analysis of the energy surface as a function of interaxial separation and axial shift.

Main Results:

  • Torsional flexibility alters the DNA recognition well, making it wider and shallower at large separations.
  • Unexpected features emerge at closer distances, including abrupt changes in azimuthal alignment.
  • The DNA recognition funnel is highly sensitive to counterion adsorption patterns on DNA.

Conclusions:

  • Torsional flexibility significantly modifies the energetic landscape of homologous DNA recognition.
  • Counterion distribution plays a critical role in shaping the DNA recognition funnel.
  • This study provides a more refined model for understanding DNA sequence recognition in recombination.