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Related Concept Videos

Homologous Recombination02:31

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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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Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
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The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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Updated: Sep 22, 2025

Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Network Formation by Cross-Hybridization of Complementary Strands to Grafted ssDNA.

S Medalion1, M Wagman1, A Y Grosberg2

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In dense DNA brushes, probe strands can bind to multiple targets, forming a cross-linked DNA network. This network formation, unlike 1:1 hybridization in low-density brushes, is influenced by system size and DNA length.

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Area of Science:

  • Biophysics
  • Materials Science
  • Molecular Biology

Background:

  • Surface-grafted single-stranded DNA (ssDNA) brushes are used in various applications.
  • In low-density brushes, complementary ssDNA probes form regular DNA duplexes via 1:1 hybridization.
  • Higher density brushes present unique hybridization behaviors due to proximity.

Purpose of the Study:

  • To investigate the phenomenon of cross-hybridization in dense ssDNA brushes.
  • To determine the conditions favoring DNA network formation over simple duplex formation.
  • To explain observed behaviors in dense DNA brush systems.

Main Methods:

  • Analysis of a 2D model of a dense DNA brush.
  • Application of analytical methods.
  • Conducting computer simulations to study system size and DNA length effects.

Main Results:

  • In dense brushes, cross-hybridization competes with 1:1 hybridization.
  • A cross-linked DNA network is formed when probe strands bind to multiple targets.
  • Network formation is dependent on system size and DNA length.
  • Cross-hybridization is predicted to almost always lead to network formation in 3D brushes.

Conclusions:

  • Cross-hybridization is a key factor in dense DNA brush behavior.
  • The formation of DNA networks in dense brushes can explain previous experimental observations.
  • Proposed experiments on DNA monolayers and concentrated solutions to validate predictions.