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Related Concept Videos

Conservative Site-specific Recombination and Phase Variation02:53

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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.
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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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Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I,...
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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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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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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Detecting and Analyzing Genetic Recombination Using RDP4.

Darren P Martin1, Ben Murrell2, Arjun Khoosal3

  • 1Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town, 7549, South Africa. darrenpatrickmartin@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|November 30, 2016
PubMed
Summary
This summary is machine-generated.

Recombination in nucleotide sequences significantly impacts evolution and challenges phylogenetic analyses. This study explores methods for detecting and analyzing recombination in sequence data.

Keywords:
BreakpointsGene conversionPhylogenetic treesRDP4Recombination

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Area of Science:

  • Evolutionary Biology
  • Molecular Evolution
  • Bioinformatics

Background:

  • Recombination is a fundamental evolutionary process affecting most species.
  • Phylogenetic methods often assume non-recombining sequences, potentially leading to inaccuracies.
  • The evolutionary impact of recombination on analytical methods is a subject of ongoing debate.

Purpose of the Study:

  • To investigate the influence of recombination on evolutionary analysis.
  • To evaluate methods for detecting and characterizing recombination in nucleotide sequences.
  • To test hypotheses regarding recombination using multiple sequence alignments.

Main Methods:

  • Examination of existing computational methods for recombination analysis.
  • Application of these methods to multiple sequence alignments.
  • Derivation and testing of recombination hypotheses.

Main Results:

  • Recombination complicates the accurate description of evolutionary history by a single phylogeny.
  • Phylogenetic approaches assuming no recombination can be undermined by actual recombination events.
  • The study assesses the utility of various available methods for recombination analysis.

Conclusions:

  • Accurate phylogenetic inference requires accounting for sequence recombination.
  • Available computational tools can be used to detect and analyze recombination.
  • Further investigation into recombination's impact on evolutionary analyses is warranted.