Homologous Recombination (Holliday model and DNA double strand repair model) and Site Specific Recombination

Homologous Recombination (Holliday model and DNA double strand repair model) and Site Specific Recombination

February 17, 2022


  • Cleavage and rejoining of DNA molecules to generate new combinations of genes
  • There are two types of recombination mechanisms occur in living system

Genetic recombination

Site specific recombination

Genetic Recombination

  • The production of gene combinations not found in the parents by the crossing over between homologous chromosomes during meiosis is called genetic recombination.
  • Genetic recombination occurs in the germ cells (during meiosis I in oocytes and spermatocytes)
  • Also called as homologous recombination as it takes place between homologous chromosomes
  • It occurs during crossing over, in which homologous regions of chromosomes are exchanged and genes are shuffled into new combinations.
  • It is an extremely important genetic process because it increases genetic variation.
  • It is an ubiquitous process occurs in every bacteria and also in eukaryotes

Models of Homologous Recombination

Holliday model (Robin Holliday 1964)

Double strand repair model

Holliday model (Robin Holliday 1964)

  • Holliday’s model explained the mechanism of HR involving the breakage, reunion, and repair of DNA molecules. The steps are as follows:
  • Recognition and alignment of homologous chromosome in two duplex chromosomes called synapsis
  • The recombination begins when an endonuclease cleaves single strands of each of the two parental DNA molecules with same polarity (breakage).
  • Segments of the single strands on one side of each cut are then displaced from their complementary strands with the aid of DNA helicases and single strand binding proteins.
  • The helicases unwind the two strands of DNA in the region adjacent to single-strand incisions.
  • In E. coli, the RecBCD complex contains both an endonuclease activity that makes single-strand breaks in DNA and a DNA helicase activity that unwinds the complementary strands of DNA in the region adjacent to each nick
  • The displaced single strands then exchange pairing partners, base-pairing with the intact complementary strands of the homologous chromosomes.
  • This process is stimulated by proteins like the E. coli RecA protein. RecA-type proteins have been characterized in many species, both prokaryotic and eukaryotic.
  • RecA protein and its homologues stimulate single-strand assimilation (a process by which a single strand of DNA displaces its homologue in a DNA double helix) by two steps.
  • In the first step, a single strand of one double helix is assimilated by a second, homologous double helix, displacing the identical or homologous strand and base-pairing with the complementary strand.
  • In the second step, the displaced single strand is similarly assimilated by the first double helix. The RecA protein mediates these exchanges by binding to the unpaired strand of DNA, aiding in the search for a homologous DNA sequence, and, once a homologous double helix is found, promoting the replacement of one strand with the unpaired strand.
  • If complementary sequences already exist as single strands, the presence of RecA protein increases the rate of renaturation by over 50-fold.
  • The cleaved strands are then covalently joined in new combinations (reunion) by DNA ligase. If the original breaks in the two strands do not occur at exactly the same site in the two homologues, some tailoring will be required before DNA ligase can catalyze the ligase step.
  • This tailoring involves the excision of nucleotides by an exonuclease and repair synthesis by a DNA polymerase.
  • The sequence of events will produce X-shaped recombination intermediates called chi forms, which have been observed by electron microscopy in several species.
  • The chi forms are resolved by enzyme-catalyzed breakage and rejoining of the complementary DNA strands to produce two recombinant DNA molecules.
  • In E. coli, chi structures can be resolved by the product of either the recG gene or the ruvC gene (repair of UV-induced damage). Each gene encodes an endonuclease that catalyzes the cleavage of single strands at chi junctions

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