DNA Recombination and Its Types: Homologous, Site-Specific, and Transposition

Recombination: originally used by geneticists to describe the outcome of crossing over between two homologous chromosomes during meiosis. Skipping effects on daughter chromosomes with a different combination of alleles compared to their parent chromosomes. By the 1960s, it was understood that the main component of cell regeneration was the subsequent breakdown and subsequent reunification of DNA molecules. Now, recombination refers to a variety of processes that involve the separation and synthesis of polynucleotides.

Three different types of recombination events:

  1. Homologous recombination
  2. Site-specific recombination
  3. Transposition

Homologous recombination

  • Occurs between segments of DNA molecules that share multiple sequences of homology.
  • Segments can be present in different chromosomes, or they can be two parts of one chromosome
  • The study of homologous regeneration has identified two important challenges for biologists
  • first challenge has been to define repetitive models.
  • The second challenge concerns the chemical processes involved in regenerative processes.

Function of these challenges has led to the realization that homologous replication is more important for cells (especially viral cells) than simply crossing  over between chromosomes. Homologous regeneration is involved in several important types of DNA repair.

Steps of Homologous Recombination

  1. Two homologous double helices are aligned
  2. Then a nuclease cleaves the two strands that have the same polarity
  3. The free ends leave their original complementary strands and undergo hydrogen bonding with the complementary strands in the homologous double helix
  4. Ligation produces a heteroduplex double helix a crucial intermediate in recombination termed the Holliday structure.
  5. The Holliday structure can be resolved by cutting and ligating either

a. two originally exchanged strands generating a pair of duplexes that are parental, except for a stretch in the middle containing one strand from each parent.

b. the originally unexchanged generating two duplexes that are recombinant, with a stretch of heteroduplex DNA.

Figure 1: Homologous recombination

Site-specific recombination

It is a recombination between two DNA molecules that have very short sequences of similarities. The two DNA partner molecules are rearranged by specific enzymes i.e. a site-specific recombinase, that acts alone or requires accessory factors to shape the DNA target performing recombination at their similar pairs of sequences or target sites. The outcome of the exchange may be excision, integration or inversion of DNA sequences.

Figure 2: Site-specific recombination between λ DNA and E. coli DNA.


Transposition means the removal and transfer of a portion of DNA from one site to another of the same or different chromosome.

  • The transferred part is accompanied by a short direct repetition performed during the conversion process.
  • Modification causes anti-retroviral drugs to fight germs and to transmit viruses to certain germs. • The cell portion of DNA associated with mutation is called a transposon or jumping gene.
  • Not a form of reunification but a process that uses renaming.

Types of mutations based on their mutation mechanism:

  1. DNA transposons that transpose replicatively: the original transposon remaining in place and a new copy appearing elsewhere in the genome
  2. DNA transposons that transpose conservatively: the original transposon moving to a new site by a cut-and-paste process
  3. Retroelements: transpose replicatively via an RNA intermediate
Figure 3: Conservation and replicative transposition

Binod G C

I'm Binod G C (MSc), a PhD candidate in cell and molecular biology who works as a biology educator and enjoys scientific blogging. My proclivity for blogging is intended to make notes and study materials more accessible to students.

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