What Is Site-Specific Recombination and What Are the Strategies Involved?


The rearrangement of genetic information within and among DNA molecules encompasses a variety of processes, collectively placed under the heading of genetic recombination. Genetic events fall into three classes-

  • Homologous Genetic Recombination - It involves the exchange of genetic information between two DNA molecules.

  • Site-Specific Recombination - exchange of genetic information occurs only at a particular DNA sequence.

  • DNA Transposition - It is different from the other two classes in the fact that it usually involves a short segment of DNA molecule that has a unique capacity to move from one location on the chromosome to another.

In this segment, we will be focusing mainly on site-specific recombination, its definition, strategies or classes, and some examples.

Definition of Site-Specific Recombination

In this type of recombination, the movement of the DNA sequence takes place at the non-homologous site in the genome which is an exchange of genetic information that takes place only at a particular DNA sequence. The movement of DNA can take place either at two different positions on the same chromosome or between two different chromosomes.

This either results in the cutting formation of inverted sequences or the integration of DNA sequences. This task is performed by a specific set of enzymes known as site-specific recombinase. They help by cleaving, exchanging, and ligating the DNA double strands. But for this enzyme to act it requires a short (20 to 200bp long), unique DNA sequence.

This type of recombination takes place in virtually all cells, filling specialized roles that vary from one species to another. The regulation of the timing and the result of the whole process is done with the help of one or more auxiliary proteins.

Different Strategies or Classes of Site-Specific Recombination

Depending on the presence of either Tyrosine or Serine in the active site there are two classes of site-specific recombination systems.

Tyrosine Class

  • A separate recombinase first recognizes and binds to each of two recombination sites on two different DNA molecules or within the same DNA.

  • One DNA strand in each site is cleaved at a specific point within the site and enzyme recombinase becomes covalently linked to the DNA at the site of cleavage through a special type of bond called phosphotyrosine bond.

  • The transient protein-DNA linkage holds on the phosphodiester bond that is lost in cleaving the DNA, therefore high-energy cofactors like ATP become insignificant in subsequent steps.

  • The cleaved DNA strands are then joined together to new partners that result in the formation of Holliday intermediate, with a new phosphodiester bond created at the expense of the protein DNA linkage.

  • In order to complete the reaction, the process must be repeated at a second point within each of the two recombination sites.

Serine Class

  • In the systems that employ an active site serine residue, both strands of each recombination site are cut simultaneously and rejoined to new patterns without the formation of any Holliday intermediate.

  • IIn both types of systems, the exchange is always reciprocal and precise, regenerating the recombination sites when the reaction is complete.

Mechanism of Action of Recombinase Enzyme System

  • Site-specific recombinases are capable of recognizing sequences of recombination sites that are partially nonpalindromic or asymmetrical and the two recombining sites align in the same orientation during the recombinase reaction.

  • The result simply depends on the orientation location of the recombination sites. If the two sites are on the same DNA molecule the reaction either inverts or deletes the intervening DNA, determined by whether recombination sites have the same or opposite orientation respectively.

  • If one or both the DNAs are circular the result is an insertion or if the sites are on different DNAs, the recombination is intermolecular.

  • Some recombinase systems are highly specific for one of these reaction types and act only on sites with particular orientations.

Example of Site-Specific Recombination

  • The first site-specific recombination studied in vitro was that encoded by bacteriophage λ.

  • When λ phage DNA enters an E. coli cell, a complex series of regulatory events take place which can have one of the two consequences.

  • The λ DNA replicates and produces more bacteriophages- or it integrates into the host chromosome and replicates passively along with the chromosome for many generations.

  • Phage-encoded λ integrase helps in the integration process by acting as recombination sites on phage and bacterial DNAs.

Significance of Site-Specific Recombination

  • Site-specific recombination can lead to DNA integration, inversion of sequences or can lead to deletion, which can play an important role in evolution by causing an alteration in DNA sequences.

  • In prokaryotes, genetic exchange mediated by site-specific recombination systems are found to play a major role in growth and adaptation mechanisms like gene expression control.

  • In bacteria, it is essential for maintaining the stability of chromosomes in order to ensure that each daughter cell receives one copy of a chromosome.


Site-specific recombination is a type of genetic recombination that involves the movement of a particular DNA sequence either at two different positions on the same chromosome or in between two different chromosomes.

This whole process of recombination takes place with the help of an enzyme system called site-specific recombinases, which has been further classified into two families namely tyrosine and serine recombinases. Elaborate research has been done and elucidated in bacteriophage λ but still, more research is going on regarding the correlation between DNA recombination process and metabolism.

Updated on: 17-May-2023


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