Genetic recombination is the process by which the combination of genes in an organism's offspring becomes different from the combination of genes in that organism. This definition is commonly used in classical genetics, evolutionary biology, and population genetics.
However, in molecular biology, recombination generally refers to the molecular process by which alleles at two genes in a linkage group can become separated. In this process alleles are replaced by different alleles from the same genes thereby preserving the structure of genes. One mechanism leading to recombination is chromosomal crossing over. In analog fashion exchange of alleles is possible between homologous sites within one DNA molecule. If the structure of genes is changed in that process it is called unbalanced recombination. Enzymes called recombinases catalyze this reaction.
Recombination is the mechanism by which organisms avoid Muller's ratchet.
Main article: Chromosomal crossover
Crossing over of two chromosomes occurs during meiosis. After chromosomal replication, the four available chromatids are in tight formation with one another. During this time, homologous sites on two chromatids can mesh with one another, and may exchange genetic information. Immediately after replication, the tetrad formed by replication contains two pairs of two identical chromatids; after crossing over, each of the four chromatids carries a unique set of genetic information.
Enzymes known as recombinases catalyze the reactions that allow for crossover to occur. A recombinase creates a nick in one strand of a DNA double helix, allowing the nicked strand to pull apart from its complementary strand and anneal to one strand of the double helix on the opposite chromatid. A second nick allows the unannealed strand in the second double helix to pull apart and anneal to the remaining strand in the first, forming a structure known as a cross-strand exchange or a Holliday junction . The Holliday junction is a tetrahedral structure which can be 'pulled' by other recombinases, moving it along the four-stranded structure.
In most eukaryotes, a cell carries two copies of each gene, each referred to as an allele. Each parent passes on one allele to each offspring. Even without recombination, each gamete contains a random assortment of chromatids, choosing randomly from each pair of chromatids available. With recombination, however, the gamete can receive a (mostly) random assortment of individual genes, as each chromosome may contain genetic information from two different chromatids.
Recombination results in a new arrangement of maternal and paternal alleles on the same chromosome. Although the same genes appear in the same order, the alleles are different. This process explains why offspring from the same parents can look so different. In this way, it is theoretically possible to have any combination of parental alleles in an offspring, and the fact that two alleles appear together in one offspring does not have any influence on the statistical probability that another offspring will have the same combination. This theory of "independent assortment" of alleles is fundamental to genetic inheritance. However, there is an exception that requires further discussion.
The frequency of recombination is actually not the same for all gene combinations. This is because recombination is greatly influenced by the proximity of one gene to another. If two genes are located close together on a chromosome, the likelihood that a recombination event will separate these two genes is less than if they were farther apart. Genetic linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome. Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart. This concept is applied when searching for a gene that may cause a particular disease. This is done by comparing the occurrence of a specific DNA sequence with the appearance of a disease. When a high correlation between the two is found, it is likely that the appropriate gene sequence is closer.
Crossover recombination can occur between any two double helices of DNA which are very close in sequence and come into contact with one another. Thus, crossover may occur between Alu repeats on the same chromatid, or between similar sequences on two completely different chromosomes. These processes are called unbalanced recombination. Unbalanced recombination is fairly rare compared to normal recombination, but severe problems can arise if a gamete containing unbalanced recombinants becomes part of a zygote. Offspring with severe unbalances rarely live through birth.
In conservative site-specific recombination, a mobile DNA element is inserted into a strand of DNA by means similar to that seen in crossover. A segment of DNA on the mobile element matches exactly with a segment of DNA on the target, allowing enzymes called integrases to insert the rest of the mobile element into the target.
Another form of site-specific recombination, transpositional recombination does not require an identical strand of DNA in the mobile element to match with the target DNA. Instead, the integrases involved introduce nicks in both the mobile element and the target DNA, allowing the mobile DNA to enter the sequence. The nicks are then removed by ligases.