Homologous Recombination from a Genetic Perspective

Recombination involves the cutting and covalent joining of DNA sequences. Recombination can occur between two different DNA molecules (intermolecular recombination) or between two regions of a single DNA molecule (intramolecular recombination). Intermolecular recombination can occur with a variety of types of DNA templates: the DNA templates may be linear DNA acquired via transduction, transformation, or conjugation, or linear chromosomes and plasmids; in bacteria with circular dsDNA chromosomes or circular plasmids, the recombination may occur between linear and circular dsDNA templates or between two circular dsDNA templates.

Some examples are shown in the cartoons below. The double-stranded DNA (dsDNA) is represented by a single line, with the donor dsDNA shown in red, the recipient dsDNA shown in black, recombinant DNA shown with a red and black line. An X represents areciprocal cross-over between the two dsDNA molecules and a half-X represents a nonreciprocal cross-over between the two dsDNA molecules.

Intermolecular recombination:

Intramolecular recombination:

Types of recombination

Genetic recombination is initiated by nicks or breaks between base pairs in the donor dsDNA. There are two common types of genetic recombination:

  1. Site-specific recombination occurs at particular DNA sequences recognized by enzymes that recognize that DNA sequence and catalyze recombination with a specific recipient DNA.
  2. Homologous recombination (sometimes called general recombination) occurs between DNA sequences that are homologous -- that is, the two DNA sequences are nearly identical.

The following discussion refers to homologous recombination (we will talk about site-specific recombination later).

Recombination frequency

Although there are some sites that are hot spots or cold spots for homologous recombination, when you consider long stretches of dsDNA the probability of a recombination event occuring between any two base pairs in the dsDNA is relatively uniform. That is, in a stretch of dsDNA the breaking and joining reaction could occur between any set of base pairs, as indicated in the figure below.

Given an equal probability of recombination between any 2 base pairs, a longer region of homologous DNA will provide many more opportunities for a recombination event. Hence, recombination between two DNA positions that are very close to each other occurs less often than recombination between two DNA positions that are farther apart -- or the further apart two DNA positions are the greater the probability that there will be a recombination event between them. (If the two DNA molecules are exactly identical, you would not be able to determine that recombination occurred by genetic approaches because the substrates and products would have the same genotype. Differences in DNA sequences that can be distinguished are called "markers".) The take-home point is that recombination frequencies are directly proportional to distance between two markers. Note that the recombination frequencies are not simply additive. In the figure below there is a 10% probability that a recombination event will occur somewhere between the two markers A and B, and a 2% probability that a recombination event will occur somewhere between the markers B and C, but a 25% probability that a recombination event will occur somewhere between the markers A and C.

However, when doing genetic crosses we typically look at how often two markers on one dsDNA molecule are co-inherited -- that is, how common are recombination events that occur on both sides of two markers so that both markers from the donor are incorporated into the recipient DNA molecule. For example, in the following figure, a recombination event with a cross-over at (i) and at (ii) would result in inheritance of A+ but not B+ or C+, a cross-over at (i) and at (iii) would result in co-inheritance of A+ and B+ but not C+, and a cross-over at (i) and at (iv) would result in co-inheritance of A+, B+, and C+. Co-inheritance frequency is inversely proportional to the distance between two DNA markers. This is a very important concept that is used extensively in genetic mapping. Because A is closer to B than to C, co-inheritance of A and B will occur much more frequently that co-inheritance of A and C.

The genetic perspective of recombination is important because it has many practical implications, such as genetic mapping. However, recombination can also be considered from a molecular perspective or from a biochemical perspective.

Some important points to remember about homologous recombination are:

  1. Homologous recombination requires substantial DNA sequence homology between the donor and recipient DNA.
  2. Recombination between any two sequences is a relatively low frequency event. (Therefore, a genetic selection is typically required to find a specific recombination event in vivo.)
  3. The co-inheritance of two genetic markers is inversely proportional to the distance between them.
  4. Homologous recombination can be prevented in a recA mutant.

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Last modified September 25, 2004