⇒ Chromosome Structure
     ⇒ DNA Replication
     ⇒ Recombination

In bacteria, pieces of DNA that can enter a cell may become part of the main chromosome or one of its plasmids. The integration process is termed genetic recombination, and it generally occurs at points where the two DNA s are nearly identical. Recombination can be beneficial because it can create new genetic information. In addition, recombination provides a mechanism by which organisms can replace genes that have been severely damaged or even deleted.

In eukaryotes, recombination leads to genetic diversity among progeny produced by sexual reproduction. During meiosis, the process of crossing over produces linkage arrangements in gametes different from those that exist in the parent. Favorable gene combinations tend to be perpetuated by natural selection. The recombination that takes place during meiosis is also a means of repairing or replacIng DNA . There are two major types of genetic recombination. Site-specific recombination requires short but identical double-stranded regions of homology between recombining molecules of DNA , and it usually changes the relative positions of chromosomal segments. General recombination occurs between homologous DNA molecules. It does not normally alter the order in which gene loci occur in their respective chromosomes but does involve DNA synthesis.

In general recombination, if the transforming DNA is single-stranded, the RecA protein binds to it, then to the bacterial chromosome and melts it while searching for a region of homology. The minimal region of homology is about 60 bp but usually involves hundreds of bases. Hydrogen bonding occurs between the transforming DNA and a complementary region of the cell's DNA . An enzyme such as UvrABC cuts away the unpaired portion of the melted DNA . A ligase repairs the nicks. If there is a mismatch, UvrABC cuts on either side of a mismatched strand, and a repair enzyme (DNA polymerase I) pushes away the mismatched strand and replaces it with new DNA that matches the complementary strand. If the transforming DNA that enters the cell is double-stranded, the RecBCD protein searches the DNA for a specific sequence called a chi (χ) site, where it cuts one strand of the DNA , creating a nick. The single stranded DNA that results is coated with RecA, which then searches the bacterial chromosome for a region of homology and the remaining steps are similar to those discussed above.

In eukaryotes, general recombination occurs when homologous chromosomes pair during prophase I of meiosis. Very large protein complexes called recombination modules are found at intervals along the synaptonemal complex, the ladderlike protein structure that develops between chromosome pairs. At each recombination module, two of the four chromatids break and rejoin with one another in crossing over. It is believed that endonucleases in the recombination modules nick a single strand of each chromatid capable of recombination and that helicases unwind the DNA , creating single-stranded regions. A protein similar to RecA is proposed to catalyze the pairing of the single-stranded DNA s to the complementary strands on the homologous chromatids. ADNA polymerase may extend the exchanged strands, and a DNA ligase is thought to eliminate the nicks in the strands. This model is referred to as the Holliday model after the geneticist who proposed it (Figure 3-4).