Factors affecting the efficiency of introducing precise genetic changes in ES cells by homologous recombination: tag-and-exchange versus the Cre-loxp system.

The introduction of genetic modifications in specific genes by homologous recombination provides a powerful tool for elucidation of structure-function relationships of proteins of biological interest. Presently, there are several alternative methods of homologous recombination that permit the introduction of small genetic modifications in specific loci. Two of the most widely used methods are the tag-and-exchange, based on the use of positive-negative selection markers, and the Cre-loxP system, based on the use of a site-specific recombinase. The efficiency of detection of targeting events at different loci using the two systems was compared. Additionally, we analysed how the distance between two gene markers placed within the region of homology of a targeting vector affects the rate at which both markers are introduced into the locus during the homologous recombination event. Our results indicate that the method based on the use of positive-negative selection markers was less efficient than the Cre-loxP based system, irrespective of locus or type of positive-negative selection. It was also determined that as the distance between the selectable marker and the genetic modification being introduced increases, there is a progressive reduction in the efficiency of detecting events with the desired genetic modification.