3. Designing Substrates for Site-Specific Recombination

Upon expression, the SSR acts upon two or more recombinase target sites (RTs) that have been introduced into the genome. Designing how the RTs are deployed in the genome is the first step. The design choices are influenced by the objective and also by certain constraints that affect the efficiency of recombination.

For both tyrosine and large serine recombinases, the site of recombination is a short crossover region of hybrid DNA composed of one strand from each of the substrate RTs. Because the recombination product must have complementarity in the crossover regions, and because none of the RTs usually employed for genetic engineering are palindromic in the hybrid region, it follows that RTs have a directionality.