Pierce et al have designed a set of recombination substrates for measuring the level of homologous recombination in vivo (Fig. 1) [25]. The DNA substrate contains a pair of mutated GFP genes (GFP encodes the easily detected green fluorescent protein), one of which contains a restriction site for I-SceI, a yeast intron encoded endonuclease with an 18 base pair recognition site. Transient transfection of an I-SceI expression vector results in the production of a DSB in the first mutated copy of GFP. One or both DNA ends formed by the break invade(s) the homologous sequence in the second mutant GFP copy, resulting in repair of the DSB via a homology-mediated gene conversion event. The configuration of the GFP construct is such that homology-mediated repair often results in the formation of a functional copy of GFP. Such events can be detected by fluorescence-activated cell sorting analysis by virtue of their expression of GFP.