Measurement of recombination frequencies between two homologous DNA segments embedded in a YAC vector

We measured the frequencies of recombination in a yeast host between two homologous segments of DNA that had been inserted with the same polarity in a yeast artificial chromosome (YAC) vector. Three kinds of YAC clones were constructed in which the gene encoding neomycin(Nm) resistance was sandwiched between two homologous segments of DNA, such as the IS3 elements of Escherichia coli or human Alu sequences. Frequencies of homologous recombination in yeast were measured in terms of loss of resistance to Nm. In the case of IS3 fragments, homologous recombination between them did occur at a relatively high frequency (5 x 10(-4). In contrast, recombination between two Alu sequences did not occur at a detectable level during a 30-day incubation. Thus, the frequency was less than 10(-5). These results indicate that the Alu sequences do not sufficiently promote the frequency of recombination between two homologous fragments in yeast as to induce rearrangements of DNA in a substantial fraction of YAC clones in libraries.