Statistical significance of partial base-pairing potential: Implications for recombination of SV40 DNA in eukaryotic cells

The frequent detection of "patchy homology" between recombining DNAs in eukaryotic systems suggests that partial sequence homology might facilitate formation of partially base-paired hybrid structures and thus define a specific target for recombination. Indeed, the extent of such "patchy homology" initially appears impressive. The question of whether such homology is statistically significant, however, has not been addressed. In this paper we compare the extent of "patchy homology" within the sequence of SV40 recombination sites and within randomly-generated sequences with the same average GC content. We have found no statistically significant differences favoring the existence of "patchy homology" within the recombining regions of SV40. On the average 50% of the bases in randomly-generated sequences with the same GC content can be paired in a pattern of "patchy homology". We have also assessed the ability of sequences near recombination junctions in SV40 to form partially base-paired intra-strand secondary structures. Again, the ability of these sequences to form such configurations was unremarkable when compared with random sequences. Thus, the notion that partial base-pairing provides specificity for sites of recombination must be considered with caution.