Simian virus 40 (SV40)-transformed cell lines, SV40 viral DNA, and SV40-based recombinant DNA vectors have been used to study both nonhomologous and homologous recombination in somatic cells (4-8, 31, 36). One outcome of these studies has been the observation that the two known genomic crossover sites for SV40 integration are associated with stretches of alternating purines and pyrimidines (8, 41). Moreover, it has been reported that an SV40 genome containing a stretch of alternating purines and pyrimidines, poly[d(pGpT) -d(pApC)] [poly(GT)], undergoes homologous recombination within the alternating purines and pyrimidines up to eight times more frequently than a control insert of the same length (43). However, though alternating purine-pyrimidine repeats may enhance the frequency of certain recombination events involving viral DNA, they are clearly not manditory. For instance, not all of the genomic integration sites utilized by DNA tumor viruses are associated with alternating purines and pyrimidines. Hayday et al. (16) and Williams and Fried (Sla) have found that these sequences are not present at the two known genomic sites selected for use during polyomavirus integration.Additional evidence, often circumstantial, linking various runs of alternating purines and pyrimidines with recombination events has been obtained from other eucaryotic recombination systems (11,19,37,38), and a review of the data linking poly(GT) sequences with recombination has been published (35). Eucaryotic organisms contain many such poly(GT) repeats dispersed throughout their genomes, ranging in size from 10 to 50 base pairs (bp) (14,15 CpG sequences are highly clustered (3). The original proposal that alternating purines and pyrimidines were hot spots for DNA exchanges was made by Slightom et al. (39), after finding a run of alternating poly(GT) residues at one end of a segment of DNA that was suggested to have recombined during duplication of the human Gz and A,, globin genes. At present, the mechanism(s) by which runs of alternating purines and pyrimidines might promote recombination in vivo is unknown.In light of these studies, we decided to test whether poly(CG) or poly(GT) residues could be shown to promote recombination in vivo. In this paper, we present studies of the effects of these two simple sequences on an intramolecular homologous recombination event between two 751-base-pair (bp) direct repeats of SV40. Recombination between the direct repeats generates wild-type (wt) SV40. Since the alternating purines and pyrimidines were cloned precisely at the border of one of the two 751-bp direct repeats, the ability of the alternating purines and pyrimidines to promote recombination in simian cells was easily assessed by following the formation of either SV40 DNA or SV40 virus.
MATERUILS AND METHODSPlasmid construction and isolation. The construction of plasmid pSVLD was as described previously (31). Plasmid pSVLD-CG64 was constructed as follows: plasmid pLP32, which has a 32-bp segment of alternating guanine and cytosine resid...