Nucleotide sequence analysis of the recombinant joints in 16 naturally arising deletion mutants of simian virus 40

Abstract

The nucleotide sequences flanking the deletions in 16 naturally arising mutant simian virus 40 (SV40) genomes were determined. The parental sequences involved in each recombinational event were reconstructed from the published sequence of wild-type SV40. No extensive homologies between the parental strands were found. Neither were there any site or sequence similarities among the deletion endpoints. Thus, neither a general homologous nor sequence-specific recombination mechanism was likely to have been involved in the formation of these deletions. In light of these findings, we propose that they may have been produced by repair and ligation of linear DNA molecules that result from the action of nonspecific cellular endonucleases. This mechanism could also account for the existence of defective SV40 genomes containing sequences of non-viral origin.