Formation of deletions after initiation of simian virus 40 replication: Influence of packaging limit of the capsid

Transfected DNA is frequently broken and rejoined in mammalian cells by recombination processes that depend on minimal nucleotide sequence homology. Although measurements of breakage and joining account reasonably well for the frequent formation of deletions during transfection, they are inadequate to explain the high frequency of deletion formation by simian virus 40 (SV40) genomes that are slightly larger than the packaging limit of the capsid. To investigate this anomaly, we constructed and transfected into CV-1 cells a series of modified SV40 genomes containing 136, 284, 460, and 656 extra base pairs in the intron of the gene encoding T antigen. These experiments indicate that the effective packaging limit of an SV40 capsid lies between 284 and 460 extra base pairs. Further analysis of these transfections suggests that molecules just above the effective packaging limit may be encapsidated and transmitted between cells at low efficiency, thereby allowing multiple rounds of replication and multiple opportunities to generate and package genomes that contain deletions. The junctional sequences in several such deletions were determined; they were similar to the junctions in deletions that were formed before replication began, suggesting that the enzymatic machinery responsible for both types of deletion may be similar.