The creation of adenovirus genomes with viable, stable, internal redundancies centered about the E2b region.

During the course of constructing new adenoviral strains by overlap recombination, we have discovered that internally redundant viable genomes can be created by end-to-end joining of the input DNA molecules. The cellular functions responsible for the end-joining activity frequently ligated the overhanging single strands of the complementary ends to form a novel restriction site at the junction. In 2 of the 17 cases analyzed in detail by restriction digestion, and some sequence determinations, the cellular functions had repaired the ends, presumably prior to end-joining. Four of the isolates had suffered deletions at the junction ranging in size from 13 to 532 bp. The isolate with the largest deletion also had an insertion of 14 bp of unknown origin at the site of the deletion. All of the redundant isolates replicated as efficiently as isogenic unit length strains, and plaque dilution titrations obeyed one-hit kinetics, showing that the redundant genomes were nondefective. Nevertheless unit-length genomes were observed at a low level (some 5 to 10% of the total) in stocks of each isolate before and after plaque purification. They presumably arose by recombination between the redundant sequences either intra- or intermolecularly. Evidence from Southern blot analysis showed that molecules with three copies of the redundant sequences also arose and could be detected both in intracellular and in capsid viral DNA. These species would arise by unequal crossing-over between redundant genomes. The efficient replication of the redundant species demonstrates that the precise spatial relationships between splice donors and acceptors on either strand, in this region of the genome, do not have to be rigidly maintained. These data suggest that it may be possible to place other genetic information between the DNA polymerase and terminal protein precursor genes and have it expressed from the major late promoter in its normal location.