Depletion between the direct repeats leads to restoration of gene function. With this system deletions are revealed as generation of phage wild type for ligase. Because good in vitro T7 DNA replication and packaging systems are available, we have also been able to apply the T7 system to an in vitro study of deletion. This allows a unique biochemical approach in a replication system where the template, precursors, chemical environment, and some of the enzymes involved can be manipulated and the effects upon deletion formation monitored. Our results show that DNA replication is apparently essential for deletion to occur.
Recombination plays a very small role in deletion.
The 3'-5' exonuclease edit function of the replicating DNA polymerase plays little or no role in deletion. But, the 5'-3' exonuclease of the host DNA polymerase does seem to be involved. The data are most consistent with slippage of the replication enzymes from one direct repeat to the downstream direct repeats and consequent loss of the genetic information between the repeats. Also, our data suggest that there may be a repair-like activity that processes DNA intermediates formed as part of the deletion process. Currently we are attempting to isolate deletion intermediates.