Southern analysis of replication-competent AAV (rcAAV) in different AAV-GFP vectors. Up to 109 viral genome particles of highly purified AAV-GFP, generated either from the 293-GFP-145 cells or from the triple-plasmid transfection method, were used to infect one 10-cm plate, which were coinfected with wild-type adenovirus at an MOI of 5 to provide helper functions for rcAAV amplification. As a positive control, wild-type AAV was also used similarly to infect the 293 cells at a total dose ranging from 1 to 1,000 infectious units per 10-cm plate along with wild-type adenovirus coinfection (see Materials and metHods). Low-molecular-weight DNA samples from the second round of amplification were isolated and subjected to Southern analysis with an AAV cap gene fragment as the probe.