Figure 3

Integrase-mediated chromosomal deletion. (A) Chromosomal deletion frequencies in 293-3BP cell lines calculated by quantitative PCR. The values represent the average of two experiments, with standard deviation bars. Cell lines were transfected with pφC31-IRES-hrGFP (dotted bars) or pR4-IRES-hrGFP (dashed bars), GFP-positive cells were sorted and expanded, and genomic DNA was harvested and analyzed by qPCR. Deletion frequency was calculated as the ratio of attR junctions amplified to total vectors present (hygromycin resistance gene amplified), multiplied by 100. (B) Representative Southern blot of deletion reaction in cell line 293-3BP6. Untransfected and Int-transfected cell lines are shown, with the expected intact (unex.) and Int-deleted bands for φC31 (φex), R4 (R4ex), and TP901-1 (TPex) indicated. Twenty μg of genomic DNA were probed with a common 1.6 kb plasmid backbone fragment.