The Alu primer binds only to cellular genomic DNA, not to integrated HIV DNA; the gag primer binds to one strand of HIV DNA. When both Alu and gag primers are used in the amplification, the original template strands and every copy are duplicated in each round, so amplification becomes exponential. Linear, one-strand amplification (i.e. primer extension) was also monitored by performing the first amplification PCR with the gag primer alone. When only the gag primer is used, only one strand of the original template DNA is copied so amplification is linear. We used the gag-only primer amplification reaction as a control because it provides the signal expected from integrated HIV DNA. While increased extension times increases the ability of Taq polymerase to make longer amplicons