Figure 1.

Scheme of differential amplification. (A) Amplification of SIVmac239Δnef. A linearized upstream primer (nef1) and hairpin-shaped primer (hs Δnef) were used to amplify a 106-bp amplicon. hs Δnef hybridizes across the junction of the deletion in nef, allowing amplification of SIVmac239Δnef in the presence of SIVmac251. A molecular beacon (mb Δnef) was used for detection of amplicons. (B) Amplification of SIVmac251. A linearized primer (nef1) and hairpin-shaped oligonucleotide (hs wt nef) were used to amplify a fragment of 142 bp. An additional PCR was performed using linearized oligonucleotides (nef3 and wt nef2), which amplify a fragment of 157 bp. Amplicons were detected using the molecular beacon (mb wt nef).