Figure 4

Estimating the frequency of v126-D/v120-A recombination with or without siRNA enrichment using semi-quantitative PCR. Schematic describing the siRNAs enrichment of v126-D/v120-A recombinants and the PCR strategy designed for their detection and quantification is shown in panel A. Virus 126-D and virus 120-A env specific primers were used to PCR amplify the env recombinant genes alongside conserved env primers amplifying all env genes (see Materials and Methods). The viruses produced in the first and second round infections (bars 1 through 6 in Figure 3C) were used as templates for this PCR of the v126-D/v120-A env or all of the env genes in the virus (i.e. v120-A + v-126-A + v126-D/v120-A + v120-A/v126-D). A PCR control involved PCR amplification of 10-fold dilutions of v120-A and v126-D env DNA in a DNA vector construct. Panel B shows the percentage of v126-D/v120-A recombinants in the total virus measured by semi-quantitative PCR.