Fig. 3.

Dimeric, cap-exposed 3G polyA^NB RNAs are not competitively packaged. (A) In vitro packaging assay via cap-dependent adaptor ligation assay comparing RNA proportions in cells to that in virus. Single nucleotide resolution allows discrimination of RNA start via comparisons to controls corresponding to HIV-1_NL4-3 5′-capped 1G (2G) and HIV-1_NL4-3 5′-capped 3G (4G). Note that a 5′ cap leads to incorporation of a G in the final PCR product obtained using the cap-dependent adaptor ligation assay employed; thus, 5′ capped 1G RNA and 3G RNAs generate products with two and four 5′ guanosines, respectively, which exhibit mobilities of noncapped 2G and 4G controls (Left-most lanes). (B) Densitometric quantification of packaging propensities (1G and 3G RNAs shown in gray and black, respectively).