Synthesis of (-)ssDNA in permeabilized NL4.3, H89-NL4.3 and PKI-NL4.3 viruses. (A) Sucrose purified NL4.3 viruses permeabilized with 0.1 mM Triton X-100 were subjected to ERT reactions run for 16 h in the presence or absence of dNTPs. Control experiments consisted of incubation of viruses with dNTPs and 20 μg/mL nevirapine (Nev). (-)ssDNA copy numbers were determined in each sample by qPCR. Values are expressed as absolute copy numbers. Error bars indicate standard deviations (n = 4). (B) PKI-NL4.3 or H89-NL4.3 particles were subjected to ERT reactions as described in (A). (C) and (D) Accessibility of ERT products synthesized in NL4.3, H89-NL4.3 and PKI-NL4.3 particles was monitored by addition 4 U DNase and 105 copies of a tracer plasmid to the reaction mixture. After DNase inactivation and nucleic acids extraction, (-)ssDNA and tracer plasmid copy numbers were determined by qPCR. Values are expressed as a percentage of DNA levels detected in no DNAse reactions.