HIV-1 proviral genomes with mutated A-loop and PBS. The A-loop (boxed) and PBS (shaded) were altered in the NL4 proviral clone to be complementary to tRNAHis, tRNAIle, tRNAMet, tRNAThr, tRNASer or tRNAGln. The NL4-WT contains a PBS and A-loop complementary to the 3' terminal 18 nucleotides and the anticodon of tRNALys,3. The NL4-His contains a PBS complementary to tRNAHis but the A-loop is complementary to the anticodon region of tRNALys,3. The remaining proviral clones contain a PBS complementary to tRNAHis with additional mutations in the A-loop to be complementary to the anticodon of the designated tRNA (e.g. NL4-His-HisAC).