Figure 4
Pathways by which the first strand transfer could generate proviruses with non-recombinant LTR and matching gag-nef pairs (panel A) or proviruses with LTR having a breakpoint at the U3/R junction and discordant gag-nef pairs (panel B). Arrows indicate 5′ to 3′ polymerisation of DNA. For clarity, synthesis of the (+) DNA strand from the central PPT is omitted. (i) After priming of reverse transcription on one RNA (blue), the transfer of synthesis blocks irreversibly (double slash) a potential ongoing reverse transcription of the second RNA (in red). (ii) Minus DNA synthesis proceeds toward the 5′ end of the gRNA. + sssDNA is synthesised on both RNAs and the tRNAs (shaded) are removed. The 5′ end of the RNAs and the corresponding + sssDNA are kept in proximity (green dotted line). (iii) Minus DNA synthesis is completed by synthesizing the (−) PBS DNA (green). Molecules no longer involved in the next steps have been omitted. (iv) Second strand transfer takes place, guided by the effect of proximity indicated by the dotted green line at step iii. (v) DNA synthesis is resumed after second strand transfer and displaces the pre-existing strands of the LTR. (vi) Synthesis of the full-length pre-proviral DNA is achieved (the strands displaced in panel B are lost – shaded –). (vii) The structure of the resulting proviral DNAs is shown. The proviral DNA in panel B will generate a breakpoint at the junction U3/R at the next generation.
