Repair of The Gaps Formed in The Strand Transfer Process ("Gap Repair")
Following the strand transfer process, the HIV-DNA and host DNA junctions have unpaired regions of DNA, referred to as DNA "gaps". In addition, the two base pairs at the end of the 5’ region of the viral DNA remain unpaired after the strand transfer. The insertion of the new HIV DNA and the remaining gaps that flank the integration site induce a host cellular DNA damage response. The host response is critical in the final step of integration, known as "gap repair". The gap repair requires at least three host enzymes - polymerase, nuclease, and ligase. In the first step of gap repair, the polymerase enzymes extend the host DNA on each end and, thus, fill in the gaps. Next, nuclease enzymes remove the 5’ dinucleotide "flaps" on the HIV DNA. Last, the DNA ligase enzymes join the remaining unbound segment of the HIV and host DNA strands. This gap repair process completes the integration of the HIV DNA into the host DNA, with the fully integrated HIV DNA now being referred to as "proviral DNA".
Read more about this topic: HIV Integration, HIV Integration Mechanism
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