Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells

A tRNA gene-like sequence has been identified near the 3′ end of HIV-1. Two segments of this sequence (motif 9 and segment 1) promoted minus strand transfer in vitro. The segments are complementary to the tRNA3Lys primer, and apparently act by binding the tRNA, thereby bringing the 3′ and 5′ ends of viral RNA into proximity for strand transfer. In this report, we used full-length HIV-1 to demonstrate biological relevance of these segments. We constructed HIV-1 genomes capable of single cycle infection and altered in one or both of two segments. We devised a real time PCR method for quantifying the amount of (−)ssDNA that completes transfer. Results showed that depending on the mutation the efficiency of transfer decreased from 9% to 26%. Alteration of segment 1 had the greatest effect. Alteration of motif 9 or both sequences also caused a reduction, but smaller than alteration of segment 1 alone.