Structures of complexes formed by HIV-1 reverse transcriptase at a termination site of DNA synthesis

This study presents structural parameters associated with termination of hu man immunodeficiency virus, type 1 (HIV-1) reverse transcriptase (RT) at Te r2, the major termination site located in the center of the HIV-1 genome. D NA footprinting studies of various elongation complexes formed by RT around wild type and mutant Ter2 sites have revealed two major structural transfo rmations of these complexes when the enzyme gets closer to Ter2. First, the interactions between RT and the DNA duplex are less extended, although the global affinity of the enzyme for this duplex is only decreased by 2-fold. Second, there is an atypical positioning of the RT RNase H domain on the D NA duplex. We interpret our data as indicating that the A(n)T(m) motif loca ted upstream of Ter2 prevents a classical positioning of the enzyme on the double-stranded part of the DNA duplex at some precise positions of elongat ion downstream of this motif. Instead, novel species of binary and/or terna ry complexes, characterized by atypical footprints, are formed. The new rat e-limiting step of the reaction, characterized in the preceding paper (Lavi gne, M., Polomack, L., and Buc, H. (2001) J. BioL Chem. 276,31429-31438), w ould be a transition leading from these new species to a catalytically comp etent ternary complex.