Exploring three-dimensional structures of the HIV-1 RNA/tRNA(Lys3) initiation complex

Human immunodeficiency virus type 1 (HIV-1) uses host tRNA as a primer for reverse transcription of its viral RNA. The 3' terminal 18 nucleotides of h uman tRNA(Lys3) are complementary to the primer binding site on the viral R NA. A secondary structure model for the HIV-1 RNA/tRNA(Lys3) initiation com plex has been proposed that includes additional base-pairing between the tR NA and the HIV-1 RNA beyond the 18 nucleotides of the primer binding site. Included in these interactions is base-pairing between the anticodon of tRN A(Lys3) and an A-rich loop in the HIV-1 secondary structure. The tRNA and H IV-1 RNA are significantly unfolded from their native structures in order t o form the initiation complex proposed in this model. We have found several problems with the proposed secondary structure in our efforts to build a t hree-dimensional model that is compatible with it. The additional interacti ons between the tRNA and viral RNA cause the structure to be topologically knotted. This poses a problem for folding of the initiation complex and tra nscription by reverse transcriptase. We have also not been able to build an y all-atom models based on known RNA structures that follow the secondary s tructure model in the extended tRNA/HIV-1 RNA complex. Finally, beyond the primer binding site interaction, subsequent biochemical and genetic studies have given further insight into the structure of the initiation complex. T hese results call into question some of the extended HIV-1 RNA/tRNA interac tions that have been proposed. (C) 1999 Academic Press.