Ultrastructure of HIV-1 genomic RNA.

The HIV-1 RNA genome is a dimer which consists of two identical strands of RNA linked near their 5' ends by a dimer linkage structure (DLS). We have structurally characterized full-length HIV-1 genomic RNA isolated from HIV-1 virions by electron microscopy. As in other retroviruses, the HIV-1 RNA genome contains a central dimer linkage structure and additional loop structures within each monomer subunit. In contrast to the DLS of other retroviruses, the DLS region of HIV-1 contains a loop of 323 +/- 44 nucleotides. The free 5' ends of the two RNA strands were not visualized, suggesting that the 5' end regions are involved in interstrand complementary base pairing. Computer modeling identified a single stable structure that was consistent with the electron microscopy data. In this model, the two RNA strands are linked at their 5' ends by two contact points derived from "kissing-loop" interactions between r-u5 and SL1 stem-loops and their counterparts on the second strand. These interactions may contribute to the formation of stable HIV-1 RNA dimers in vivo.