Structure of the HIV-1 5′ Untranslated Region Dimer Alone and in Complex with Gold Nanocolloids: Support of a TAR–TAR-Containing 5′ Dimer Linkage Site (DLS) and a 3′ DIS–DIS-Containing DLS

The formation of a genomic RNA dimer is critical for the HIV-1 replication cycle, and dimerization is known to initiate within the 5′UTR (5′ untranslated region) of the viral RNA. However, the 5′UTR constitutes the 335 terminal nucleotides, and because of this considerable size, it has been difficult to study the global structure using conventional structural methods. Here, the atomic force microscope has been used to directly visualize the dimer formed from RNAs including HIV-1 nucleotides 1–744. Gold nanocolloids were deposited on the primer binding site regions in the dimer as an internal control. The dimer showed distinct ring morphology with up to two gold nanocolloids deposited within the ring and one or two strands extending from the ring. This morphology implies a dimer including a DIS-DIS (dimerization initiation site)-containing 3′ dimer linkage site (DLS) and a TAR-TAR (trans-activation region)-containing 5′DLS. Furthermore, the dimer was formed under the influence of Mg2+ and was imaged with an atomic force microscope under buffer conditions. The overall ring morphology containing a 5′DLS and a 3′DLS with one or two strands extending from it was conserved in these atomic force microscopy images. This indicates that the observed dimer morphology is physiologically significant. Moreover, evidence of multiple dimer interstrand contacts downstream of the major splice donor were observed, which indicates a component in the selection of full-length genomic RNA in dimer formation during virion packaging.