Structure and sequence motifs in the HIV-1 RNA genome

The untranslated leader of the HIV-1 RNA genome contains some 350 nucleotides and is highly conserved among virus isolates. Several characteristic hairpin structures that regulate important virus replication steps, such as dimerization and packaging in virion particles, are clustered in this leader. In this thesis, we demonstrate that the single-stranded sequences flanking these hairpins also play critical roles in these HIV-1 RNA processes. By exploring the sequence space of these single-stranded regions that is compatible with virus replication, we demonstrate that sequences compatible with efficient virus replication do not affect the surrounding RNA structure. These results emphasize the importance of a correct leader RNA structure. We describe that a correct RNA secondary structure also prevents excessive splicing and is therefore important for the regulation of HIV-1 splicing. Furthermore, the effect of a drug belonging to a new class of antivirals was tested on the HIV-1 RNA-mediated processes. These drugs mislocalize the viral RNA genome outside the capsid core in virion particles and inhibit reverse transcription. We demonstrate that all essential RNA and enzyme components for reverse transcription are present in these virions and hypothesize that the spatiotemporal regulation of reverse transcription is disturbed by the mislocalization of these components.