HIV RNA dimerisation interference by antisense oligonucleotides targeted to the 5′ UTR structural elements

The HIV-1 genome consists of two identical RNA molecules non-covalently linked by their 5′ unstranslatable regions (5′ UTR). The high level of sequence and structural conservation of this region correlates with its important functional involvement in the viral cycle, making it an attractive target for antiviral treatments based on antisense technology. Ten unmodified DNA antisense oligonucleotides (ODNs) targeted against different conserved structural elements within the 5′ UTR were assayed for their capacity to interfere with HIV-1 RNA dimerisation, inhibit gene expression, and prevent virus production in cell cultures. The results show that, in addition to the well-characterised dimerisation initiation site (DIS), targeting of the AUG-containing structural element may reflect its direct role in HIV-1 genomic RNA dimerisation in vitro. Similarly, blocking the 3′ end sequences of the stem-loop domain containing the primer biding site interferes with RNA dimerisation. Targeting the apical portion of the TAR element, however, appears to promote dimerisation. ODNs targeted against the conserved polyadenylation signal [Poly(A)], the primer binding site (PBS), the major splicing donor (SD) or the major packaging signal (Psi), and AUG-containing structural elements led to a highly efficient inhibition of HIV-1 gene expression and virus production in cell culture. Together, these results support the idea that ODNs possess great potential as molecular tools for the functional characterisation of viral RNA structural domains. Moreover, the targeting of these domains leads to the potent inhibition of viral replication, underscoring the potential of conserved structural RNA elements as antiviral targets.

► ODNs targeting functional HIV-1 5′ UTR structural RNA domains interfere with the viral RNA dimerisation process. ► The AUG-containing structural domain may play a direct role in triggering RNA dimerisation. ► The 3′ end of the PBS structural domains promotes RNA dimerisation in a non-functional DIS background. ► Targeting of genomic structural RNA domains by antisense ODNs promote a potent inhibition of viral replication. ► Conserved structural RNA elements are excellent antiviral targets.