Development of Fluorescence and SANS Methods for Characterizing Structural Changes Associated with HIV-1 Genomic RNA Dimerization

 

Andrea L. Szakal, Susan Krueger, and John P. Marino

 

During virus assembly, all retroviruses, including HIV, specifically encapsidate two copies of full-length viral genomic RNA in the form of a non-covalently linked RNA dimer.  A number of studies suggest that dimerization is mediated through a sequence in the 5’-untranslated region (UTR) of the genomic RNA, but the structures formed by this RNA and the in vivo mechanism by which genome dimerization occurs are still not well understood.  We will present results from measurements using small-angle neutron scattering (SANS) and fluorescence that have been applied to analyze the structure of the 5’-UTR of the genomic HIV-1 RNA and guide the building of structural models that can be tested in vivo.  We have applied these techniques to probe the 5’-UTR as both a monomer and a dimer, and also in the absence and presence of the HIV-1 nucleocapsid protein, NCp7, which has been implicated as an RNA chaperone in the genome dimerization process.   Knowledge of these structures could potentially guide the development of novel therapeutics that target HIV-1 genomic RNA before packaging and/or upon introduction to the cell after infection, and may lead to new treatments for other retroviruses as well.