Imaging Retroviral RNA Genome Heterodimers Using Bimolecular Fluorescence Complementation (BiFC)

Retroviruses are single-stranded RNA viruses that package two copies of their positively stranded RNA genomes as a non-covalent dimer into newly formed virions. This process is evolutionarily conserved, and disruption of genome dimerization results in production of non-infectious virus particles. Genome dimers can be packaged as homodimers, containing two identical RNAs, or heterodimers, consisting of two genetically distinct copies. Genome dimerization generates genetic diversity, and different retroviruses have preferences for the type of genome dimers packaged into virions. We developed a novel imaging approach to specifically label and detect retroviral genome heterodimers in cells using a modified bimolecular fluorescence complementation (BiFC) technique. This method utilizes viral genomes encoding two different RNA stem-loop cassettes that each specifically binds to an RNA-binding protein conjugated to a split fluorophore. When two genetically different genomes are within close proximity, the fluorophore halves come together to reconstitute fluorescence. These BiFC-labeled RNA dimers can be visualized and tracked in living cells and interact with retroviral Gag proteins. This method has the advantage of low background fluorescence and can be applied to the study of dimeric or double-stranded RNAs of viruses and other organisms.