UC San Diego

Phylogenetic analysis and sequence alignments with other Flaviviruses have led us to identify a putative promoter motif located in a putative three-way junction of the 5’UTR RNA, called Stem Loop A (SLA), which allows for binding of the RNA-dependent RNA polymerase (RdRp), and thus replication of the viral RNA genome. To support this hypothesis through structural and biochemical characterization of this domain, milligrams of the SLA RNA were 

produced by in vitro transcription to then crystallize and determine its structure by X-ray diffraction. Determining the structure of the Zika virus SLA domain would contribute to our understanding of its mechanism of action. Although sufficient amounts of RNA were produced for crystallography, diffracting crystals have not yet been obtained. Additionally, a FRET assay has been developed and successfully used to confirm that the SLA domain of the Zika virus adopts a bent three-way junction conformation. FRET experiments with antisense DNA as surrogate ligands to parts of the SLA RNA suggest that the FRET assay will be useful in the future to discover small molecule ligands that alter and capture the SLA three-way junction in a non-functioning conformation.