Characterization of RNA aptamer binding to Rift Valley fever virus nucleocapsid protein

Rift Valley fever virus (RVFV) is a mosquito-borne virus that can cause hemorrhagic fever in humans and miscarriage in livestock. There is currently no cure for RVFV. Viral nucleocapsid protein (N) binding to viral RNA is crucial for RVFV replication, transcription, and genome protection. If N-RNA binding is prevented, RVFV will be unable to propagate in a host. This suggests that disruption of N-RNA interaction is a good potential therapeutic strategy for a new class of antiviral drugs. To exploit this target, molecular details about how N recognizes its preferred RNA binding sites must be elucidated. The Lodmell laboratory previously discovered a small RNA shown to bind N with high affinity called MBE87. MBE87 structure contains two GAUU nucleotide motifs. We have collaborated with Dr. Douglas Raiford in the Computer Science Department at UM to design RNAs with the same predicted secondary structure as MBE87 but with GAUU motifs at different positions in the structure. We hypothesize that the position of the GAUU motif is important for recognition by N and thus for viral functions. Using MBE87 and an RNA devoid of GAUU motifs as controls, electrophoretic mobility shift assays were performed to determine if the position of the GAUU motif within the RNA sequence affects N-RNA binding affinity. We performed the binding experiments in the presence and absence of suramin, a drug recently shown to inhibit RVFV replication. Our results suggest that suramin acts as a competitive inhibitor that binds to the site on N where aptamer RNA also binds. Because suramin binds at a site that at least overlaps with the aptamer RNA binding site, it had a stronger inhibitory effect on weaker-binding aptamers. When completed, this research will lend insight into how N recognizes preferred viral or host RNA binding sites and will pave the way toward development of drugs that target N protein