title: Characterization of RNA aptamers directed against the nucleocapsid protein of Rift Valley fever virus.
abstract: Nucleocapsid protein (N) is an essential RNA binding protein in many RNA viruses. During replication, N protein encapsidates viral genomic and antigenomic RNA, but not viral mRNA or other cellular RNAs. To discriminate between different species of RNA in a host cell, it is likely that N interacts with specific sequences and/or secondary structures on its target RNA. In this study, we explore the RNA binding properties of N using both natural and artificially selected RNAs as ligands. We found that N binds to RNAs that resemble the terminal panhandle structures of RVFV genomic and antigenomic RNA. Furthermore, we used SELEX to isolate RNA aptamers that bound N with high affinity and determined that N specifically recognizes and binds to GAUU and pyrimidine/guanine motifs. Interestingly, BLAST analysis revealed the presence of these motifs within the coding region of the viral genome, suggesting that N may interact with non-terminal viral RNA sequences during replication. Finally, the aptamer RNAs were used to construct a sensitive fluorescence based sensor of N binding with potential applications for drug screening and imaging methodologies.
authors.affiliation: Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Ellenbecker
authors.forename: Leila
authors.initials: L
authors.lastname: Sears
authors.forename: Ping
authors.initials: P
authors.lastname: Li
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Lanchy
authors.forename: J Stephen
authors.initials: JS
authors.lastname: Lodmell
mesh_terms: D052157:Aptamers, Nucleotide / Q000235:genetics; D001483:Base Sequence; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D019590:Nucleocapsid Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D012295:Rift Valley Fever / Q000821:virology; D012296:Rift Valley fever virus / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D019590:Nucleocapsid Proteins; D012367:RNA, Viral