Characterization of RNA aptamers directed against the nucleocapsid protein of Rift Valley fever virus

Mary Ellenbecker, Leila Sears, Ping Li, Jean Marc Lanchy, J. Stephen Lodmell

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


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.

Original languageEnglish
Pages (from-to)330-339
Number of pages10
JournalAntiviral Research
Issue number3
StatePublished - Mar 2012


  • Nucleocapsid
  • RNA aptamer
  • Rift Valley fever virus


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