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

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• 作者：Mary Ellenbecker^a ; Leila Sears^a ; Ping Li^b ; Jean-Marc Lanchy^a ; J. Stephen Lodmell^a ; ^{stephen.lodmell@umontana.edu}
• 关键词：Rift Valley fever virus ; Nucleocapsid ; RNA aptamer ; SELEX
• 刊名：Antiviral Research
• 出版年：2012
• 期刊代码：7_01663542
• 类别：imm
• 出版时间：March, 2012
• 卷：93
• 期：3
• 页码：330-339
• 文件大小：1795 K

摘要

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.