The majority of the nucleotides in the top loop of the genomic 3' terminal stem loop structure are cis-acting in a West Nile virus infectious clone.
The flavivirus genome RNA terminates with a conserved 3' stem loop (SL) structure that was shown to be essential for virus replication. A stretch of conserved nts is located in the top loop (TL) of this structure. Mutation of the TL nts (5' ACAGUGC 3') in a WNV infectious clone indicated that 3 of the 7 TL nts (5' ACAGUGC 3') are critical for virus replication. Mutation of 3 of the other nts reduced the efficiency of virus replication. The four 5' TL nts are conserved in both mosquito- and tick-borne flavivirus genomes, while the TL 3' C is conserved in mosquito-borne viruses. The conservation of two or three G-C base pairs in the TL flanking sequences suggests that a stable stem is necessary for precise presentation of the TL sequence. The TL may participate in RNA as well as protein interactions.
Elghonemy
Salwa
S
Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA.
Davis
William G
WG
Brinton
Margo A
MA
D000818:Animals; D017124:Conserved Sequence; D006224:Cricetinae; D016679:Genome, Viral; D007668:Kidney; D009154:Mutation; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D013329:Structure-Activity Relationship; D014779:Virus Replication; D014902:West Nile virus / Q000737:chemistry* / Q000235:genetics / Q000502:physiology
D012367:RNA, Viral