Abstract
Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region. Chemical mapping data combined with thermodynamic energy minimization were used in secondary structure prediction. Sequence/structure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conserved between influenza virus type A strains. Microarray mapping and RNase H cleavage identified accessible sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA. Antisense oligonucleotides were designed based on the secondary structure model and tested against influenza virus in cell culture. Inhibition of influenza virus proliferation was noticed, identifying good targets for antisense strategies. Effective target sites fall within two domains, which are conserved in sequence/structure indicating their importance to the virus.
Highlights
Influenza is a common disease that spans the globe and is dangerous for human health and life
Oligonucleotides are a major focus of drug development; numerous clinical trials have been performed and many oligonucleotide therapeutics are in phase III development
A 121 nt conserved structural motif from the segment 5 (+)RNA was used to design effective antisense oligonucleotides against a modified, single-cycle infectious influenza A virus strain. This highlights the importance of this motif in virus proliferation and highlights a new method for the design of Antisense oligonucleotide (ASO) based on target RNA secondary structure[8]
Summary
Influenza is a common disease that spans the globe and is dangerous for human health and life. In the case of mRNA, conserved structural motifs were discovered using sequence/structure comparisons, an analysis of the constraints of RNA folding on codon evolution, and were confirmed by the study of RNA models in vitro in segment 8, 7 and 58,9,14,15 and experiments in vivo[2]. A 121 nt conserved structural motif from the segment 5 (+)RNA was used to design effective antisense oligonucleotides against a modified, single-cycle infectious influenza A virus strain. This highlights the importance of this motif in virus proliferation and highlights a new method for the design of ASOs based on target RNA secondary structure[8]. Segment 5 (+)RNA, which is rich in predicted structural motifs, was selected for the full-length analyses of (+)RNA structure: to validate/model these motifs in the context of the full-length sequence
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