RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference

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Mol Ther Nucleic Acids. 2019 Dec 24;19:627-642. doi: 10.1016/j.omtn.2019.12.018. [Epub ahead of print] RNA Secondary Structure Motifs of the Influenza A Virus as Targets for siRNA-Mediated RNA Interference.

Piasecka J¹, Lenartowicz E¹, Soszynska-Jozwiak M¹, Szutkowska B¹, Kierzek R¹, Kierzek E².
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Abstract

The influenza A virus is a human pathogen that poses a serious public health threat due to rapid antigen changes and emergence of new, highly pathogenic strains with the potential to become easily transmitted in the human population. The viral genome is encoded by eight RNA segments, and all stages of the replication cycle are dependent on RNA. In this study, we designed small interfering RNA (siRNA) targeting influenza segment 5 nucleoprotein (NP) mRNA structural motifs that encode important functions. The new criterion for choosing the siRNA target was the prediction of accessible regions based on the secondary structure of segment 5 (+)RNA. This design led to siRNAs that significantly inhibit influenza virus type A replication in Madin-Darby canine kidney (MDCK) cells. Additionally, chemical modifications with the potential to improve siRNA properties were introduced and systematically validated in MDCK cells against the virus. A substantial and maximum inhibitory effect was achieved at concentrations as low as 8 nM. The inhibition of viral replication reached approximately 90% for the best siRNA variants. Additionally, selected siRNAs were compared with antisense oligonucleotides targeting the same regions; this revealed that effectiveness depends on both the target accessibility and oligonucleotide antiviral strategy. Our new approach of target-site preselection based on segment 5 (+)RNA secondary structure led to effective viral inhibition and a better understanding of the impact of RNA structural motifs on the influenza replication cycle.
Copyright ? 2019 The Author(s). Published by Elsevier Inc. All rights reserved.


KEYWORDS:

NP; RNA structure; antisense oligonucleotides; influenza; influenza inhibition; modified siRNA; nucleoprotein; siRNA

PMID: 31945726 DOI: 10.1016/j.omtn.2019.12.018
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