Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides
Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides
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DOI：
10.1038/s41598-019-40443-7
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发表时间：
2019-03-07
影响因子：
4.6
通讯作者：
Kierzek, Elzbieta
中科院分区：
文献类型：
--
作者：
Michalak, Paula;Soszynska-Jozwiak, Marta;Kierzek, Elzbieta
流感病毒会引起季节性流行病和危险的大流行病爆发。它是一种具有分段基因组的单链 (-) RNA 病毒。基因组病毒 RNA (vRNA) 的八个片段形成病毒体，然后在宿主细胞中转录和复制。 vRNA 的二级结构是病毒生物学的重要调节因子，可以成为寻找新疗法的目标。本文基于甲型流感化学图谱数据、自由能最小化和结构序列保守分析，确定了片段5 vRNA的二级结构。揭示的二级结构具有圆形折叠，具有先前报道的狭长图案和独特的新颖结构域。碱基对的保守度平均为 87%，许多结构基序高度保守。等能量微阵列作图用于另外验证二级结构并发现容易结合短寡核苷酸的区域。基于建模二级结构和微阵列图谱设计的反义寡核苷酸可抑制甲型流感病毒在 MDCK 细胞中的增殖。最有效的寡核苷酸可将病毒滴度降低约 90%。这些结果定义了对病毒功能可能重要的 A 型结构区域的普遍性，以及反义治疗的新靶标。
Influenza virus causes seasonal epidemics and dangerous pandemic outbreaks. It is a single stranded (-) RNA virus with a segmented genome. Eight segments of genomic viral RNA (vRNA) form the virion, which are then transcribed and replicated in host cells. The secondary structure of vRNA is an important regulator of virus biology and can be a target for finding new therapeutics. In this paper, the secondary structure of segment 5 vRNA is determined based on chemical mapping data, free energy minimization and structure-sequence conservation analysis for type A influenza. The revealed secondary structure has circular folding with a previously reported panhandle motif and distinct novel domains. Conservations of base pairs is 87% on average with many structural motifs that are highly conserved. Isoenergetic microarray mapping was used to additionally validate secondary structure and to discover regions that easy bind short oligonucleotides. Antisense oligonucleotides, which were designed based on modeled secondary structure and microarray mapping, inhibit influenza A virus proliferation in MDCK cells. The most potent oligonucleotides lowered virus titer by similar to 90%. These results define universal for type A structured regions that could be important for virus function, as well as new targets for antisense therapeutics.