Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin （HA） cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in...

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Bibliographic Details
Published in:Chinese science bulletin 2008-02, Vol.53 (3), p.377-383
Main Authors: Zhang, SuXia, Wang, Xin, Chen, XueFeng, Cao, Huai, Zhang, Wen, Liu, CiQuan
Format: Article
Language:English
Subjects:
Avian influenza virus
Chemistry/Food Science
Earth Sciences
Engineering
H5N1病毒
Humanities and Social Sciences
Life Sciences
multidisciplinary
Physics
RNA
Science
Science (multidisciplinary)
二级结构
氨基酸
禽流感
红血球凝聚素分裂位点
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Summary:Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin （HA） cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in an iterative extension process. Statistical analysis of the sequences showed that the HA cleavage site basic amino acids favor the adenine-rich codons, and the corresponding mRNA fragments are mainly in the folding states of single-stranded loops. Our sequential and structural analyses showed that to prevent and control these highly pathogenic viruses, that is, to inhibit the gene expression of avian influenza virus H5N1 subtypes, we should consider the single-stranded loop regions of the HA cleavage site-coding sequences as the targets of RNA interference.
ISSN:1001-6538
1861-9541
DOI:10.1007/s11434-008-0119-6