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

作　　者：ZHANG SuXia WANG Xin CHEN XueFeng CAO Huai ZHANG Wen LIU CiQuan 

机构地区：[1]Modern Biological Research Center, Yunnan University, Kunming 650091, China [2]Henan Medical School, Kaifeng 475300, China [3]Tangdu Hospital, Fourth Military Medical University, Xi'an 710033, China [4]Deparment of Cell Biology and Medical Genetics, Kunming Medical College, Kunming 650031, China [5]Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China [6]Center for Theoretical Biology, Peking University, Beijing 100871, China

出　　处：《Chinese Science Bulletin》2008年第3期377-383,共7页

基　　金：the National Natural Science Foundation of China(Grants No.90208018,39970412and90303018);the CAS Knowledge Innovation Project Cross-Frontier Project(No.KJCX1-08)

摘　　要：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.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.

关 键 词：禽流感 H5N1病毒 红血球凝聚素分裂位点 RNA 二级结构 氨基酸 

分 类 号：S855.3[农业科学—临床兽医学]