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以A型流感病毒为研究样本,分析了同义密码子使用偏性对RNA二级结构的影响,为进一步研究同义密码子存在的意义及A型流感病毒RNA特征提供一些理论依据。收集整理了NCBI中收录的全部A型流感病毒的核酸序列信息,计算了每一条核酸序列的RNA二级结构,计算出RNA环结构含量和茎结构含量及折叠自由能。在此基础上,计算了RNA二级结构的柔性。同时,计算了每一条核酸序列的相对同义密码子使用值。由此,建立了A型流感病毒RNA二级结构数据库。分析每条核酸序列的相对同义密码子使用值与RNA的环结构、茎结构及柔性之间的关系。分析结果表明,50%的氨基酸的相对同义密码子使用值与RNA茎结构含量和环结构含量显著相关;60%的氨基酸的相对同义密码子使用值与单位平均折叠自由能显著相关;50%的氨基酸的相对同义密码子使用值与RNA柔性显著相关。进一步分析发现,与茎结构含量和环结构含量都显著相关的密码子,它们的相对同义密码子使用值与两种结构含量的相关性截然相反,而且发现,在所选的参量中,RNA柔性与相对同义密码子使用值显示出更好的相关性。结果证实,对于A型流感病毒,同义密码子的使用偏性对RNA二级结构存在很大的影响。
A type A influenza virus was used as a sample to analyze the influence of synonymous codon usage bias on RNA secondary structure. This study provides some theoretical basis for further study of the significance of synonymous codons and the RNA characteristics of influenza A virus. The information of the nucleic acid sequences of all influenza A viruses collected in NCBI was collected and the RNA secondary structure of each nucleic acid sequence was calculated. The contents of RNA ring structure and the content of stem structure and the free energy of folding were calculated. On this basis, the flexibility of RNA secondary structure was calculated. At the same time, relative synonymous codon usage values for each nucleic acid sequence were calculated. Thus, a type A influenza virus RNA secondary structure database was established. The relationship between the relative synonymous codon usage of each nucleic acid sequence and the loop structure, stem structure, and flexibility of the RNA was analyzed. The results showed that relative synonymous codon usage of 50% of amino acids was significantly correlated with the contents of RNA stem structure and the content of ring structure. The relative synonymous codon usage of 60% of amino acids was significantly correlated with the average free energy of unit folds. The relative synonymous codon usage values of% amino acids were significantly correlated with RNA flexibility. Further analysis revealed that codons that were significantly associated with both the content of stalk and the content of ring structure were opposite in their relative synonymous codon usage values from the two structural contents and found that among the parameters selected, RNA Flexibility and relative synonym usage values showed better correlation. The results confirm that the use of synonymous codons for the influenza A virus has a large effect on RNA secondary structure.