[Influence of Synonymous Codon Bias on the RNA Secondary Structure in Influenza-A Viruses]

Influenza-A viruses were selected as samples. Then, the relationship between synonymous codon bias and mRNA secondary structures was analyzed. Our data will provide a theoretical basis for further research on the synonymous codon and RNA properties of the influenza-A virus. Information on the nucleic-acid sequence of all influenza-A viruses in the National Center for Biotechnology Information was collected. The secondary structure of each nucleic-acid sequence was predicted. Then, the loop structure, stem structure, and free replicating energy of RNA were calculated. Based on this information, the specific flexibility of RNA was worked out. Simultaneously, the synonymous codon bias in each nucleic-acid sequence was counted. A database on the RNA secondary structure of the influenza-A virus was set up. Then, the relationship between the synonymous codon bias and the content of loop structure, stem structure, and flexibility were analyzed.Codon usage of 50% of amino acids was correlated significantly with the content of stem structure or the content of loop structure.Also,60% of amino acids were correlated significantly with average unit folding free energy. In addition, codon usage of 50% of amino acids was correlated significantly with the specific flexibility of RNA. For codons that were correlated significantly with stem structure and loop structure, the correlation between their usage with two types of structural content was completely contrary .Also, the correlation between specific flexibility with synonymous codon bias was better than that observed for other parameters. These results suggest that synonymous codon usage bias has important influences on RNA secondary structure.