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Most stable G‐quadruplex structures are selectively avoided at the codon level

The coding region (CDS) of mRNA is known to be less structured compared to the untranslated regions (UTRs) primarily to reduce any structural interference with the translation process. Translational rate and open reading frames have been shown to be affected by the secondary structures present within the CDS. However a systematic and comprehensive analysis of secondary structure avoidance is difficult as some of the common secondary structures such as hairpins can be formed by a wide range of sequence combinations. Using a G‐quadruplex (GQ) as the secondary structure we studied the evolutionary selectivity against the GQ structures within the CDS. G‐quadruplexes are well‐known secondary structures adopted by RNA and have been shown to control translation. Since the GQs have defined sequence requirements, they provide an excellent platform for investigation of the selectivity of such structures at the codon level. Using a bioinformatics approach we studied the frequencies of GQs within the CDS of a variety of species. We discovered that the most stable GQs are significantly avoided within the CDS by evolutionary pressure. Further we showed that the avoidance of GQs at the codon level correlates to the stability of such structures. Finally we established that the translation is affected by the stable GQs that are present within the CDS. This work not only provides a comprehensive analysis on how the stable secondary structures are avoided within the CDS throughout the evolution but also broadens the current understanding of codon usage as they relate to structure‐function relationship of RNA.