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Background: The secondary structure and complexity of mRNA influences itsaccessibility to regulatory molecules (proteins, micro-RNAs), its stability andits level of expression. The mobile elements of the RNA sequence, the wobblebases, are expected to regulate the formation of structures encompassing codingsequences.  Results: The sequence/folding energy (FE) relationship was studied bystatistical, bioinformatic methods in 90 CDS containing 26,370 codons. I foundthat the FE (dG) associated with coding sequences is significant and negative(407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are ableto form structures. However, the FE has only a small free component, less than10% of the total. The contribution of the 1st and 3rd codon bases to the FE islarger than the contribution of the 2nd (central) bases. It is possible toachieve a ~ 4-fold change in FE by altering the wobble bases in synonymouscodons. The sequence/FE relationship can be described with a simple algorithm,and the total FE can be predicted solely from the sequence composition of thenucleic acid. The contributions of different synonymous codons to the FE areadditive and one codon cannot replace another. The accumulated contributions ofsynonymous codons of an amino acid to the total folding energy of an mRNA isstrongly correlated to the relative amount of that amino acid in the translatedprotein.  Conclusion: Synonymous codons are not interchangable with regard to theirrole in determining the mRNA FE and the relative amounts of amino acids in thetranslated protein, even if they are indistinguishable in respect of amino acidcoding.

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases