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Based on the secondary structural model of MS2 RNA, it is shown that, in base-pairing regions of the RNA, there is a bias in the use of synonymous codons which favours C and/or G over U and/or A in the third codon positions, and that in non-pairing regions, there is an opposite bias which favours U and/or A over C and/or G. This nature is interpreted as a result of selective constraint which stabilises the secondary structure of the single-stranded RNA genome of the MS2 phage.

Secondary structure of MS2 phage RNA and bias in code word usage