[The context analysis of polynucleotide sequences. II. Inverted repeats and complementary palindromes in...

A new approach to the reconstruction of the RNA secondary structure is suggested on the basis of the method of contextual analysis of polynucleotide sequences. The coding gene regions of beta-, beta'-, sigma-subunits of E. coli RNA polymerase and of phage T7 RNA polymerase were analysed. The clusters of non-random inverted repeats were found in all these genes. The mRNA coded by them can be folded into compact secondary structures. The latter are formed by quite long helices with a few cases of mispairing.