The Palindromic Triplets and Pairs

The type of pairs found meaningful for initiating the coding process is configured as perfect palindromes, containing the same bases in the extremities, which we shall call the fishing triplets (see Guimaraes et al., 2007). Among all types of triplet pairs, the palindromic configuration is the one guaranteeing full and long-lasting single-strandedness which is a requisite for their ability to produce stable dimers through the formation of the mini-helices. Considering the restriction of accepting only the perfect standard base pairs, it is indicated that the palindromic coding was developed before the exclusion of A from the 5' position of the triplets. The exclusion of 5' A became necessary in the complex boxes due to its wide wobbling possibilities that would produce ambiguity in their decoding. In our scheme, the mechanism of 5' A exclusion may have been initiated as early as in the stage of incorporation of the two acidic amino acids, sharing the UC box. The remaining 5' G solved the ambiguity problem and was enough for decoding. The later extension of the 5' A exclusion to all boxes may have been due to its benefit to the regulatory mechanisms, when some perfect palindromes (ANA:UNU) yielded to imperfect ones (GNA:UNU), with the consequent acceptance of G:U pairings.

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