<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Our studies on the bases of codons from 11 completely sequenced archaeal genomes
show that, as we move from GC-rich to AT-rich protein-coding gene-containing
species, the differences between G and C and between A and T, the purine load (AG
content), and also the overall persistence (i.e. the tendency of a base to be followed
by the same base) within codons, all increase almost simultaneously, although the
extent of increase is different over the three positions within codons. These findings
suggest that the deviations from the second parity rule (through the increasing
differences between complementary base contents) and the increasing purine load
hinder the chance of formation of the intra-strand Watson–Crick base-paired
secondary structures in mRNAs (synonymous with the protein-coding genes we dealt
with), thereby increasing the translational efficiency. We hypothesize that the ATrich
protein-coding gene-containing archaeal species might have better translational
efficiency than their GC-rich counterparts.</p>
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Comp Funct Genomics. 2003 Feb; 4(1):56-65