Amino Acid Coding

It is known that tRNAs can form dimers through the pairing of complementary anticodons. The thermal stability of the dimers is high, equivalent to the formation of about seven base-pairs in the common RNA helices (Grosjean et al., 1986; Grosjean and Houssier 1990). It is indicated that the type of mini-helix formed either has a peculiar stability by itself or receives additional support, either from special base modifications or from other bases in the anticodon loop, besides the anticodon triplets. Thermal stability of dimers of present day tRNAs is also not much influenced by the G + C contents of the triplets, but there are indications that early coding might have been influenced by this character (Ferreira and

Cavalcanti, 1997), its main feature being that all boxes at the core of the matrix are simple. Our model requires a perfect palindromic topology in the triplet pairs and obeys only partially the thermodynamic stability principle: in each of the sectors, the initial boxes are at the core and the last ones to be filled with attributions are at the tips.

The tRNA dimers are considered proto-ribosomes and proto-mRNAs. In ribos-omes, the two tRNAs are front to back in the A and P sites, guided by the codons in the mRNA (Fig. 1). In the dimers, the anticodon loops are associated head to head through a mini-helix and the anticodons are simultaneously codons for each other, making unnecessary the presence of an external template, and the tRNA acceptor ends hang to different sides. In both cases the two tRNAs are held together in a stable structure so that the acceptor ends are placed in contact and the trans-ferase reaction facilitated. This reaction is driven towards peptide synthesis due to the peptide bond being covalent and the dimer association dynamic, dependent only on hydrogen bonds. Polymerization of peptides works as a sink, providing a suction force to the system. This force works as long as there are dimers of ac-tRNAs. Dimers of an ac-tRNA and a non-acylated tRNA may be inhibitory when the concentration of the latter is higher. When only one synthetase is available, acylating one tRNA type, the system may be de-repressed when a second synthetase arises with specificity for the other tRNA in the pair. In this way, dimerization is also a driving force for the fixation of catalysts that can acylate the second member of a pair. In this double-catalyst situation, there are difficulties in deciding which came first since the concentrations of the members of the pair will fluctuate and tend to get equilibrated; any decision on which came first relies upon external factors. A limited complementary behavior of the amino acids being recruited into the code is seen, when the amino acids follow the hydropathies of the tRNAs in the pairs.

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