posted 01. February 2006 16:52                    

quote:

---

...no one has discovered a persuasive chemical connection between any particular triplet of nucleotides and the amino acid that this triplet codes for.

---

posted 03. February 2006 16:20                    

quote:

---

I propose that a 3x4 structure is the minimal requirement for a system that codes for at least 20 amino acids, while still preserving the matching helical structure of DNA.

---

posted 06. February 2006 22:09                   

quote:

---

To summarize: on the basis of newly selected site structures, there presently appear to be three classes of amino acids. Arginine behaves straightforwardly; it follows the natural example of the group I active center and strongly overrepresents its codons (but not anticodons) within its binding sites. A second anticipated type includes glutamine and phenylalanine; with due allowance for the fact that these are negative results, these amino acids have no detectable relation to their coding sequences. The comment about negative results is not trivial; the glutamine codon CAG turns up in an RNA recognition domain for gln-cyanomethyl ester (61), adjacent to a metal site required for a 50 self-aminoacylation reaction. This association is a reminder that negative results can always be superceded. However, these amino acids might have been assigned their codons on another basis (such as preservation of protein structures) during the later evolutionary history of the code (27). Finally, the data suggest an unanticipated class of amino acids—isoleucine and tyrosine are bound in sites containing disproportionate numbers of both codon and anticodon sequences (though the potentially complementary triplets are not paired). The genetic code therefore seems, in part, stereochemical. It is based on primordial RNA-like amino acid binding sites whose parts seem to have been adapted to become the mRNAs and tRNAs of a later, more evolved translation apparatus. To return to the argument about RNA activities, the need for primitive RNA-based coding could be met with ordered amino acid binding sites as peptide templates (114), as well as in other ways (97).

---

posted 11. March 2006 20:27                   

quote:

---

For this discussion, we revisit the occurrence of codons and anticodons in amino acid–binding sites isolated by selection amplification (SELEX), combining all data in our possession. We now know of 43 recently selected and characterized binding sites for 8 amino acids in RNAs with 2791 total initially randomized nucleotides. Our intent here is to use these data conservatively to arrive at minimal estimates for the probability of the calculated associations (26). To estimate the probability of observed associations between coding triplets and binding sites, we considered only those sequences for which direct experimental information about the binding sites was available (chemical protection/modification/interference mapping, conservation, or NMR).We considered only independently derived structures in which the binding site occurred in backgrounds with no significant sequence identity. For example, the minimal isoleucine site has been isolated at least 63 times, and the minimal histidine site has been isolated at least 54 times. However, only a minority of individually characterized examples are used for calculations in Table 1. Inclusion of other independent isolates would increase the statistical significance of the results (diminish the probabilities) by many orders of magnitude.

To calculate probabilities, we assigned each aptamer nucleotide to one of four categories: both triplet and binding-site nucleotide, triplet and not a binding-site nucleotide, not a triplet nucleotide but a binding-site nucleotide, or neither triplet nor binding-site nucleotide, depending on whether it was in a coding triplet (either a codon or an anticodon for the cognate amino acid) and whether it was in the experimentally determined binding site. These four counts were pooled across sequences for the same amino acid, and subjected to the G test for independence (with the Williams correction), which tests whether the proportion of binding site nucleotides that participate in coding triplets exceeds the proportion of nucleotides in flanking sequences that participate in coding triplets. The G test is similar to but more accurate for small samples than the chi-squared test traditionally used in genetics. Thus, the nonbinding parts of the aptamers act as an internal control for all manipulations and for the net nucleotide composition. Counts are pooled across codons or anticodons and across all aptamers for one amino acid to increase sensitivity.

To compare results across multiple analyses (different amino acids, codons, and anticodons), we used Fisher’s method for combining independent tests of a hypothesis. We combined the tests for codons and anticodons for each amino acid and combined the tests for all amino acids to get overall estimates of the probabilities bearing on the escaped triplet hypothesis (Table 1). We emphasize a few aspects of these results. 1. Codons and cognate binding sites are not independent sequences, and the association between anticodons and newly selected aptamer binding sites is even more unlikely. 2. Not all amino acids show codons or anticodons concentrated in their binding sites, and codons and anticodons are not necessarily associated. Arginine sites improbably contain only codons; tryptophan and histidine sites contain only an excess of anticodons. 3. For both codons and anticodons, there are significant arguments for more than one single amino acid. The argument for codons could rest on arginine or isoleucine alone, whereas the argument for anticodons could be based only on isoleucine, tyrosine, or tryptophan. Thus, the evidence for triplet association with binding sites does not rely completely on any particular selection, any particular amino acid, or indeed on experimentation by any one laboratory. 4. Conversely, the argument can be made from the most significant single amino acids without reference to pooled data—arginine for codons and isoleucine for anticodons would serve well. Thus, the major conclusions can be supported using homogeneous subsets of the data and do not emerge only by combining disparate experiments. 5. There are true negatives, such as glutamine anticodons and histidine codons, indicating that this set of techniques does not unexpectedly force a positive result. 6. Only one amino acid, glutamine, shows no significant associations with either codons or anticodons. Stereochemical associations seem the rule rather than the exception. 7. The amino acid sites showing strong associations with cognate triplets are chemically varied; basic, polar, aliphatic, and aromatic side chains are detected. 8. Positive triplets do not have any obvious sequence or compositional properties, being AU-rich, GC-rich, and mixed. 9. Controls using arbitrarily derived triplets with the same compositions, such as reversed codons (25), do not concentrate in amino acid–binding sites.

In summary, current evidence, construed in a way that minimizes its signifi- cance, supports significantly elevated codon concentration in the binding sites for isoleucine, and arginine as well as elevated anticodon concentration for six of the eight amino acids, with the exceptions of glutamine and arginine. It is intriguing that the one exception to stereochemical origin is glutamine, an amino acid for which the evidence of coevolution (see above) is among the strongest. The overall probability that codons and anticodons for eight amino acids are independent of their selected cognate binding sites (counting favorable and unfavorable cases together) is exceedingly low, 5.4 x 10^-11.

Although the numerical details may change with addition of data, the overall trends to association of codons with a few kinds of amino acids and anticodons with the sites for many or most amino acids appear secure by normal standards (Table 1). Because these sequences were selected requiring only affinity for free amino acids, there seems no simple or otherwise plausible alternative to the idea that progenitor structures that bound amino acids gave rise to the coding triplets of the present genetic code.

---