Wobbling of What

A simple explanation for the symmetry of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. The facts revealed in this study offer a new insight into physical mechanisms of the functioning of the genetic code. The wobble hypothesis, which was first proposed more than 40 years ago [1], can explain two events: 1) formation of the uracil­guanine pair as a result of codon­anticodon interaction in the third position and 2) encoding of isoleucine by three codons (for the universal genetic code). This hypothesis is based on two statements: in the third position of the codon nucleotides can “wobble”, and inosine can form pairs with uracil, cytosine, and adenine. Neither of these statements is necessary for explaining the abovementioned events, and the wobble hypothesis is just wrong. Once we admit this, we can get a better insight into the structure and functioning of the genetic code. What makes the uracil­guanine pair possible? Uracil can exist either in the enol form or in the keto form. Uracil in the enol form can make two and even three hydrogen bonds with guanine, while uracil in the keto form would be able to make only one hydrogen bond. One can say that the enol form of uracil is stabilized by its interaction with the complementary guanine. The keto­enol tautomerism is a well­studied process and chemists will understand me without any further proofs. The molecular basis of the wobble hypothesis has been criticized by other researchers [2], but I’d like to add a few comments. Watson first considered nucleotide formulae in the enol form as the more probable, guided by reference books of that time [3]. Fortunately, I can give convincing arguments using commonly available information. Codon­anticodon interaction results in the formation of a short segment of the double helix. In the case of GC­rich codons, opposite to uracil in the third position of the codon there is inosine in the anticodone. Crick’s wobble hypothesis [1] allows a solution for this pair only by wobbling the third nucleotides of the codon and the anticodon. However, in the double helix, their position is also stabilized by stacking. If stacking exerts significant influence so that wobbling becomes impossible, then no uracil­ inosine complementarity is possible for the keto form of uracil, i.e. there cannot be any hydrogen bonds. If in this case uracil is in enol form, in the state that most closely imitates cytosine, two hydrogen bonds can be established, without a nucleotide shift. If C­I are Watson­Crick’s pairs and U­I pairs are formed in accordance with the wobble hypothesis, it is not clear why these codons are always indistinguishable, although they have different conformations, which can be stabilized. Crick’s hypothesis would be valid if cytosine and uracil were opposed by the same anticodon but as a component of different tRNAs, which would stabilize different conformations of the anticodon. This, however, is not so – the same tRNA always “confuses” cytosine with uracil in the third position of the codon. With the keto­enol tautomerism, both codons have the same conformation. Why is uracil opposed by inosine in some anticodons and by guanine in others? According to Crick’s hypothesis, inosine and guanine are indistinguishable to uracil. If we suppose the presence of the enol form of uracil, we can suggest that inosine emerged in anticodons in an evolutionary way because in this case the guanine amino group could not form a hydrogen bond. That is, in this case inosine (guanine without an amino group) is sufficient. Weakening and possible disruption of the hydrogen bond that has been formed involving the amino group must cause more than just binding of vacant hydrogen bonds to water molecules. Binding of two water molecules will transform the amino group from an active helper into an active obstacle. I should add that the enol form of uracil can be registered in NMR spectra, which makes the necessary experiments easy to perform. Incorporation of thymine into DNA may be accounted for as follows. Methylation could favor further stabilization of uracil in the keto form. Oxygen is an electron acceptor while the methyl group an electron donor, so the presence of the methyl group reduces the probability of the proton being near oxygen [4]. Let us now discuss the second part of Crick’s hypothesis: why is isoleucine encoded by three codons? A more general question is: why are methionine and tryptophan encoded without degeneracy, by one codon each? To answer this question, we have to refer to another study published in 1966 – Yu.B. Rumer’s study of the symmetry of the genetic code table. Let us consider the table of the genetic code letter doublets as it was proposed by Yu.B. Rumer [5, 6] (Table 1). The author focused his attention on the presence of the letter doublets (i.e. the first two nucleotides of the triplet, called “roots” by Yu.B. Rumer) and their ability or inability to encode just one amino acid. Of 16 letter doublets, 8 were strong (encoding just one amino acid) and 8 were weak (encoding more than one amino acid). Please note that this symmetry is characteristic of almost all dialects of the genetic code. The only exception has been comprehensively studied [7] and is accounted for by a mutation in aminoacyl­tRNA­synthetase, i.e. it is not related to the anticodon recognizing the codon.