Analysis of action of wobble nucleoside modifications on codon-anticodon pairing within the ribosome

Wobble rules for modified residues in the first anticodon position are derived. All known modifications are considered individually. Stereochemical analysis was made taking into account the interaction between the ribosomal A and P-site bound codon-anticodon duplexes. The wobble base-pair was considered as the right one if its formation did not lead to an uncompensated loss of hydrogen bonds or polar atom-ion bonds. From this requirement it follows that all modifications of U should restrict its translational specificity to purines (with the exception of xo5U, which should decode A, G and U). The restriction is carried out in a unified way: modifications inhibit the large propeller twist resulting from an increase of about 35 degrees in the torsion angle of the anticodon wobble base, interacting with the third codon base via a hydrogen-bonded water molecule. Such a twist is required to avoid a loss of the hydrogen bond of the bonded water molecule. The modifications in S2U, Se2U and Um should weaken their pairing with G, because they deform one of the two hydrogen bonds of the guanine NH2 group. G should be recognized by Se2U better than by S2U for the reason that the hydrogen bond Se...HN is weaker than the hydrogen bond S...HN. Among the modifications of C and G only that in k2C has a pronounced effect on wobble. The nucleoside k2C should pair only with A. The N-2 atom of k2C should be in the pyramidal state. The consequences following from the interduplex interaction are formulated. According to one of them, adenosine in the wobble position of the P-site tRNA should destabilize the A-site duplex. This can serve as an explanation for the fact that adenosine is very rarely observed in the anticodon wobble position.