Degeneracy of the genetic code and stability of the base pair at the second position of the anticodon

Abstract

With an analysis of the structural constraints of the anticodon-codon interaction within the decoding center of the ribosome, we show that the extent of degeneracy at the third position of the anticodon is determined by the level of stability of the base pair at the second position.

Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation

“…It has also been suggested to occur in chloroplasts (Shinozaki et al, 1986) and supported by in vitro experiments using wheat (Triticum aestivum) germ extracts and bean (Phaseolus vulgaris) chloroplast tRNAs (Pfitzinger et al, 1990). Further analysis showed that two out of three critically depends on the stability of the second base pair formed between the codon and anticodon and that this stability is influenced by the structure of the tRNA anticodon loop (Lehmann and Libchaber, 2008).…”

“…This tRNA lacks a uridine at position 34 required for superwobble but can form the strong Watson-Crick pairing at positions 35 and 36 (Figure 1) required to stabilize codon-anticodon pairing when there is a mismatch at the third position (Lehmann and Libchaber, 2008). However, tobacco cptRNA Gly (GCC) is apparently unable to decode by two out of three, despite that positions 2 and 3 of the anticodon are cytidines (Rogalski et al, 2008).…”

“…This could be because, in cp-tRNA Gly (GCC), U 32 and A 38 can form a strong Watson-Crick pairing, whereas C 32 and A 38 in cp-tRNA Arg (ACG) can only form a single weak hydrogen bond (Auffinger and Westhof, 1999). To allow two out of three, the N 32 -N 38 pair has to be non-Watson-Crick to allow the flexibility of the anticodon loop required for proper stacking of the bases (Lehmann and Libchaber, 2008).…”

Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

“…Recently, a molecular mechanism was reported explaining this pattern based on hydrogen bonding interactions (Lehmann and Libchaber 2008). When the first two nucleotides of a codon form six hydrogen bonds with the anticodon, the codon box is a family box (codons CCN, CGN, GCN, and GGN).…”

“…When the first two nucleotides of a codon are able to make five hydrogen bonds with the anticodon, the codon box is a family box only if the middle base of the codon is a pyrimidine (codons UCN, CUN, ACN, and GUN). This is caused by the stabilization of the position of the purine that forms the middle base of the anticodon by a long-range intramolecular hydrogen bond from U 33 (Lehmann and Libchaber 2008).…”