Wobble base pair

There are not 64 different tRNAs, one for each codon, but instead the tRNAs are capable of unconventional base pairing ( wobble ) with the codons during translation of the mRNA. 

FIGURE 1.7 Base pairing schemes of Watson-Crick and non-Watson-Crick types. Among the non-Watson-Crick base pairs, wobble pairs are formed by H-bonds between tautomeric forms of hydroxyl (OH) and imino (NH) groups. Non-Watson-Crick base pairs also comprise Hoogsteen base pairs and reverse Watson-Crick base pairs which form the basal structural units in triplex DNA and In parallel-stranded DNA (psDNA), respectively. 

Bases do not always pair according to the Watson—Crick base pairing rule. There are a variety of alternative H-bonded base pairing arrangements called non-Watson—Crick or wobble base pairs. Wobble base pairs occur at a high... 

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

Watson-Crick wobble base pair mismatch mismatch mismatch... 

Figure 3 Cognate and near-cognate codon-anticodon interactions. The anticodon ioop of tRNA is shown as an example interacting with various codons on the mRNA. In correct, cognate codon-anticodon pairings, two Watson-Crick base pairs can be formed in the first two positions while the third position contains either a Watson-Crick or a wobble base pair.

I I I I I Watson-Crick pairs G-U wobble base pair /WWW exon... 

Murphy, F. V., 4th Ramakrishnan, V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat. Struct. Mol. Biol. 2004,11, 1251-1252. 

Wobble Base pairing rules used for position... 

Figure 12-1. Codon-anticodon base pairing. Special wobble base-pairing rules apply to the third (3 ) position of the codon. The first (S ) position of the tRNA anticodon is frequently inosine (I) to provide this flexibility in hydrogen bonding.

Note X and Y denote bases complementary to and capable of strong Watson-Crick base pairing with X andY respectively, Wobble bases—in the 3 position of codons and 5 position of anticodons—are shaded in pink. 

Wobble Nontraditional base-pairing between the 5-nucleotide (first nucleotide) of the anticodon with the 3 -nucleotide (last nucleotide) of the codon. I = inosine. 

The "wobble" hypothesis states that the first (5 ) base of the anticodon is not as spatially defined as the other two bases. Movement of that first base allows nontraditional base-pairing with the last (31) base of the codon, thus allowing a single tRNA to recognize more than one codon for a specific amino acid. 

Crick or wobble (GU) base pairing in the stems. This requires certain relationships in the sequences of the DNA in the genes that encode these molecules as discussed in Section E,3. Because of the base-pairing requirements, some of the bases in the stems protrude as bulges and fail to form pairs. Often, it is possible to find more than one reasonable structure, each having some bases unpaired.328... 

While tRNAs consist largely of loops and stems containing Watson-Crick base pairs, they also contain Hoogsteen pairs, wobble pairs, and triplets such as the following. 

The 3 terminal redundancy of the genetic code and its mechanistic basis were first appreciated by Francis Crick in 1966. He proposed that codons and anticodons interact in an antiparallel manner on the ribosome in such a way as to require strict Watson-Crick pairing (that is, A-U and G-C) in the first two positions of the codon but to allow other pairings in its 3 terminal position. Nonstandard base pairing between the 3 terminal position of the codon and the 5 terminal position of the anticodon alters the geometry between the paired bases Crick s proposal, labeled the wobble hypothesis, is now viewed as correctly describing the codon-anticodon interactions that underlie the translation of the genetic code. 

Examples of standard (a) and wobble (b and c) base pairs formed between the first base in the anticodon and the third base in the codon. 

Wobble. A proposed explanation for base-pairing that is not of the Watson-Crick type and that often occurs between the 3 base in the codon and the 5 base in the anticodon. 

Figure 13.1 (A) Structure of 2-aminopurine and its base pairing partners. For reference, a G U wobble pair is shown. (B) Jablonski diagrams...

Most amino acids in proteins are specified by more than one codon (i.e. the genetic code is degenerate). Codons that specify the same amino acid (synonyms) often differ only in the third base, the wobble position, where base-pairing with the anticodon may be less stringent than for the first two positions of the codon. 

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