Abstract
Codon recognition occurs during protein synthesis with the aminoacyl-tRNA bound in the recognition (or R) tRNA-binding site. The recognition site is thought to be located on the external surface of the smaller ribosomal subunit distal from the interface between subunits, where the aminoacyl (A) and peptidyl (P) tRNA-binding sites are located. A molecular model describing the switching of the aminoacyl-tRNA from the R site to the A site is proposed. Details of the model include codon recognition at the R site by an aminoacyl-tRNA with its anticodon loop in the 5' stacked conformation; movement of the aminoacyl-tRNA from the R site to the A site by a switching in the anticodon loop from the 5' stacked conformation to the 3' stacked conformation; and recognition of the correct reading frame by a base-pairing interaction between the A and P site tRNAs that involves trans pairing of the invariant bases U-33 of both molecules.
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