Contributions to selective binding of aromatic amino acid residues to tRNA^Phe

The binding of aromatic amino acid amides to two fragments of tRNA^Phe has been measured, in order to explore contributions to selective interactions of amino acid residues with tRNA^Phe. Measurements of the Wye base fluorescence demonstrate that the isolated anticodon loop of tRNA^Phe (15 nucleotide residues) has a binding constant K = 75 M^-1 for Phe-amide, which is only slightly lower than that observed previously for the complete tRNA^Phe (K = 100 M^-1). The hexamer G_mAAYA,ψ - possessing most residues of the loop, but without loop structure - shows a further reduced binding constant of 42 M^-1. According to these data, part of the selective interaction results from the special loop structure and another part probably from the nature of the Wye base. The particular influence of the loop structure is also demonstrated by binding experiments performed in the presence of Mg²⁺. As expected, addition of Mg²⁺ decreases the binding affinity of the aromatic amino acid amides. Moreover, Mg²⁺ at concentrations ≥ 0.3 mM induces cooperative binding of the amides to the anticodon loop similar to that found previously for the complete tRNA^Phe, whereas the hexamer does not show any indication for cooperativity. A special coupling of Mg²⁺ and amide binding to the anticodon loop is also indicated by inhibition of Mg²⁺ binding in the presence of amides, which is much stronger than expected for a simple salt effect. These results demonstrate a complex coupling of Mg²⁺ and amide binding to different conformational states of the anticodon loop, which resembles an allosteric type of reaction mechanism.