Luminescence and binding studies on tRNA-Phe.

The phenylalanine transfer RNA of baker's yeast (tRNA(Phe)) contains a base Y of unknown molecular structure next to the anticodon triplet. Since the base Y fluoresces at room temperature (lambda(max) = 431 nm), its emission properties offer a unique tool for studying conformational and binding properties of tRNA(Phe). The results obtained by these experiments include the following: (1) The quantum yield of fluorescence of Y in tRNA(Phe) (phiF) is 0.07 +/- 0.01 at high Mg(2+) concentrations (>10(-2)M) and about half that at 10(-3)M or less, indicating a [Mg(2+)]-dependent conformational change of the anticodon loop. (2) The fluorescence of Y isolated from tRNAPhe (Y(+)) is red-shifted by 15 nm compared to Y in tRNA(Phe) which suggests a stacked (more hydrophobic) environment for Y in the intact anticodon loop. phiF of Y(+) is 0.035. (3) The solvent isotope effect phiF(D(2)O)/phiF(H(2)O) is 1.5 for tRNA(Phe) and 1.9 for Y(+) i.e., Y in tRNA is still hydrated. (4) The temperature dependence of phiF in a polar glass shows that quenching occurs only at temperatures at which the glass has sufficiently low viscosity to permit solvent shell relaxation in the excited state. The low-temperature (80 degrees K) fluorescence is blue shifted (lambda(max) = 409 nm) and the phosphorescence has a decay time of 1.5 seconds, a threshold at 392 nm and a spectral shape like that of guanine. (5) In the presence of 10(-2)M Mg(2+) penta-uridylate, which contains the codon triplet, a small blue shift and a decrease in phiF are observed. This shift can be used to establish the formation of a binary complex between the codon and the anticodon with an association constant of 4 x 10(2)M(-1), approximately. A similar complex is formed with poly-uridylate but not with poly-cytidylate. In the absence of Mg(2+) the binary complex is not formed.