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.

Binding Sites↗

PubMed1970

Synthetic spectroscopic models related to coenzymes and base pairs. VII. Stacking interactions in tRNA; the "bend" at dimethylguanosine.

We have examined the stacking interactions of N(2)-dimethyl-guanosine with the nucleosides, e.g., adenosine and cytidine, found adjacent to it in certain tRNA's, by the use of model compounds in which the trimethylene bridge was substituted for the ribose-phosphate-ribose linkage. From the hypochromism exhibited by synthetic 9-[3-(aden-9-yl)propyl]-2-dimethylaminopurine-6-one (IV) and by 9-[3-(cytos-1-yl)propyl]2-dimethylaminopurin-6-one in aqueous solution (VI) it is appearent that the interaction is at least as great between the N(2)-dimethylguanine moiety and adenine or cytosine as between guanine and these two bases. The fluorescence and phosphorescence emission spectra were obtained in ethylene glycol-water glass at 80 degrees K. The exciplex fluorescence observed for both bi-molecules (IV and VI) containing the N(2)-dimethylguanine unit provides further evidence for stacked chromophores.

Adenine↗

PubMed1970

[Current trends of phosphotherapy].

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Adolescent↗