Spectroscopic properties of oligonucleotides excised from the anticodon region of phenylalanine tRNA from yeast

✍ Scribed by Alfred Maelicke; Friedrich Von Der Haar; Friedrich Cramer

• Publisher: Wiley (John Wiley & Sons)
• Year: 1973
• Tongue: English
• Weight: 882 KB
• Volume: 12
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.1973.360120104

✦ Synopsis

Abstract

Ultraviolet absorption and static fluorescence properties of hexanucleotide (Gm‐A‐A‐Y‐A‐ψ__p__) and a dodecanucleotide (A‐Cm‐U‐Gm‐A‐A‐Y‐A‐ψ‐m^5^C‐U‐Gp) excised from the anticodon region of phenylalanine tRNA from yeast have been studied with respect to temperature, pH, ionic strength, and Mg^2+^ concentration. At low temperature these oligomers have a largely stacked structure. Only the melting data of the dodecanucleotide in absence of Mg^2+^ fit a two‐state model. From the different melting behavior of the oligonucleotides after excision of base Y, a rodlike structure of the hexanucleotide produced by stacking interactions can be concluded. The Y fluorescence increase produced by Mg^2+^ has been used to evaluate the binding equilibria between Mg^2+^ and the oligonucleotides. One strong binding site per oligonucleotide and a greater number of weak binding sites have been found. The fluorescence of the free base Y is not influenced by Mg^2+^. The dodecanucleotide enhances the ethidium fluorescence to the same extent as tRNA^Phe^ and produces comparable shifts in the excitation and emission spectra. Therefore a double helical structure for this oligomer under the assay conditions is suggested. Only weak binding of ethidium to the hexanucleotide is observed, indicating that intercalation of the dye into its structure is not favored. The data show the decisive role of the nucleobase Y in maintaining a rigid stacked structure of the anticodon nucleotides. This structure is stabilized by high ionic strength, Mg^2+^, and ethidium.