Yeast tRNALeuUAG. Purification, Properties and Determination of the Nucleotide Sequence by Radioactive Derivative Methods

Abstract

A second major species of leucine tRNA, tRNA^Leu_UAG (formerly designated tRNA^Leu_CUA) was purified from baker's yeast in a three‐step procedure entailing BD‐cellulose chromatography in the presence and absence of Mg²⁺ and Sephadex G‐100 gel filtration. Results of aminoacylation and partial RNase T₁ digestion experiments showed that this tRNA retains a native conformation under conditions that denature yeast tRNA^Leu_m5CAA (tRNA^Leu₃). The primary structure of baker's yeast tRNA^Leu_UAG was elucidated by application of sensitive radioactive isotope derivative (‘postlabeling’) methods. Complete RNase T₁ and A and partial RNase U₂ fragments, prepared from non‐radioactive tRNA and 5′‐half and 3′‐half molecules, were separated by two‐dimensional polyethyleneimine‐cellulose anion‐exchange thin‐layer chromatography and isolated by a novel micropreparative procedure affording high yields of these compounds in sufficient purity for subsequent tritium derivative analysis. Base composition and sequence of oligonucleotides were analyzed by tritium derivative methods. Molar ratios of the fragments were determined from the radioactivity of ³H‐labeled nucleoside trialcohols in combination with base analysis. 2′‐O‐Methylated guanosine was characterized using the [γ‐³²P]ATP/polynucleotide kinase reaction. The analysis of classical complete and partial RNase digests by the tritium derivative methods yielded the complete nucleotide sequence of the RNA. A total of about 20 A₂₆₀ units of the RNA was used for analysis, i.e. considerably less material than required for conventional spectrophotometric analysis. A different sequencing approach, consisting of a combination of ‘readout sequencing’ with tritium sequencing of complete RNase T₁ and A fragments, was applied to the 3′‐half molecule. The 3′‐half molecule was labeled with ³²P at its 5′ terminus, partially degraded with RNases T₁, U₂, and Phy₁ and with alkali, and subjected to polyacrylamide gel electrophoresis. The sequence was read off the gel on the basis of cleavage patterns and size of the fragments. While the readout procedure provided only the positions of A, U, C, and G residues in the chain, additional information from tritium derivative analysis was utilized to define the positions of the modified nucleosides. The readout sequencing procedure was found to require less than 0.01 A₂₆₀ unit of RNA and the analysis of the complete fragments about 6 A₂₆₀ units. Interesting structural features of tRNA^Leu_UAG are (a) the location of unique, leucine tRNA isoacceptor‐specific sequences next to U‐8, a constant nucleotide participating in synthetase recognition, (b) the occurrence of 1‐methyladenosine in the T loop, a modification not present in the structurally related tRNA^Leu_m5CAA, and (c) the unusual presence of an unmodified uridine in the first position of the anticodon, which may be related to the unusual coding properties reported for this tRNA.