On the Structure of Yeast tRNA^Phe

Abstract

The availability of (yeast)tRNAPhe for helix formation with complementary oligoribonucleotides has been explored by equilibrium dialysis studies. Oligoribonucleotides complementary to sequences which are double-stranded, according to the cloverleaf model of tRNAPhe, did not bind. Two regions of tRNAPhe were fully acessible to oligonucleotide binding: (a) the 3'-terminus; (b) the sequence (3'-5')U-G-A-A-Y (33-37) of the anticodon loop. Two other regions were accessible to oligonucleotide binding: (a) part of the extra arm; (b) the (3'-5')T-Y-C sequence of the ribosylthymine loop. However, the binding constants of trimers and tetramers complementary to these parts of tRNAPhe are very low.The data indicate that the anticodon loop of tRNAPhe has an asymmetric structwe, which is not compatible with the Fuller-Hodgson model. The low binding constants for oligonucleotides complementary to the extra arm or to the TpVpC sequence are discussed. They seem to be due either to sterical hindrance or to different conformations of tRNA. I n the latter case, one conformation would be accessible to complementary oligonucleotides for helix formation, the other would not. Present available oligonucleotide binding data of four tRNAs suggest that each tRNA has an individual pairing scheme, according to which the loops of the cloverleaf contribute to the three-dimensional structure.Although many properties of tRNA have been clarified, the three-dimensional structure of tRNA is far from known. The results of a variety of physicochemical measurements have led to ample evidence that tRNA has a structure of higher order than a loose combination of helical segments as is proposed by the general cloverleaf model [I-31. Several models of the tertiary structure of tRNA have recently been proposed in order to obtain a correlation between molecular structure and biological function of this molecule. However, none of them is apparently consistent with all the available data, which are pertinent for the actual three-dimensional structure of tRNA (for review, see [I]). This lack in understanding the structure of tRNA is mainly due DefiniGon. Azao unit; the quantity of material contained in 1 ml of a solution which has an absorbance of 1 a t 260 nm when measured in a 1-cm path-length cell.to the fact that it is not known what segments or parts of the loops of the cloverleaf are involved in the organization of the higher ordered structure of tRNA.Recently, it has been shown that it is possible to explore, in partially double-stranded RNA molecules, single-stranded regions by complementary oligonucleotide binding [4 -81. Oligonucleotides of three units interact with available complementary regions of RNA to such a degree that the association constant can be readily measured by equilibrium dialysis. We applied this methodology to see what regions of (yeast) tRNAPhe are open, unshielded and unpaired and are thus available for oligonucleotide binding. It is apparent that this method can only be used to detect sequences, which are not shorter than three ...

Complementary trimer binding to transfer‐RNAVal1

“…Oligo-. nucleotide binding studies to E. coli tRNAMet,E, coli tRNA Tyr [3], and yeast tRNA Phe [8]. have shown, that these tRNA's have an asymmetric anticodon loop structure.…”

“…T~OC Pu represents the sequence which is common to all tRNA's so far sequenced. Since in the four tRNA's examined by oligonucleotide binding studies [2,3,8], T~OC is available to complementary GAA binding, it might indicate a common environment as well as function of this particular tRNA sequence.…”

Effective binding of oligonucleotides to the anticodon of a tRNA without stimulation of tRNA binding to 30 S ribosomes

“…The increased complex formation with U-U-C-A cannot be explained by a higher population of the stacked conformer in the tetranucleotide as compared to the trinucleotide, because U-U-C-C shows a lower association constant as compared to U-U-C-A [2].…”

“…It has been shown that complementary tetranucleotides only bind effectively to the C-C-A end and the anticodon region of the tRNA [1,2]. Extensive studies have been performed using either oligonucleotides and cognate tRNAs or tRNA pairs with complementary anticodons to elucidate the structural details for codon-anticodon recognition [3][4][5]7].…”

Interaction of actinomycin D with yeast ribosomal RNA

“…Equilibrium dialyses were performed in plexiglass cells, as in [7]. The solvent for all experiments was 0.2 M NaCl + 0.04 M MgClz + 1 mM sodium phosphate (pH 7.4).…”