Yeast tRNAphe

Satisfactory fits of the fluorescence decays for ethidium bound to yeast tRNAPhe and E. coli tRNA al require (at least) two exponentials in the sum response S(t) [cf. Eq. (4.56)] under all conditions studied.0 870 88) The normalized amplitudes and lifetimes for tRNA 1 (extrapolated to zero concentration) are S° = 0.917, r, = 25.6ns and S02 = 0.082, t2 = 5.6 ns.(187) The results for tRNAPhe are similar.(188) This requirement for two (or more) exponentials is unequivocal evidence for at least two ethidium binding sites. The dominant component has a lifetime similar to, but slightly longer than, that of ethidium intercalated in DNA and is taken to represent ethidium... 

Removal of endogeneous Mg2+ by rigorous treatment (heating to 80 °C in the presence of 10 mM EDTA) introduces a fundamental difference between yeast tRNAPhe and E. coli tRNA]781, although their xR values remain... 

FIGURE 27-13 Three-dimensional structure of yeast tRNAphe deduced from x-ray diffraction analysis. The shape resembles a twisted L. (a) Schematic diagram with the various arms identified in Figure... 

The results of these efforts show that no method of tRNA recognition is universal.2443 In some cases, e.g., for methionine- or valine-specific tRNAs, the synthetase does not aminoacylate a modified tRNA if the anticodon structure is incorrect. Although the anticodon is 7.5 ran away from the CCA end of the tRNA, the synthetases are large enzymes. Many of them are able to accommodate this large distance between a recognition site and the active site (Fig. 29-9A). For some other tRNAs the anticodon is not involved in recognition 245 For yeast tRNAphe residues in the stem of the dihydrouridine loop and at the upper end of the amino acid acceptor stem seem to be critical.241... 

FIGURE 28.11 Phenylalanine tRNA from yeast, (a) A schematic drawing showing the sequence of bases. Transfer RNAs usually contain a number of modified bases ( gray circles). One of these is a modified guanosine (G ) in the anticodon. Hydrogen bonds, where present, are shown as dashed lines, (b) The structure of yeast tRNAphe as determined by X-ray crystallography. 

Schleich, H. G., Wintermeyer, W., and Zachau, H. G. (1978). Replacement ofwybutine by hydrazines and its effect on the active conformation of yeast tRNAPhe. Nucleic Acids Res. 5, 1701-1713. 

Figure 11.1 Atomic resolution structure of yeast tRNAPhe (PDB accession code 1TRA), rendered as black sticks and reconstructed density (red transparent surface). The reconstructed density was generated from the filtered consensus bead model by smoothing with a Gaussian kernel. Figure adapted from Lipfert ct al. (2007b).

Yeast tRNAphe Romer and Hach (1975) Mixed Na+/Mg2+ AG, fMg2+... 

Furthermore, the high efficiency of Mg2+ is more pronounced for more compact/complex structures. For example, for a simple 24-bp DNA duplex, 0.4 mMMg2+ is equivalent to 20 mMNa+ in ionic neutralization, that is, 0.4 mM Mg2+ and 20 mMNa+ can cause the same neutralization for the phosphate charges. In contrast, the 76-nt yeast tRNAphe, a more complex structure, 0.4 mMMg2+ is equivalent to 32 mM, a much higher Na+ concentration (Bai et ah, 2007 Romer and Hach, 1975). 

Finally, NMR data can be used in combination with data of other methods to determine solution structures of nucleic acids. For example, the homology model of E. coli tRNAVal based on the X-ray structure of yeast tRNAphe was refined based on experimental RDC data and small angle X-ray scattering (SAXS) data.296... 

R.S., Jack, A., Further refinement of the structure of yeast tRNAphe./. Mol. Biol. 124, p. 523- Copyright 1978, with permission... 

Brown, R. S., B. E. Hingerty, J. C. Dewan, et al. 1983. Pb(ll)-Catalysed Cleavage of the Sugar-Phosphate Backbone of Yeast tRNAPhe—Implications for Lead Toxicity and Self Splicing RNA. Nature 303 543-546. 

Two of the partially resolved >P signals of yeast tRNA at 40.5 MHz were observed by Hayashi et al. (1977) to have quite different T, values. Assuming a single isotropic motion model, it was concluded from T, and NOE measurements that both the CSA and dipolar mechanisms contribute to relaxation at 40.5 MHz, with the dipolar contribution being the greatest. Applying the isotropic motion model to the experimental T, and NOE vdues, it was estimated that the P correlation time was 3 ns in yeast tRNAPhe. 

Figure 29-7 (A) Generalized cloverleaf diagram of all tRNA sequences except for initiator tRNAs numbered as in yeast tRNAae (Fig. 5-30). Invariant bases A, C, G, T, U, and semivariant bases Y (pyrimidine base), R (purine base), H (hypermodified purine base). The dotted regions (a, P, variable loop) contain different numbers of nucleotides in various tRNA sequences. See Rich.179 (B) L form of the yeast phenyl-alanine-specific tRNAphe. The structure is the same as that in Fig. 5-31 but has recently been redetermined at a resolution of 0.20 nm.175 The new data revealed the presence of ten bound Mg2+ ions (green circles) as well as bound spermine (green).

Of interest are imidazo[l,2-u] purine substances from the so called wye-family, isolated from phenylalanine-transfer-ribonucleic acid (tRNAphe) of various sorts of yeast 4,9-dihydro-4,6-dimethyl-l//-imidazo[l,2-a]purine-9-one ( wye , 162a) 4,9-dihydro-4,6-dimethyl-3-/I-D-ribofuranosyl-3/7-imidazo[l,2-(2]purine-9-one ( wyo-sine fluorescent Y-nucleoside from Candida albicans tRNAphe, 162b) methyl... 

A more precise and detailed X-ray study of tRNAphe from yeast has now been performed by Robertus et al. (23) Although the overall shape of the molecule resembles that advanced by Kim et al. (22), many details are significantly different [Fig. 8.10(b)]. Thus, the -T- -C-G loop seems to be paired with the bases 18 and 19, the two Guo of the dihydro Urd loop. The acceptor stem and the -T- -C-G helix form a continuous helix, while the D-helix is perpendicular to... 

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