Dihydrouridine , tRNA

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

A. Primary tRNA transcript. B. Functional tRNA after posttranscriptional modification. Modified bases include D (dihydrouridine), (pseudouridine), and m. which means that the base has been methylated. 

Figure 5-51 (A) The low-field region of the one-dimensional H NMR spectrum of E. coli tRNAjVal at 27°C in H20. Resonances are identified by letters A - X. (B) NOESY spectrum of the same tRNA under similar conditions showing the imino-imino NOEs. In the lower right sector the connectivity traces of the acceptor helix and dihydrouridine helix are shown as solid and dotted lines, respectively. In the NOESY sample the two protons in peak EF are partially resolved whereas the two protons in peak T have coalesced. (C) NOESY spectrum of E. coli tRNA,Val at 32°C showing the imino and aromatic proton regions. AU-type imino protons have been connected horizontally by a dotted line to the cross-peak of their proximal C2-H or C8-H in the 7 to 9 ppm region, which has been labeled with the corresponding lower-case letter. From Hare et al.669 Courtesy of Brian Reid.

The complete tRNA contains 75 nucleotides. Sketch the rest of the molecule in the cloverleaf representation. Label the 5 and 3 ends and the dihydrouridine and T /C loops. What are the last three nucleotides at the 3 end ... 

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... 

Garey, J.R. and Wolstenholme, D.R. (1 989) PlatyheIminth mitochondrial DNA evidence for early evolutionary origin of a tRNA(ser AGN) that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons. Journal of Molecular Evolution 28, 374-387. 

Transfer RNA (tRNA) molecules mediate translation of the nucleic acid genetic code into the amino acid building blocks of proteins, thus ensuring the survivability of cells. The dynamic properties of tRNA molecules are crucial to their functions in both activity and specificity. This chapter summarizes two methods that have been recently developed or improved upon previous protocols to introduce fluorophores to site-specific positions in tRNA. One method enables incorporation of fluorophores carrying a primary amine (such as proflavin or rhodamine) to dihydrouridine (D) residues in the tRNA tertiary core, and a second method enables incorporation of pyrroloC and 2-aminopurine to positions 75 and 76, respectively, of the CCA sequence at the 3 end. These site-specific fluorophore labeling methods utilize tRNA transcripts as the... 

Xing, F., Martzen, M. R., andPhizicky, E. M. (2002). A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 8, 370-381. 

Following synthesis, nucleotides in the tRNA molecule may undergo modification to create unusual nucleotides such as 1-methylguanosine (m G), pseudouridine (4/), dihydrouridine (D), inosine (I) and 4-thiouridine (S4U). 

Figure 10.29 Diagram of tRNA from yeast, specific for alanine. I, inosine V pseudouridine mG, methylguanosine m2G, dimethylguanosine T, ribothymidine hU, dihydrouridine ml, methylinosine.

Figure 5 Structural features of the tRNA from E. coli. Elements involved in recognition by seryl-tRNA synthetase are shaded, antideterminants against recognition by EF-Tu are hatched. The modified bases are D dihydrouridine F pseudouridine i A isopentenyl-adenosine T ribothymidine. Tertiary interactions involving base pairing are indicated by lines, those with intercalations by arrows...

Figure 29.3. Alanine-tRNA Sequence. The base sequence of yeast alanyl-tRNA and the deduced cloverleaf secondary structure are shown. Modified nucleosides are abbreviated as follows methylinosine (ml), dihydrouridine (UH2),...

Figure 3-12. The cloverleaf structure of tRNA. Bases that commonly occur in a particular position are indicated by letters. Base-pairing in stem regions is indicated by lines between strands, xy = pseudouridine T = ribothymi-dine D = dihydrouridine.

Posttranscription modification of tRNA The synthesis of tRNA involves modification of some uridine nucleotides to unusual nucleotides, such as pseudouridine, ribothymidine, and dihydrouridine. 

Transfer RNA (tRNA) molecules transport amino acids to ribosomes for assembly into proteins. Comprising about 15% of cellular RNA the average length of a tRNA molecule is 75 nucleotides. Because each tRNA molecule becomes bound to a specific amino acid, cells possess at least one type of tRNA for each of the 20 amino acids commonly found in protein. The three-dimensional structure of tRNA molecules, which resembles a warped cloverleaf (Figure 17.22), results primarily from extensive intrachain base pairing. tRNA molecules contain a variety of modified bases. Examples include pseudouridine, 4-thiouridine, 1-methylguanosine, and dihydrouridine ... 

C, G, and U residues are modified in most tRNAs (see key). Dihydrouridine (D) is nearly always present in the D loop likewise, ribothymidine (T) and pseudouridine ( k) are almost always present in theT kCG loop. Yeast alanine tRNA, represented here, also contains other modified bases. The triplet at the tip of the anticodon loop base-pairs with the corresponding codon in mRNA. (b) Three-dimensional model of the generalized backbone of all tRNAs. Note the L shape of the molecule. [Part (a) see R. W. Holly et al., 1965, Science 147 1462 part (b) from J. G. Arnez and... 

---