5,6-Dihydrouridine

C9H14KN2O9P,0.5 HjO Dihydrouridine 3 -(potassium phosphate), hemihydrate (KURDMP)191... 

Nucleosides, Nucleotides, Derivatives, and Related Compounds. — 5-Substituted uracils were examined for conformational dependence on the substituents, uridine 5 -phosphate disodium salt, 2 -deoxyuridine 5 -phosphate disodium salt, " 6-methyl-2 -deoxyuridine, 5-C-acetyl-2 -deoxyuridine, dihydrouridine 3 -phosphate potassium salt, 5-hydroxymethyl-2 -deoxyuridine, 4-thio--uridine, 2,5 -anhydro-2, 3 -0-isopropylidene-2-thiouracil, 2,2 -an-hydro-1 - 3-D-arabinofuranosyl-2-thiouracil. ... 

If polyribonucleotides are treated simultaneously with methoxylamine and bisulphite, cytidine residues are converted into 5,6-dihydro-7V4-methoxycytidine-6-sulphonate,154 and uridine into 5,6-dihydrouridine-6-sulphonate.155 Treatment with dilute ammonia regenerates the uridine residues, leaving the dihydrocytidine derivatives unaffected. When only the cytidine residues have been derivatized, pancreatic ribonuclease becomes uridyl ribonuclease, since it is unable to cleave the chain on the 3 -side of the modified cytidine.154 This allows the isolation of blocks of modified cytidine residues. T2 ribonuclease may also be used. Alternatively, a ribonuclease from Physarum polycephalum has been found to hydrolyse CpX links very slowly, allowing the isolation of cytidine blocks.156 If both uridine and cytidine residues are modified, T2 ribonuclease acts as puryl ribonuclease, allowing the isolation of cumulative blocks of pyrimidines.155 This ability to alter the specificity of nuclease cleavage is a useful tool in sequence analysis. 

The following synthesis of cyclo-5,6-dihydrouridine is self-explanatory. ... 

Catalytic reduction of cytidine in water over rhodium on alumina yields the tetrahydro derivative [l-(/3-D-ribofuranosyl)-4-aminotetrahydropyrimidin-2(l//)-one] and l-( 3-D-ribofuranosyl)tetrahydropyrimidin-2(l/0-one as the major products [680]. The former hydrolyses readily to give tetrahydrouridine,which is a potent inhibitor of human liver deaminase. The latter compound is also formed by sodium borohydride reduction of 5,6-dihydrouridine. 

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). 

Pulse radiolysis experiments have shown that "OH radical adds preferentially at C5 of the uracil moiety, giving rise to the reducing 5-hydroxy-5,6-uracil-6-yl radical. Interestingly, the two cis diastereomers of 6-hydroperoxy-5-hydroxy-5,6-dihydrouridine, two of the expected final products of the latter radicals in aerated aqueous solutions, have been prepared by trifluoroacetic acid treatment of uridine (3, R = H, = ribose) in the presence of H202 (equation 14). The mechanism of the reaction that involves transient formation of an epoxide-type intermediate followed by nucleophilic attack by a perhy-droxyl group at C6 presents similarities with the substitution of thymine bromohydrin by... 

Hydrogenation of uridine 5 -(a-D-glucopyranosyl pyrophosphate) over rhodium on alumina resulted in the 5,6-dihydrouridine derivative229,324 (75). Several modifications in the heterocyclic base of adenosine 5 -(a-D-glucopyranosyl pyrophosphate) have been described. 

The effect, on substrate properties, of structural changes in the nucleoside residue, as studied with uridine 5 -(a-D-glucopyranosyl pyrophosphate) 4"-epimerases from liver339,364,394 and mung bean,364,377 is qualitatively similar to that just discussed for uridine 5 -(a-D-glu-copyranosyl pyrophosphate) dehydrogenase. The enzymes tolerate various substitutions at C-6 and C-5 (such as those resulting in derivatives of 5,6-dihydrouridine, 6-azauridine, and 5-methyluridine)... 

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... 

Cathou et al. (459) found that the Cotton effect near 270 nm in the ORD spectrum of RNase disappeared on interaction with either 2 -CMP or 3 -CMP. The X-ray studies (120) (see Fig. 23) clearly show that no tyrosine residues are in close contact with the substrate. Thus the change in rotatory behavior must reflect either (1) a shift in protein structure on association of the nucleotide or (2) the induction of a Cotton effect of the opposite sign in the bound nucleotide. In the independent spectral and chemical studies of Irie and Sawada (480), the reduced nucleotide 5,6-dihydrouridine-2 (3 )-phosphate, known to interact with the enzyme, showed no difference spectrum. With nucleotides containing... 

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... 

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