Pseudouridines

Ribosomal RNAs characteristically contain a number of specially modified nucleotides, including pseudouridine residues, ribothymidylic acid, and methylated bases (Figure 11.26). The central role of ribosomes in the biosynthesis of proteins is treated in detail in Chapter 33. Here we briefly note the significant point that genetic information in the nucleotide sequence of an mRNA is translated into the amino acid sequence of a polypeptide chain by ribosomes. 

Eurther quantum chemical studies involving uracil derivatives concern the conformations and properties of uridines [98CEJ621,98JA5488,98JOC1033, OOJCS (P2)677], the nucleophilic attack in pseudouridine synthases [99JA9928], and the aza analogs of uracil [99JST349]. 

Posttranslational modification of preformed polynucleotides can generate additional bases such as pseudouridine, in which D-ribose is linked to C-5 of uracil by a carbon-to-carbon bond rather than by a P-N-glycosidic bond. The nucleotide pseudouridylic acid T arises by rearrangement of UMP of a preformed tRNA. Similarly, methylation by S-adenosylmethionine of a UMP of preformed tRNA forms TMP (thymidine monophosphate), which contains ribose rather than de-oxyribose. 

Nucleic acids contain, in addition to A, G, C, T, and U, traces of 5-methylcytosine, 5-hydroxymethylcyto-sine, pseudouridine ( P), or N-methylated bases. 

Since no human enzyme catalyzes hydrolysis or phos-phorolysis of pseudouridine, this unusual nucleoside is excreted unchanged in the urine of normal subjects. 

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

Isoxazole (as well as isoxazoline, and isoxazolidine) analogues of C-nucleosides related to pseudouridines 25 and 27 have been regioselectively synthesized by 1,3-dipolar cycloaddition (1,3-DC) of nitrile oxides (and nitrones) derived from uracyl-5-carbaldehyde 24 and 2,4-dimethoxypyrimidine-5-carbaldehyde 26 respectively <06T1494>. 

This Section is concerned with the synthesis of C-nucleosides having the Type A arrangement of atoms attached to the glycosylic carbon atom, and covers the synthesis of pseudouridine (1), show-... 

A substantial improvement was reported by D. M. Brown and coworkers,156 who used the more readily hydrolyzable tert-butyl pyrimidine derivative (222) in a condensation reaction with the aldehydo-D-ribose derivative 223. Acid hydrolysis of the epimeric mixture (224) gave pseudouridine and its a anomer in 18 and 8%... 

In the course of their studies of pseudouridine,164 Asbun and S. B. Binkley183 reported the synthesis of 5-/3-D-arabinofuranosyl- and 5-/3-D-xylofuranosyl-uracil (258 and 259) by the acid-catalyzed ring-closure of the corresponding alditol derivatives. The configuration at the anomeric carbon atom was determined on the basis of optical rotatory dispersion studies. 

David and Lubineau191 reported the synthesis of pseudocytidine [5-/3-D-ribofuranosylcytosine (270)] and its a anomer by a procedure analogous to that used in preparing pseudouridine.155-157 Thus, 2,4 3,5-di-O-benzylidene-a/de/iydo-D-ribose (223) was condensed with the dilithio derivative of 2-0,4-N-(trimethylsilyl)cytosine, and the resulting, epimeric, acyclic derivatives were subjected to acid-catalyzed cyclization. The anomeric configuration of the free C-nucleosides was ascertained by spectroscopic methods and by their transformation into a- and /3-pseudouridine in the presence of nitrous acid. The anomeric 5-(/3-D-ribofuranosyl)isocytosines have also been prepared by Fox and coworkers.1913... 

The reaction of 1,3-dipolar cycloaddition of enantiopure cyclic nitrones to protected allyl alcohol, is the basis of stereoselective syntheses of bicyclic N, O-iso-homonucleoside analogs (747), of isoxazolidine, to analogs of C-nucleosides related to pseudouridine (748) and to homocarbocyclic-2 -oxo-3 -azanucleosides (749) (Fig. 2.36). 

PUA Putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase E(MFP)AB 5(5) 3(3) ... 

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). 

The tRNAs undergo post-transcriptional modification to produce specialized bases, such as pseudouridine, dehydrouridine, and methylcytosine. 

Alternatively, lactone 392 was condensed with 2-furaldehyde, and the aldol adduct was dehydrated to give 394. Treatment of 394 with methanolic sodium methoxide afforded the methyl ester 395, which, after (trialkylsilyl)ation, was transformed by ozonolysis into the unstable keto ester 396. Compound 396 was converted into showdomycin, as well as into some 6-azapseudouridines.261 A number of a,a -dibro-moketones react262 with furan, to give substituted analogs of the bicy-elic ketone 390. Appropriately substituted substrates have been converted,263 by way of Baeyer-Villiger oxidation and treatment of the resulting lactone with tcrt-butoxybis(dimethylamino)methane, into pseudouridines 397 modified at C-5. 

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