Pseudo-uridine

A good source of uncommon bases is tRNA. It provides substrates for studying the effect of base on the rate of hydrolysis. Baev et al. (62) showed that V2-dimethylguanylyl-(3 -5 )-cytidine-3 phosphate (G2m-pCp) was hydrolyzed much slower than the usual GpCp. Venkstern (63) reported that Tp was hydrolyzed very slowly. Naylor et al. (64) found that Cp was hydrolyzed with half the rate of CpU. The same group of workers introduced (64, 65) a chemical block on uridine and pseudo-uridine residues by reacting RNA with l-cyclohexyl-3-(2-morpho-liny]-(4)-ethyl)-carbodiimide metho-p-toluene sulfonate. The modification of the uridine residues completely blocked the action of venom exonuclease and also blocked the action of pancreatic RNase. 

Most tRNAs are 7495 nucleotides in length, and differ by the number of nucleotides in the variable loop. The TyC loop is named for the presence of an invariant pseudo-uridine base modification (y) and the D loop contains several dihydrouridine residues. 

The reaction of 1,1.3,3-tetrabromopropanone with furan derivatives has been used to prepare C-methyl analogues (46) and (47) of pseudo-uridine (Scheme 11), and the related C-hydroxymethyl analogues (48) were similarly prepared. ... 

Figure 29-2. Sequence and projection of the conformation of the phenyl alanine specific f-RNAP " of yeast. D, Dihydrouridine DiMeG, 2,2-dimethylguanosine 2 OMeC, 2 methyl cytidine ij/, pseudo-uridine (base bonded to the sugar group via C ).

Deoxy- and 5 -deoxy-5 -halo-derivatives of pseudo-uridine(5- 5-D-ribo-furanosyluracil) have been prepared by conventional methods, with the 5 -fluoro-derivative being prepared from 2, 3 -0-isopropylidene-pseudo-uracil by reaction with 7V,A -diethyl-iV-(2-ehloro-l,l,2-trifluoroethyl)amine as a less conventional fluorinating reagent. Other papers report on the five possible A -monomethyl formycins and the tautomeric equilibrium between the 7- and 8-protonated forms of formycin (25). Further references to antibiotic C-nucleosides are made in Chapter 18. 

A stereocontrolled general synthesis of C-nucleosides from non-carbohydrate materials has been described, illustrated in Scheme 9 for pseudo-uridine derivatives (69) (R = H, Me, CsHn, or Ph R = H) a branched-chain sugar derivative (69) (R = R = Me) was analogously prepared. 2-Thio-pseudouridine and pseudoisocytidine were also obtained from the intermediate (70) (R = R = H) using thiourea and guanidine respectively in place of urea, and this intermediate was also converted to the maleimido C-nucleoside, showdomycin. ... 

Initial studies carried out in our laboratories served to confirm that the Eu(III) texaphyrin 8b is in fact capable of catalyzing the hydrolysis of phosphate diesters. For instance, using the ammonium salt of uridylyl-3, 5 -uridine (UpU) as a substrate, it was found that this particular texaphyrin is able to effect catalytic hydrolysis (as judged by a controlled HPLC product analysis) with a pseudo-zero order rate of (9.1 1.6) x lO mMh By comparison, under identical conditions, Eu(N03)3, was found to effect UpU hydrolysis with a pseudo-zero order rate of (2.7 0.2) X lO mMhwhile Morrow s Eu(III) hexaamine Schiff base complex ("EuHAM"),27e one of the better alternative systems known, induced hydrolysis with a corresponding rate of (4.1 0.4) x lO mMh- Additionally, these same studies served to confirm that the Eu(III) texaphyrin complex 8b is far more stable in solution than the corresponding HAM-derived product. Thus, from both a kinetic efficacy and intrinsic stability perspective, the Eu(III) texaphyrins appear to be the best metal-based systems for use in antisense applications. 

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