Uridine -, hydrolysis rate

The benzylidene acetal is cleaved by acidic hydrolysis (e.g., 0.01 N H2SO4, 100°C, 3h, 92% yield 80% AcOH, 25°C, f,/2 for uridine - 60b h, conditions that do not cleave a methylenedioxy group. The rate of acid-catalyzed hydrolysis of benzylidene acetals increases as the size of the substituent R increases. The second-order rate constant k, on going from R — Me to R — f-amyl, increases about 100-fold, indicating that steric effects play a large role in determining hydrolysis rates. ... 

These were originally prepared by Khorana as selective protective groups for the 5 -OH of nucleosides and nucleotides. They were designed to be more acid-labile than the trityl group because depurination is often a problem in the acid-catalyzed removal of the trityl group. Introduction of p-methoxy groups increases the rate of hydrolysis by about one order of magnitude for each p-methoxy substituent. For 5 -protected uridine derivatives in 80% AcOH, 20°, the time for hydrolysis was... 

It remains unclear whether or not the rate of cleavage of the gly-cosyl bond in sugar nucleotides depends upon the structure of the nucleotide residue, and the same uncertainty is true for other reactions that affect the glycosyl group no systematic kinetic studies have been reported. However, it may be noted that there appears to be no essential difference between the rates of acidic hydrolysis of the 5 -(a-D-glucopyranosyl pyrophosphates) of uridine and N3-methyluridine, 331... 

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. 

These groups were prepared to examine the relative acid lability to the classic iso-propylidene group. They are formed from the corresponding dimethyl ketals in acetonitrile with CSA as a catalyst in 95%, 88%, 70% yield, respectively. The relative rates for the hydrolysis of the uridine derivatives in TFA/H20/MeOH at 30° were examined and the results are reported in the following table. ... 

Modulated acid lability of protecting groups is extremely important in ribonu-cleoside synthesis. A comparison of the relative rates of hydrolysis of a some diarylmethylene protecting groups for the 2 3 -cu-diol system of uridine shows that aryl substitution achieves much greater add lability than the conventional isopropylidene group. Comparison of the half-times for the hydrolysis of the di-(p-anisyl)methylene (B), xanthen-9-ylidene (C) and 2,7-dimethylxanthen-9-yli-dene (D) acetals in trifluoroacetic acid/water/methanol (1 2 7 v ) at 30 revealed that the 2J-dimethylxanthen-9-ylidene system is 20 times more labile than the isopropylidene acetal. 

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. 

The alkaline hydrolysis of isopropyl, 2-ethoxyethyl, 2,2-dichloroethyl, and 2,2,2-trichloroethyl uridine 3 -thiomonophosphates (86a-d), similar to a series of aryl analogues (86e) studied previously, proceeded via a transient pentacoordinated dianionic thiophosphorane intermediate (87) to yield, via the formation and ring-opening of a 2, 3 -cyclic thiophosphate (88), a mixture of 2 - and 3 -thiophosphates, (89) and (90) (Scheme 24). For the alkyl esters (86a-d), the breakdown of the thiophosphorane intermediate (87) was rate determining, but for the aryl esters (86e), which have better leaving groups, its formation was rate determining. " ... 

Adenosine 2 - and 3 -monophosphate monomethyl and monoisopropyl esters undergo isomerization and hydrolytic cleavage to the 2, 3 -cyclic phosphate and the alcohol at comparable rates under acidic conditions, whilst at neutral pH, a pH-independent phosphate migration prevails.197 However the hydrolysis of the 2-chlorophenyl ester of uridine-3 -phosphate to 2-chlorophenol and uridine monophosphates is rapid compared with the phosphate migration under acidic conditions. 198 These studies have been extended to the interconversion and hydrolysis of 2 ,5 - and 3 ,5 -dinucleoside phosphates, where for adenosine systems, acid-catalysed depurination competed with phosphate migration and hydrolysis at pH<3.i99... 

The rate of acidic hydrolysis was found [37] to increase by approximately one order of magnitude for each /r-methoxy substituent introduced. Thus the times required for the complete hydrolysis, in 80% acetic acid at room temperature, of 5 -protected uridine derivatives were found [37] to be trityl, 48 hr. monomethoxytrityl, 2 hr dimethoxytrityl, 15 min trimethoxytrityl, 1 min. The introduction of /)-methoxy substituents also leads [37] to progressively more reactive triaryl-methyl chlorides. Khorana and his co-workers have used the mono- and di-methoxytrityl protecting groups widely in oligonucleotide synthesis [39]. 

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