Nucleosides lability

For nonvolatile or thermally labile samples, a solution of the substance to be examined is applied to the emitter electrode by means of a microsyringe outside the ion source. After evaporation of the solvent, the emitter is put into the ion source and the ionizing voltage is applied. By this means, thermally labile substances, such as peptides, sugars, nucleosides, and so on, can be examined easily and provide excellent molecular mass information. Although still FI, this last ionization is referred to specifically as field desorption (FD). A comparison of FI and FD spectra of D-glucose is shown in Figure 5.6. 

The FAB source operates near room temperature, and ions of the substance of interest are lifted out from the matrix by a momentum-transfer process that deposits little excess of vibrational and rotational energy in the resulting quasi-molecular ion. Thus, a further advantage of FAB/LSIMS over many other methods of ionization lies in its gentle or mild treatment of thermally labile substances such as peptides, proteins, nucleosides, sugars, and so on, which can be ionized without degrading their. structures. 

Both FI and FD provide good molecular mass information, but few if any fragment ions, and allow thermally labile substances such as peptides, nucleosides, and glycerides to be examined, as well as inorganic salts. 

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... 

DNA is not susceptible to alkaline hydrolysis. On the other hand, RNA is alkali labile and is readily hydrolyzed by dilute sodium hydroxide. Cleavage is random in RNA, and the ultimate products are a mixture of nucleoside 2 - and 3 -monophosphates. These products provide a clue to the reaction mechanism (Figure 11.29). Abstraction of the 2 -OH hydrogen by hydroxyl anion leaves a 2 -0 that carries out a nucleophilic attack on the phosphorus atom of the phosphate moiety, resulting in cleavage of the 5 -phosphodiester bond and formation of a cyclic 2, 3 -phosphate. This cyclic 2, 3 -phosphodiester is unstable and decomposes randomly to either a 2 - or 3 -phosphate ester. DNA has no 2 -OH therefore DNA is alkali stable. 

Bemdl S, Herzig N, Kele P et al (2009) Comparison of a nucleosidic vs non-nucleosidic postsynthetic click modification of DNA with base-labile fluorescent probes. Bioconjug... 

Cytidine is the most labile of the four nucleosides (see Sect. 6.2). It deaminates spontaneously to uridine (t1/ = 340 years at pH 7 and 298 K). This was possibly the reason that cytidine was not present in the original genetic material on the primeval Earth. 

The isomerism existing between the pairs of nucleotides was attributed to the different locations of the phosphoryl residues in the carbohydrate part of the parent nucleoside,49 63 since, for instance, the isomeric adenylic acids are both hydrolyzed by acids to adenine, and by alkalis or kidney phosphatase to adenosine. Neither is identical with adenosine 5-phosphate since they are not deaminated by adenylic-acid deaminase,68 60 and are both more labile to acids than is muscle adenylic acid. An alternative explanation of the isomerism was put forward by Doherty.61 He was able, by a process of transglycosidation, to convert adenylic acids a" and 6 to benzyl D-riboside phosphates which were then hydrogenated to optically inactive ribitol phosphates. He concluded from this that both isomers are 3-phosphates and that the isomerism is due to different configurations at the anomeric position. This evidence is, however, open to the same criticism detailed above in connection with the work of Levene and coworkers. Further work has amply justified the original conclusion regarding the nature of the isomerism, since it has been found that, in all four cases, a and 6 isomers give rise to the same nucleoside on enzymic hydrolysis.62 62 63 It was therefore evident that the isomeric nucleotides are 2- and 3-phosphates, since they are demonstrably different from the known 5-phosphates. The decision as to which of the pair is the 2- and which the 3-phosphate proved to be a difficult one. The problem is complicated by the fact that the a and b" nucleotides are readily interconvertible.64,64... 

The position was somewhat clarified by the isolation of 2- and 3-O-phos-phonucleosides from ribonucleic acid hydrolyzates in 92 to 100% yields,134 and also by the demonstration that 5-O-phosphonucleosides are also present in enzymic digests.49, 197 Yet this information gave no indication of the nature of the alkali-labile linkages. Thus, while the majority of the experimental evidence pointed to the phosphoryl residues as being doubly esterified with adjacent nucleosides, two facts remained apparently inexplicable on the basis of this type of structure. First, ready fission by alkalis, and secondly, the absence of 5-phosphates from alkaline hydrolyzates and their presence in enzymic digests. Both these facts have been explained by Brown and Todd in the following way.92... 

The vast majority of research focused on selenium in biology (primarily in the fields of molecular biology, cell biology, and biochemistry) over the past 20 years has centered on identification and characterization of specific selenoproteins, or proteins that contain selenium in the form of selenocysteine. In addition, studies to determine the unique machinery necessary for incorporation of a nonstandard amino acid (L-selenocysteine) during translation also have been central to our understanding of how cells can utilize this metalloid. This process has been studied in bacterial models (primarily Escherichia colt) and more recently in mammals in vitro cell culture and animal models). In this work, we will review the biosynthesis of selenoproteins in bacterial systems, and only briefly review what is currently known about parallel pathways in mammals, since a comprehensive review in this area has been recently published. Moreover, we summarize the global picture of the nonspecific and specific use of selenium from a broader perspective, one that includes lesser known pathways for selenium utilization into modified nucleosides in tRNA and a labile selenium cofactor. We also review recent research on newly identified mammalian selenoproteins and discuss their role in mammalian cell biology. 

Despite the fact that secondary hydroxyl groups of nucleosides also react with 23 (see later), selective iodination of only the primary hydroxyl group in some unprotected, pyrimidine nucleosides can also be achieved.82 Thus, brief treatment of thymidine with 1.1 mol-equivalents of 23 in N,N-dimethylformamide gave crystalline 5 -deoxy-5 -iodothymidine in 63% yield. It was even possible to effect some selective iodination of the 5 -hydroxyl group of 2,2 -anhydrouri-dine without excessive cleavage of the (quite labile) anhydro linkage. 

Dilute perchloric acid or trichloroacetic acid, or ethanol, is usually employed for extraction of the glycosyl esters of nucleoside pyrophosphates from biological materials.19 The high lability of these compounds in acidic media (see Section IV, p. 356) leads to unavoidable losses during extraction with acids. Extraction with ethanol can lead to difficulties, as ethanol may not completely inactivate pyrophosphatases present in the tissue the action of these enzymes may result in partial degradation of the nucleoside pyrophosphate derivatives. Such a situation has been encountered particularly with plant tissues.20... 

Preparative, paper-chromatography is frequently used for further fractionation of the resulting mixtures. The high lability of glycosyl esters of nucleoside pyrophosphates seriously limits the choice of solvent systems. Systems used most commonly are neutral or slighdy acidic mixtures of ethanol with ammonium acetate,24,25 or weakly acidic solvents based on 2-methylpropionic acid.26 A solvent system containing morpholinium borate has also been found extremely useful.27... 

The high lability of glycosyl esters of nucleoside pyrophosphates strongly limits the possibilities for their chemical modification. However, some conversions may be accomplished on a preparative scale. 

The most commonly used thiation reagents (see [166] for a discussion about thiation reagents) and particularly P4Sl0 and its surrogates are not suitable for acid-labile compounds. Some mild methods have been devised, for instance the conversion of nucleosides to thionucleosides [167], an example of which is given here. The nucleoside (protected on the sugar... 

The scarcity of studies of glycofuranosides in the literature may be attributed to several factors their lability to acid (excepting pyrimidine nucleosides), their formation in complex mixtures with unwanted byproducts, their low melting points, and sometimes, their reluctance to crystallize. In the present Chapter, Tables XII-XIV list most of the knqwn crystalline glycofuranosides, together with some that are presumably pure but have not yet been crystallized. 

With the same protocol, a heterocyclic dibenzoate 86 derived from furan in one step has been efficiently desymmetrized to provide facile entry to either D or L nucleosides (see Scheme 8E.10). As depicted in Scheme 8E.10, the catalyst derived from ligand 71 gave rise to high enantioselectivities in the alkylation with both a purine 83 and a pyrimidine 87 [62], Subsequent allylic alkylations with an achiral ligand introduced the tartronate and aminomalonate moieties to furnish enantiomerically pure Ci s-2,5-disubstituted-2,5-dihydrofurans 89 and 91, respectively. Only six steps from furan were required to synthesize the alio and talo isomers of the nucleoside skeleton of the polyoxin-nikkomycin complexes. It should be noted that the corresponding enzymatic desymmetrization of substrate 86 is impossible because the product is labile. 

For the removal of this protecting group, tetrabutylammonium fluoride in oxolane is the most frequently used [388, 389, 409-411]. A much simpler reagent to prepare, potassium fluoride — crown ether, has been introduced for the same purpose [427]. Silyl group at 0-2 of nucleosides is cleaved more rapidly [411] than at 0-5. Acyl migrations occurred under the tetrabutylammonium fluoride-catalyzed desilyla-tion [432, 434, 443], Differencies between the primary and secondary position were also observed for acid- or base-catalyzed solvolysis [391, 409-412], 5 -0-(7ert-butyl-dimethylsilyl)nucleosides are much more labile towards acid than either 2 - or 3 -silyl ethers [391, 410-412], whereas the situation is reversed for base hydrolysis [411], /V-Bromosuccinimide in aqueous DMSO is another alternative for the removal of this type of silyl group [444]. 

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