Mononucleotides synthetic

The synthetic scheme typically involves chain-extending addition of protected mononucleotides to a nucleoside bound covalentiy at the 3 -hydroxyl to an inert siUca-based soHd support, such as controlled pore glass (Fig. 11). The initial base-protected 5 -O-dimethoxytrityl (DMT) deoxynucleoside is linked to the soHd support via the reaction of a siUca-bound amino-silane and the -nitrophenylester of the 3 -succinylated nucleoside, yielding a 3 -terminal nucleoside attached to the soHd support (1) (Fig. 11). Chain elongation requites the removal of the 5 -DMT protecting group. 

The major intermediates in the biosynthesis of nucleic acid components are the mononucleotides uridine monophosphate (UMP) in the pyrimidine series and inosine monophosphate (IMP, base hypoxanthine) in the purines. The synthetic pathways for pyrimidines and purines are fundamentally different. For the pyrimidines, the pyrimidine ring is first constructed and then linked to ribose 5 -phosphate to form a nucleotide. By contrast, synthesis of the purines starts directly from ribose 5 -phosphate. The ring is then built up step by step on this carrier molecule. 

Figure 4.3 The synthesis of an oligonucleotide from an activated mononucleotide, (a) Adenonine triphosphate (ATP), the substrate of enzymatic nucleic-acid synthesis. (b) An imidazolide of a nucleotide of the kind used in many non-enzymatic template-directed reactions, (c) The synthetic reaction leading to the formation of a trinucleotide. (Modified from Orgel, 2002.)...

These early contributions were later supplemented by a comprehensive article on the mononucleotides by Ueda and Fox.4 The present article is an extension of these articles to chemical synthesis of oligo-and poly-nucleotides, and it is hoped that, in conjunction with the earlier articles, it will provide the organic chemist with a reasonable appreciation of some of the challenges, both past and present, of the synthetic chemistry of the nucleic acids. 

The Wlds mutation is dominant and has been mapped to the distal end of chromosome 4 (Lyon et al., 1993), where there is an 85-kb tandem triplication that results in the production of an abnormal fusion protein (Conforti et al., 2000). This fusion protein contains the intact enzyme nicotinamide mononucleotide adenylyl transferase (NMNAT), which functions in the synthetic pathway for nicotinamide adenine dinucleotide (NAD+), as well as the ubiquitination factor E4b (UbE4b). 

A large number of stable conformations of both natural and synthetic DNA have been observed. They may be characterized in terms of gross structural parameters such as N, the number of molecular asymmetric units in K turns of the helix h, the axial rise per residue and r, the axial rotation per residue. Both right- and left-handed helices have been observed [13, 43]. In typical cases the molecular asymmetric unit is a mononucleotide but dinucleotide asymmetric units have been found in molecules in which the chemical repeat consists of two nucleotides [11]. The nucleotide conformations can be related to the different helical parameters both in terms of the backbone and conformational angles and features such as the sugar pucker and the base-pair displacement and orientation with respect to the helix axis. 

The A, B and C forms have been observed from fibers of both natural and synthetic DNAs. The A-form [5] is a right-handed helix with eleven nucleotides in one turn of the helix (h = 2.56 A, r = 32.7°) (Fig. 1). The asymmetric unit is a mononucleotide. In common with all the conformations described here, the molecule contains a family of diad rotation axes perpendicular to the helix axis which relates one chain of the double helix backbone to the other. Therefore, the two backbones run in opposite directions with respect to the helix axis. 

Although most polynucleotides are naturally occurring prodncts (for which the term nncleic acid is best reserved), many synthetic polynucleotides, generally of lower molecular weight, have now been prepared and smdied. Very short chains, obtained either synthetically or by breakdown of natnral polynucleotides, which contain just a few mononucleotide units, are often called ohgonncleotides. 

Because it is very polar, cAMP hardly penetrates the cell membrane. Synthetic derivatives of cAMP with organic acid substituents are more lipophilic, and therefore display greater permeation. Most commonly used of these is A/, 0 -dibutyryladenosine 3, 5 -monophosphate (DBcAMP). A number of other 3, 5 -mononucleotides with special functions (e.g. 3, 5 -GMP) occur naturally. 

Both flavin adenine dinucleotide (FAD) and flavin adenine mononucleotide (FMN)-containing DIs are found, some specific for NAD, whereas others for NADP. They have been used for staining dehydrogenase-rich tissues and in attempted appKcations for the regeneration of the cofactor such as in bioelectroanalytical devices and flow systems (see following text) and in bioorganic synthetic reactions. 

Synthetic polynucleotide complexes have been shown to be effective immune response modulators in animals and man (Braun et al. 1971, Johnson 1979). The polynucleotides are formed foUowing the action of an enzyme, polynucleotide phosphor-ylase on the synthetic mononucleotide diphosphates. Complexing takes place following the mixing of polymers composed of opposite base pairs. Two have been utilised, polyinosinic acid complexed with polycytidylic acid (poly I poly C) and polyad-enylic acid complexed with polyuridylic acid (poly A poly U). The single strands mononucleotides are ineffective. 

Ribonucleic Acid. A major contribution to the formulation of RNA structure was the demonstration that alkaline hydrolysis of RNA quantitatively liberates about equal amounts of mononucleotide isomers of all four bases 103). Although it was readily established that none of these mononucleotides is the 5 -phosphate isomer, it was not until some years later that Cohn and associates 103) by controlled degradation experiments, and Brown and associates 121) by the synthetic route, established that the products were isomers involving phosphate attachment at positions 2 and 3 of the ribose. Of equal significance was the discovery 161) that hydrolysis of RNA by the enzyme phosphodiesterase (snake venom or intestinal) liberates mononucleotides exclusively of still another type, the 5 -mono-nucleotides. It was thus necessary to establish the mechanisms which could account for one phosphodiester structure in the RNA chain giving rise to three isomers of each mononucleotide. 

Other synthetic pathways, of course, are possible, and it has been speculated that perhaps nicotinamide reacts with ribose-1, 5-diphosphate to give nicotinamide mononucleotide and inorganic orthophosphate. The formation of nicotinamide mononucleotide has been observed in intact red cells incubated with nicotinamide and glucose. ... 

X-Ray difiiaction studies of natural (Fuller etal., 965) and synthetic (Leslie et al., 1980) DNA fibers have shown that depending on its base sequence, water content, and counterion, DNA can adopt at least four diflfeient conformations A, B, C, and D forms. Since the early 1970s it has become evident through CD spectroscopy (Pohl and Jovin, 1972 Ivanov et al., 1973) that DNA secondary structure also varies in solution. However, owing to the limited resolution of X-ray fiber diflBraction, the DNA models thus derived were sequence-averaged and each had a uniform backbone conformation with a mononucleotide repeat unit (Fig. 3). Circular dichroism also has the drawback that detailed structures of DNA in solution cannot be... 

Modified nucleoside monophosphates. The number of naturally occurring nucleotides is relatively few. However, synthetic chemistry is now capable of offering an unlimited number of modified nucleoside monophosphates for biological studies or medicinal exploitations. Based upon their chemical moieties (base, sugar and phosphate), it is natural for this paper to discuss all of the three corresponding modifications. In this section the focus will be on base-modified and sugar-modified mononucleotides. Phosphate-modified mononucleotides will be dealt with in Sections 2 and 3. 

Since the bases encode genetic information, any base modification would have significant biological consequences and offer great synthetic opportunities for novel mononucleotides with useful chemical or physical properties. For instance, base-modified nucleotides are reported as potent medicinal or diagnostic agents. 

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