Phosphoramidates, nucleotide synthesis

The first application of this reaction for the synthesis of sugar nucleotides was reported in 1958, when Moffatt and Khorana269 prepared uridine 5 -(a-D-glucopyranosyl pyrophosphate) (5) in 59% yield from uridine 5 -phosphoramidate (58). Other examples of similar... 

The synthesis of a nucleotide-like phosphoramidite building block in which the nucleic base has been replaced by a tert-butyldimethylsilyl-protected styrene glycol (47) has been described. After its incorporation in an oligonucleotide by automated synthesis, the terminal alcohol has been oxidized with NaI04 after fluoride deprotection. A similar phosphoramidate in which the nucleic base has been replaced by an alkyl diol (48) has been incorporated in an oligonucleotide and further conjugated with biotin after oxidation to the aldehydic functional-ity. ... 

Nucleoside S -phosphoramidates have proved to be useful intermediates in the synthesis of nucleoside 5 -pyrophosphates and nucleotide coenzymes. Nucleoside phosphoramidates may also be prepared by treatment of a nucleoside 5 -phosphate with ammonia in the presence of N, IV -dioyclohexylcarbodiimide [R. W. Chambers and J. G. Moffatt, J. Am. Chem. Soc., 80, 3752 (1958)]. 

The chemical synthesis of uridine 5-(a-D-glucopyranosyl pyrophosphate) has been effected by condensing a-n-glucopyranosyl phosphate with uridine 5-phosphate in the presence of dicyclohexylcarbodiimide. The yield of glycosyl nucleotide in this reaction is very low, primarily because dicyclohexylcarbodiimide promotes the formation of n-glucose cyclic 1,2-phosphate in preference to the formation of the pyrophosphate bond. In an improved synthetic method, the nucleotide is first converted to a phosphoramidate (5) or phosphoromorpholidate (6), by condensation in the presence of dicyclohexylcarbodiimide with ammonia or morpholine, respectively. 

There have been two reports of the synthesis of di- and oligonucleotides with P-NH-5 -phosphoramidate intemucleotide links 134.135 in one approach 135 a Staudinger-type reaction is used to form the link (Scheme 15). Another paper has reported the synthesis of building blocks for 5 -amino- and 5 -mercapto-ollgodeoxy nucleotides. 136... 

Herdewijn and co-workers have been for some time investigating alternative nucleotide building blocks suitable for synthesis of oligonucleotides based on nucleoside phosphoramidates. Here they have shown that the iminodipropionic acid derivative (5) is a good substrate for HIV-1 RT resulting in -fl primer extension of 91% at 50 pM concentration. Similar results were found for the pyrophosphate mimic (6) with HIV-1 RT. They have also shown that the L-Ala phosphoramidate derivatives are also substrates for HIV-1 RT and for various DNA polymerases. ... 

The first syntheses of chiral [ 0, 0]phosphodiesters were performed independently and reported simultaneously in 1980 by Stec and co-workers (Baraniak et al., 1980) and by this laboratory (Gerlt and Coderre, 1980). The efforts of both laboratories were directed toward the synthesis of oxygen chiral 3, 5 -cyclic nucleotides Stec prepared the Sp diastereomer of cyclic [ 0, 0]AMP, and we reported both diastereomers of cyclic [i6o,i 0]dAMP. Both laboratories utilized the Wittig-Staudinger reaction to introduce the heavy oxygen isotope into the precursor iV-phenyl phosphoramidates of the cyclic nucleotides. In this chemistry, a primary phos-phoramidate is reacted with a strong base, such as NaH, to remove the... 

This chapter reviewed selected papers published in 2012 on the chemical synthesis and biological, particularly medicinal, applications of nucleotides and oligonucleotides. The term nucleotide is the central point of the chapter. As a nucleotide has a nucleoside in its make-up and plays its functional roles as part of oligonucleotides, some relevant aspects of nucleosides and oligonucleotides are also included in this chapter. For its intended functions, a nucleotide can be presented in several forms, such as phosphoramidite, phosphoramidate, phosphonate and triphosphate, their relationships can be summarized in the Scheme below. 

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