Nucleobases, 2 -deoxyribonucleoside

Scheme 9.1 Multi-step enzymatic process for the production of 2 -deoxyribonucleoside from glucose, acetaldehyde and a nucleobase through the reverse reactions of2 -deoxy-ribonucleoside degradation.

Biochemical Retrosynthesis of 2 -Deoxyribonucleosides from Glucose Acetaldehyde and a Nucleobase Three-Step Multi-Enzyme-Catalyzed Synthesis... 

Scheme 9.4 Biochemical retrosynthesis of 2 -deoxyribo-nucleosides from glucose, acetaldehyde and a nucleobase (adenine) through the glycolytic pathway and the reverse reactions of 2 -deoxyribonucleoside degradation.

One-Pot Multi-Step Enzymatic Synthesis of 2 -Deoxyribonucleoside from Glucose, Acetaldehyde and a Nucleobase... 

The one-pot multi-step enzymatic process described above seemed still impractical on an industrial scale due to the low amount of 2 -deoxyribonucleoside accumula-hon and the low molar yield to added nucleobase (yield to adenine was 33.3%). In addition, it required three kinds of catalyst cells (baker s yeast, deoxyriboaldolase-or phosphopentomutase-expressing E. coli and commercial nucleoside phosphory-lase). It is difficult and complicated to operate the multi-catalysts. If the molar yield of 2 -deoxyribonucleoside to the most expensive material, nucleobase, was improved and the number of catalysts could be reduced, a practical enzymahc process could be developed. 

Figure 9.1 2 -Deoxyribonucleoside production from glucose, acetaldehyde and a nucleobase in a one-pot (substrate-feeding) reaction.

Hanson, A. A., Rogan, E. G., and Cavalieri, E. L. (1998). Synthesis of adducts formed by iodine oxidation of aromatic hydrocarbons in the presence of deoxyribonucleosides and nucleobases. Chem Res Toxicol 11, 1201-1208. 

Among the variety of methods that have been developed to quantify nucleobase deamination products, including simple HPLC quantification [134], 32P-postlabe-ling of 2 -deoxyribonucleosides released from DNA [135] and uptake and labeling of DNA with [3H]uridine [136] or [3H]2 -deoxyuridine [137], all lack the specificity and sensitivity required to detect background levels of dU in DNA. This problem has been overcome with the development of methods involving gas or liquid... 

IMPROVEMENT OF THE ONE-POT MULTISTEP ENZYMATIC PROCESS FOR PRACTICAL PRODUCTION OF 2 -DEOXYRIBONUCLEOSIDE FROM GLUCOSE, ACETALDEHYDE, AND A NUCLEOBASE... 

Instead of altering nucleobases, several methods to address the sugar phosphate backbone of nucleic acids have been published. One approach, reported by Nagahara et al., is to incorporate a fully protected 2 -deoxyribonucleoside H-phosphonate into the oligonucleotide by means of an automated solid-phase... 

Suau T, Alvaro G, Benaiges MD et al. (2006) Influence of secondary reactions on the synthetic efficiency of DHAP-aldolases. Biotechnol Bioeng 93 48-55 Takayama S, McGarvey GJ, Won CH (1997) Microbial aldolases and transketolases new biocatalytic approaches to simple and complex sugars. Ann Rev Microbiol 51 285-310 Tischer W, Ihlenfeldt HG, Barzu O et al. (2001) Enzymatic synthesis of deoxyribonucleosides from deoxyribose 1-phosphate and nucleobase. Int. Patent WO014566. 

High yields of separable anomeric mixtures of regiospecifically N-9 purine and N-1 pyrimidine 2 -deoxyribonucleosides can be obtained by interaction of l-C)-acetyl-3,5-di-C>-benzoyl-D-ribofuranose with a silylated nucleobase under phase-transfer conditions using dibenzo-18-crown-6 and potassium iodide in acetonitrile-toluene.An asymmetric route to nucleosides from non-carbohydrate precursors is outlined in Scheme 4.53 i OH OH... 

Seela F, Xu K, Chittepu P, Ming X (2007) Fluorinated 7-deazapurine 2 -deoxyribonucleosides modification at the nucleobase and the sugar moiety. Nucleosides Nucleotides Nucleic Acids 26 607-610... 

A reversed-phase chromatography technique for the preparative separation of polar compounds has been demonstrated with the separation of a simple nucleoside mixture. A group separation of the 2 -deoxyribonucleoside, nucleotide and nucleobase constituents of normal and modified nucleic acids was achieved by gel permeation chromatography, and further separation was achieved on a hydrophilic acrylate polymer operating in the partition mode. Mononucleotides are selectively bound at low pH to Fe(ni) immobilized on agarose gel due to their free phosphate ester group, and can be recovered with a neutral eluant. Nucleosides and molecules with phosphate diester groups are not retained. ... 

In this chapter, the preparation of monochlorophosphoramidite and phosphorodiamidite derivatives and their application toward a general synthesis of deoxyribonucleoside phosphoramidites will be delineated from representative literature procedures. The synthetic protocols provided herein should allow the preparation of a myriad of deoxyribonucleoside phosphoramidite monomers having any modification of the following entities nucleobases, nucleobase-protecting... 

To facilitate the design of deoxyribonucleoside phosphoramidite analogs, information regarding the activation of deoxyribonucleoside phosphoramidites will be provided to emphasize the importance imparted by the steric bulk of the substituents attached to the phosphorus center and to specific nucleobases on the coupling rates. The capping and oxidation steps of the synthetic cycle will also be discussed in relation to the potential formation of side products during oligonucleotide synthesis. 

The steric bulk of substituents at the exocyclic amino function of the guanine nucleobase has been shown to affect significantly the coupling rates and efficiency of the deoxyribonucleoside phosphor-amidites 18 and 19 (Fig. 7) - Specifically, the activation of 18... 

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