6-Deoxynucleosides synthesis

In the diester method a deoxynucleoside-5 -monophosphate is condensed with the 3 -OH group of a deoxynucleotide to produce a 3, 5 -phosphodiester. This is illustrated by a general method for dinucleotide synthesis developed by H.G. Khorana (K.L. Agarwal, 1976). One N-... 

All DNA polymerases are single-minded—they can do it only one way. Each dNTP (deoxynucleoside triphosphate) is added to the 3 -OH group of the growing chain so that all chains grow from the 5 end in the dirction 5 to 3. Since strands are antiparallel, the template strand is read in the 3 to 5 direction. This is true of both DNA and RNA synthesis. Most of what you need to know about DNA replication can be summarized in a single picture. 

DNA-directed DNA polymerases [EC 2.7.7.7], also called DNA nucleotidyltransferases (DNA-directed), are enzymes that catalyze the DNA template-directed extension of the 3 -end of a nucleic acid strand one nucleotide at a time. Thus, n deoxynucleoside triphosphates produce n pyrophosphate (or, diphosphate) ions and DNA . This enzyme cannot initiate the synthesis of a polymeric chain de novo it requires a primer which may be DNA or RNA. RNA-directed DNA polymerases [EC 2.7.7.49], also referred to as reverse transcriptases, DNA nucleotidyltransferases (RNA-directed), and revertases, are enzymes that catalyze the RNA template-directed extension of the 3 -end of a nucleic acid strand one nucleotide at a time. Thus, n deoxynucleoside triphosphates produce n pyrophosphate (or, diphosphate) ions and DNA . As was the case above, this enzyme cannot initiate the synthesis of a polymeric chain de novo it requires a primer which may be DNA or RNA. 

Regulation of ribonucleotide reductase by both positive feedback from ATP and negative feedback by various 2 -deoxynucleoside triphosphates (eg, dATP) is tightly coupled to the need for DNA synthesis. 

The synthesis of some dinucleoside phosphates has been achieved1680 by the reaction of 5 -chloro-5 -deoxynucleosides with nucleotide anions. In that work, the 5 -chloro-5 -deoxynucleosides were conveniently obtained by treatment of the corresponding 2, 3 -0-isopropylidene-nucleoside with thionyl chloride. 

Other useful targets for pharmaceutical agents are thymidylate synthase and dihydrofolate reductase, enzymes that provide the only cellular pathway for thymine synthesis (Fig. 22-49). One inhibitor that acts on thymidylate synthase, fluorouracil, is an important chemotherapeutic agent. Fluorouracil itself is not the enzyme inhibitor. In the cell, salvage pathways convert it to the deoxynucleoside monophosphate FdUMP, which binds to and inactivates the enzyme. Inhibition by FdUMP (Fig. 22-50) is a classic example of mechanism-based enzyme inactivation. Another prominent chemotherapeutic agent, methotrexate, is an inhibitor of dihydrofolate reductase. This folate analog acts as a competitive inhibitor the enzyme binds methotrexate with about 100 times higher affinity than dihydrofolate. Aminopterin is a related compound that acts similarly. 

Because coupling is not always quantitative, the non-reacted terminal deoxynucleoside must be excluded from the following synthesis cycles. Otherwise deletion sequences will render the isolation of the pure final product difficult. Therefore a capping step (step 3) follows, e.g., acetylation with acetic anhydride and N,N-dimethyl-4-pyridinamine (DMAP) in dioxane. Capping times should be as short as possible, especially with 2-cyanoethyl phosphite tri-esters, which are sensitive to bases such as DMAP. 

As a direct result of these anhydronucleoside studies, methods have been developed126,262 for the chemical synthesis of 2-deoxynucleosides of pyrimidines. It was noted126 that the 2-O-tosyluridine derivative LXXXVI, when caused to react with sodium iodide in hot 2,5-hexanedione (acetonylace-tone), is converted into a 5-0-acetyl-2-deoxy-2-iodo nucleoside which, upon reduction under alkaline conditions, yields 2-deoxyuridine (V, R = H). In analogous fashion, the 5-O-acetyl derivative of l-/S-D-ribofuranosyl-thymine68 is converted by sodium iodide to CVI which, after deacetylation followed by reduction in the presence of palladium catalyst, yields thymidine (V, R = CH,).126... 

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