Deoxyribose, equilibrium forms

Deoxy sugars, as we saw in Section 25.7, have an oxygen atom "missing." That is, an —OH group is replaced by an -H. The most common deoxy sugar is 2-deoxyribose, a monosaccharide found in DNA (deoxyribonucleic acid). Note that 2-deoxyribose exists in water solution as a complex equilibrium mixture of both furanose and pyranose forms. 

The enzyme DERA, 2-deoxyribose-5-phosphate aldolase (EC 4.1.2.4), is unique among the aldolases in that the donor is an aldehyde. In vivo it catalyzes the reversible aldol reaction of acetaldehyde and D-glyceraldehyde 3-phosphate, forming 2-deoxyribose 5-phosphate, with an equilibrium lying in the synthetic direction (Scheme 5.41). DERA, the only well-characterized member of this type I aldolase, has been isolated from both animal tissue and microorganisms.67... 

The deoxyribose residues that are generated at sites of base loss in DNA exist in equilibrium between the closed furanose form and the open aldehyde form (13) (Fig. 3). The 3 phospho-diester bonds associated with the latter are labile and are readily hydrolyzed by -elimination during which the pentose carbon tothe aldehyde is activated at alkaline pH and at increased temperatures (13). The same reaction proceeds at a reduced rate at neutral pH. At physiologic pH and temperature, a site of base loss in DNA has an estimated average lifetime of 400h (14). 

The aspect of a reversible reaction of fluorinase was of major importance for further optimizations and by addition of the enzyme L-amino acid oxidase (L-AAO) the oxidative removal of formed L-methionine was enabled. In this way, the equilibrium of the reaction was pulled toward 5 -[ F]FDA and allowed very high radiochemical yields of 95% within 1-2 h. Accordingly, the F-labeled compounds 5 -[ F]fluoro-5 -deoxyinosine (5 -[ F]FDI) (O Fig. 42.30h), 5 -[ F]fluoro-5 -deoxyribose phosphate (O Fig. 42.30c)y and 5 -[ F]fluoro-5 -deoxyribose (O Fig. 42.30d) were successfully produced from 5 -[ F]fluoro-5 -deoxyadenosine (Deng et al. 2006, Onega et al 2009, 2010). In the base-swap strategy, the 5 [i F]fluoro-5 -deoxyribose phosphate O Fig. 42.30c) could be further transformed into... 

Wong and coworkers reported one-pot aldol reactions catalyzed by a deoxyribose-5-phosphate aldolase (DERA), in which 2 eq of acetaldehyde was added in sequence to two-carbon aldehyde acceptors to afford six-membered lactol derivatives 126 (Figure 4.35). The DERA-catalyzed reaction is an equilibrium process the intermediate four-carbon adduct 127 is reversibly formed under the reaction conditions. The second condensation between this intermediate and a second equivalent of acetaldehyde drives the equilibrium favorably due to the stability of the cydized lactol product 126. DERA has been expressed in E. coli [158,159]. 

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