2-Deoxyribose formation

Aldolases catalyze asymmetric aldol reactions via either Schiff base formation (type I aldolase) or activation by Zn2+ (type II aldolase) (Figure 1.16). The most common natural donors of aldoalses are dihydroxyacetone phosphate (DHAP), pyruvate/phosphoenolpyruvate (PEP), acetaldehyde and glycine (Figure 1.17) [71], When acetaldehyde is used as the donor, 2-deoxyribose-5-phosphate aldolases (DERAs) are able to catalyze a sequential aldol reaction to form 2,4-didexoyhexoses [72,73]. Aldolases have been used to synthesize a variety of carbohydrates and derivatives, such as azasugars, cyclitols and densely functionalized chiral linear or cyclic molecules [74,75]. 

It has been recently shown that the selective alkylation and strand scission of deoxytetranucleotide d(GTAG)-27 chosen as DNA model, results from the formation of covalent adducts 28 and 29 on the N-7 of guanine and N-3 of adenine with opening of the cyclopropane ring, respectively. Thermal treatment of 28 (90 °G, 5 min) afforded the d(deoxyribose-TAG) 30 with liberation of N-7 alkyl-guanine 31, while treatment of 29 provided the d(GT-deoxyribose-G) 32 and the N-3 alkyladenine 33 [27]. The stabilities of adducts 28 and 29 were tj/2 = 31 h and 3.2 h, respectively therefore, the cleavage reaction of adduct 29 proceeds much faster than that of 28, Eq. (11) [27]. 

In contrast to transketolase and the DHAP-dependent aldolases, deoxyribose aldolase (DERA) catalyzes the aldol reaction with the simple aldehyde, acetaldehyde. In vivo it catalyzes the formation of 2-deoxyribose-5-phosphate, the building block of DNA, from acetaldehyde and D-glyceraldehyde-3-phosphate, but in vitro it can catalyze the aldol reaction of acetaldehyde with other non-phosphorylated aldehydes. The example shown in Scheme 6.28 involves a tandem aldol reaction... 

The mechanism involves participation of the free 2 -OH of the ribose groups and formation of cyclic 2, 3 -phosphates and is similar to that of pancreatic ribo-nuclease (Chapter 12). Because deoxyribose lacks the free 2 -OH, the phosphodiester linkages in DNA are quite stable in base. 

The formation of deoxyribose, die pentose moiety of deoxyribonucleic acid, can occur directly from ribose while the latter is in the form of a nucleotide diphosphate. Deoxyribose-5-phosphate can also be formed by condensation of acetaldehyde and glyceraldehyde-3-phosphate. 

For the sake of simplicity in illustrating A -glycoside formation in DNA, we shall show the type of bonding involved for the sugar and base components only (i.e., the deoxyribose nucleoside structure). Attachment of 2-deoxyribose is through a NH group to form the /3-N-deoxyribofuranoside (Section 20-5) ... 

CH,Br + H20 - CH3OH + HBr. nucleoside A combination of an organic base and a ribose or deoxyribose molecule, nucleosynthesis The formation of elements, nucleotide A nucleoside with a phosphate group... 

The rate constants for the reactions between OH and a range of ethers and hydroxy ethers have been reported at 298 K233 as well as those for reactions between dimethyl ether and methyl f-butyl ether over the range 295-750 K.234 Data from the former study show deviations from simple structure-activity relationships which were postulated to arise due to H-bonding in the reaction transition states.233 The atmospheric lifetime of methyl ethyl ether has been determined to be approximately 2 days.235 Theoretical studies on the H-abstraction from propan-2-ol (a model for deoxyribose) by OH have been reported using ab initio methods (MP2/6-31G ).236 The temperature dependence (233-272 K) of the rate coefficients for the reaction of OH with methyl, ethyl, n-propyl, n-butyl, and f-butyl formate has been measured and structure-activity... 

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