The Purine Bases

This enzyme, sometimes also called the Schardinger enzyme, occurs in milk. It is capable of " oxidising" acetaldehyde to acetic acid, and also the purine bases xanthine and hypoxanthine to uric acid. The former reaction is not a simple direct oxidation and is assumed to take place as follows. The enzyme activates the hydrated form of the aldehyde so that it readily parts w ith two hydrogen atoms in the presence of a suitable hydrogen acceptor such as methylene-blue the latter being reduced to the colourless leuco-compound. The oxidation of certain substrates will not take place in the absence of such a hydrogen acceptor. 

Imidazole can be A -allylated. The A -glycosylimidazole 299 is prepared by regiospecific amination at the anomeric center with retention of configuration. Phenoxy is a good leaving group in this reaction[181]. Heterocyclic amines such as the purine base 300 are easily allylatedfl 82]. 

The exocychc nitrogens on cytosine and the purine bases must be protected during the synthesis. The search is ongoing for protecting groups that are subject to fewer side reactions and that can be removed more easily in the final deprotection step (34). 

Binding of cisplatin to the neighbouring bases in the DNA disrupts the orderly stacking of the purine bases when it forms a 1,2-intrastrand crosslink, it bends the DNA helix by some 34° towards the major groove and unwinds the helix by 13°. These cross-links are believed to block DNA replication. 

Human tissues can synthesize purines and pyrimidines from amphibolic intermediates. Ingested nucleic acids and nucleotides, which therefore are dietarily nonessential, are degraded in the intestinal tract to mononucleotides, which may be absorbed or converted to purine and pyrimidine bases. The purine bases are then oxidized to uric acid, which may be absorbed and excreted in the urine. While little or no dietary purine or pyrimidine is incorporated into tissue nucleic acids, injected compounds are incorporated. The incorporation of injected [ H] thymidine into newly synthesized DNA thus is used to measure the rate of DNA synthesis. 

Figure 34-8. Formation of uric acid from purine nucleosides byway of the purine bases hypoxanthine, xanthine, and guanine. Purine deoxyribonucleosides are degraded by the same catabolic pathwayand enzymes,all of which existin the mucosa of the mammalian gastrointestinal tract.

Hydrolytic cleavage of the glycosidic bond holding the DNA bases to the sugar-phosphate backbone is typically a very slow process under physiological conditions (pH 7.4 37°C). Loss of the pyrimidine bases cytosine and thymine occurs with a rate constant of 1.5 X 10 s (ty2 = 14,700 years), while loss of the purine bases guanine and adenine proceeds slightly faster, with a rate constant of 3.0 X... 

The bulk effect of water as a solvent is rather dramatic since it causes a drastic reduction of the nucleophilicity of 9-methyladenine N1 and even more of 9-methylguanine 06. As a result, there is a reversal of the nucleophilicity order of the purine bases passing from gas phase to aqueous solution. In fact, in solution, methyladenine is more nucleophilic than methylguanine. Moreover, oxygen and N7 nucleophilic centers of 9-methylguanine compete almost on the same footing in solution (Table 2.2) and also the reactivity gap between N1 and N7 of 9-methyladenine is highly reduced in comparison to the gas phase. 

Nucleotides can be linked together into oligonucleotides through a phosphate bridge at the 5 position of one ribose unit and the 3 position of another. The purine bases, adenine and guanine, have two heterocyclic rings, while the pyrimidines cytosine, thymine, and uracil have one. The structure of adenosine monophosphate is shown in Figure 11. 

Adenine phosphoribosyltransferase (APRT) deficiency is an inherited disorder of purine metabolism and is inherited in an autosomal recessive manner (K18, V7). This enzyme deficiency results in an inability to salvage the purine base adenine, which is oxidized via the 8-hydroxy intermediate by xanthine oxidase to 2,8-di-hydroxyadenine (2,8-DHA). This produces crystalluria and the possible formation of kidney stones due to the excretion of excessive amounts of this insoluble purine. Type I, with virtually undetectable enzyme activity, found predominantly in Caucasians, is found in homozygotes or compound heterozygotes for null alleles. Type II, with significant APRT activity, found only in Japan, is related to a missense mu-... 

Figure 11-4. Molecular orbitals for the purine bases adenine and guanine...

Figure 11-8. Structures of representative conical intersections Sj/Sq in the purine bases, 9H-adenine and 9H-guanine. Adenine structures (a,b) are taken from Ref. [138]. Guanine structure (c) is taken from Ref. [171]...

Shukla and coworkers have studied the excited states of purine bases, adenine and guanine, in water using CIS with the self-consistent reaction field (SCRF) to model the water [217,218], Tomasi and coworkers have also studied the purine bases... 

Interestingly, the nucleophilic addition of water in the sequence of events giving rise to 41 represents a relevant model system for investigating the mechanism of the generation of DNA-protein cross-links under radical-mediated oxidative conditions [80, 81]. Thus, it was shown that lysine tethered to dGuo via the 5 -hydroxyl group is able to participate in an intramolecular cyclization reaction with the purine base at C-8, subsequent to one electron oxidation [81]. 

GG8, the radical cation must traverse five A/T base pairs. Electrochemical measurements in solution have shown that the purine bases (A and G) have considerably lower Eox than the pyrimidines (C and T), with the Eox of G estimated to be about 0.25 V below that of A [20]. It is not very likely that the Eox of bases in DNA will be the same as they are in solution, but it is generally assumed that the order of Eox will remain the same. Consequently, the radical cation at Gi of AQ-DNA(l) must traverse a bridge of five A bases to reach GG8. The process whereby the radical cation crosses such bridges has been a major point of debate in consideration of long distance radical cation migration mechanisms in DNA this issue will be discussed fully below. 

In a typical experiment a portion of the 5 -labeled single-stranded DNA is reacted with dimethylsulfate under conditions where many but not all of the purine bases react. This reagent alkylates the N7 position... 

As A. and B. Pullman showed more than 40 years ago, the purine base adenine occupies a unique situation in the purine family in comparison to the other purines, it has the greatest resonance energy per -electron, i.e., it is more stable, and thus likely to have been incorporated preferentially into biomolecules (Pullman, 1972). 

The purine base guanine is also formed in concentrated solutions of ammonium cyanide, i.e., the same substance which became known from Or6 s adenine synthesis. Or6, as well as Stanley Miller, was involved in a new series of experiments (Levi et al., 1999). The yield of guanine is, however, 10 10 times lower than that of adenine surprisingly, the synthesis is just as effective at 253 K as at 353 K. Low temperatures seem conceivable in certain parts of Earth as well as on the Jovian moon Europa (see Sect. 3.1.5) or in the Murchison meteorite. 

This study again shows the prime importance of the purine base adenine, whether in the vastness of interstellar space or in the biochemical processes taking place in a single cell (Glaser et al 2007). 

Figure 1.53 The purine bases are subject to bromination reactions at the C-8 position, forming an important reactive intermediate for derivatization purposes.

Consistent with the experimental data, mutation of the purine base nitrogens, i.e. N, 3N, 7N and 9N, showed that replacement of N, 3N and 9N with CH had little effect on binding affinity whereas a similar replacement of 7N led to a loss of 2.8 kcal/mol. The 0.6 kcal/mol gain in affinity for the 1-deaza and 3-deaza AMP analogues was consistent with the hydrophobic nature of this portion of the binding site cavity and the absence of hydrogen bond donors in the vicinity of either heteroatom. 

Scan of Residues in the Purine Base Binding Region... 

The tautomerisation of the purine bases adenine and guanine and of the pyrimidine bases thymine, cytosine, and uracil has important implications in molecular biology, and the occurrence of rare tautomeric forms of these bases has been suggested as a possible cause of spontaneous mutagenesis (Lowdin, 1965 Pullman and Pullman, 1971 Kwiatowski and Pullman, 1975). Three of the most likely tautomers for cytosine are shown in [87]—[89], together with the less likely imino forms [90] and [91] (Scanlan and Hillier,... 

Several adducts can be formed by binding of cisplatin to DNA [41] the most important are the intrastrand adjacent 5 -GG adduct, intrastrand adjacent 5 -AG, and nonadjacent intrastrand di-dentate adduct GXG (where X=any base), at 65%, 25% and 6%, respectively (Fig. 4.1). The remaining part consists of cisplatin monofunctionally bound to G, and interstrand bifunctional G-G adducts at 3%. The adducts are, according to experimental evidence, formed exclusively at the N7 position of the purine bases A and G exposed in the major groove of the DNA helix the other possible sites of complexation are either exposed in the too narrow minor groove or involved in the base-pairing of the two strands. 

P2J2A Z = 8 Dx = 1.931 R = 0.034 for 2,321 intensities. There are two molecules in the asymmetry unit, and both exhibit the syn disposition (—84.5°, + 76.1°) for the base. The conformation of the D-ribosyl group is 3T4 (28.5°, 39.4°) in molecule A and 3T2 (359.9°, 36.2°) in molecule B. The exocyclic, C-4 -C-5 bond torsion-angle is gauche+ for both molecules (55.2°, 59.7°). The purine bases of the crystallograph-ically independent molecules are paired by N-l-H 0-6 hydrogen bonds across a pseudo-two-fold axis. The bases are stacked such that the Br atoms are tucked under the pyrimidine moiety of the adjacent... 

Diaminobenzoic acid (DABA) reacts with aldehydes of the form RCH CHO to produce a strongly fluorescent compound. Acid-catalysed removal of the purine base from the nucleic acid exposes the 1 and 2 carbons of deoxyribose... 

Inosine monophosphate (contains the purine base hypoxanthine) is the precursor for AMP and GMP. 

Figure 10.8 A summary of the reactions involved in the degradation of nucleic acid, nucleotides, nucleosides and purine and pyn midine bases. Nucleic add is hydrolysed by nucleases to form nucleotides, which are hydrolysed to nucleosides. The latter are split into ribose 1-phosphate and a base. The purine bases are converted to uric acid and ammonia. Uric acid is excreted. The pyrimidine bases are converted to 3-carbon intermediates (malo-nate semialdehyde and methylmalonate semialdehyde). The nitrogen is released as ammonia or used to convert oxoglutarate to glutamate.

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