Cytosine hydrate

The behavior of cytosine and cytidylic acid during photolysis are quite different existing reports about the behavior of cytosine are contradictory. It should be noted that neither the cytosine hydrate nor the dimer has been isolated from photolyzed solutions nor identified by comparison with known substances. Early work7 reports that photolysis of cytosine in solution resulted in a decrease in absorption at 270 nm, and an increase at 240 nm. This transformation was partly reversible at room temperature,7 but the reversal was prevented by the presence of 0.1M NaCl. The quantum yield for disappearance of cytosine was about 1 to 2 x 10-3. 

Oxoguanine Thymine glycol Cytosine hydrate FaPy-G FaPy-A... 

Another type of photochemical reaction involving a pyrimidine base is the addition of a molecule of water across the 5,6 double bond of C to yield a 5,6-dihydro-6-hydroxy derivative called the cytosine hydrate. The quantum yield for the formation of cytosine hydrates in UV-irradiated DNA is greater in single-stranded than in duplex-DNA (45). Hydrates of cytosine, deoxycytidine, CMP, or dCMP are unstable, readily reverting to the parent form by rehydration (45). However, their half-life is dramatically increased in DNA, and cytosine hydrate may be the major nondimer C photoproduct. Cytosine hydrate can undergo deamination and dehydration to yield uracil (1). The hydrate of 5-methylcytosine may undergo deamination to yield 5-thymine hydrate, which can convert to thymine upon dehydration (1). 

Intramolecular photocycloaddition occurs with thymine derivatives and related compounds. Thus, the bis thymine dimer (116) is formed on irradiation at 254 nm of (117). Zinc complexes of 1,4,7,10-tetraazacyclododecane inhibit the intramolecular photodimerisation of the thymidilyl thymidine (118) and the same complexes are active in cleaving cyclobutane systems (119). Conventional (2+2)-cycloaddition does not occur on irradiation of (120) but instead the main product is the cytosine hydrate accompanied by the (6-4)-photoproduct (121). Dimerisation is reported to occur on irradiation in an acidic medium. 

Deoxycytidine (dCyd) (14 in Scheme 2) is also an excellent target for one-electron oxidation reactions mediated by triplet excited menadione. On the basis of extensive identification of dCyd photooxidation products, it was concluded that this nucleoside decomposes by competitive hydration and deprotonation reactions of cytosine radical cations with yields of 52% and 40%, respectively [53]. It was also found, on the basis of 180 labeling experiments, that hydration of cytosine radical cations (15) predominantly occurs... 

An amino or hydroxy group facilitates 5-bromination even in aqueous solution. A -bromosuccinimide (NBS) and molecular bromine are the commonest reagents used. In uracils, cytosines, and barbituric acids, products of both addition and substitution can be identified in aqueous solution, and 5,5-dibromo products are common. In the bromination of uracils, addition products, including covalent hydrates, form rapidly, and the acid-catalyzed dehydration step to 5-bromouracils is much slower. Cytosine and related compounds behave similarly <1994HC(52)1, 1996CHEC-II(6)93>. 

Only a confused picture is revealed by these essentially qualitative studies. Many questions are left unanswered. The probable formation of uracil hydrate in cytosine photolysis has not been reported and the question of dimer formation, either in solution or in ice, is still unresolved. There are thus large gaps in our knowledge about the photolysis of cytosine and cytidine. Much more detailed work has been carried out on cytidylic acid and on dinucleotides of cytosine (Sect. XI-C). 

Ultraviolet light photolysis of CpC (16c) leads to the formation of mono- and dihydrates and dimers of the cytosine residue. Since saturation of the 5,6-double bond labilizes the 4-amino group, deamination also takes place readily with the formation of hydrates and dimers also of UpC, CpU, and UpU. A chart of those products which have been separated and identified is shown in Figure 21.74 The starting material, CpC, was labeled with 32P. The products were separated by various... 

An attempt has been made to apply the Cohen and Reiss theory to dimer and hydrate formation in RNA.158 The results were inconclusive, probably because of a poor choice of example. Application of the theory to RNA was complicated by the necessity of estimating the distribution of uracil residues on the chain. The results are made still more tentative by the fact that Tanaka ignored the probability of dimer formation between cytosine residues, mixed dimers between cytosine and uracil, and hydrate formation in cytosine as well as the resultant deamination phenomena. A better choice of example would have been poly-uridylic acid. 

Irradiation of air-free solutions of pyrimidines can give products resembling some of those produced by ultraviolet light, but probably by a quite different mechanism. Irradiation of 1,3-dimethyluracil with 200 kV X-rays produces not only the expected 5,6-glycol, but also 6-hydroxyl-l,3-dimethyl-5-hydrouracil, the same isomer as the UV-produced hydrate discussed elsewhere in this chapter. The yield of the hydroxy compound is low, G = 0.35 molecules/100 eV absorbed. Cytosine glycol is formed in gamma-irradiated cytosine solutions, and this deaminates completely to the uracil glycol. These products are probably formed by addition of an OH to the 6-position of the pyrimidine and then dismutation of hydroxy radical. The major products formed in the radiolysis of air-free solutions of pyrimidines or purines have not yet been identified. 

Becker et al.174 find that the photoproduct of cytidine-3 -phosphate is the photohydrate. The quantum yield is dependent on the pH, and is higher for the neutral form than for the acidic form. Albert176 has published a review article on nonphotolytic hydration of the C=N bond in many heteroaromatic substances, a reaction similar in many respects to photohydration of the pyrimidines. Shapiro and Klein175 report that cytidine and cytosine are deaminated at 95°C by a variety of aqueous buffers. The reaction is pH sensitive. 

Product analyses of hydrated DNA, irradiated at room temperature, yield substantial quantities of 5,6-dihydrothymine[18] as expected from ESR results which show large amounts of T(C6)H however, substantial quantities of 5,6-dihydrocytosine and its deamination product 5,6-dihydrouracil are also found [Swarts S, unpublished results]. These results suggest that at higher temperatures the activation barrier to protonation of one-electron reduced cytosine at a carbon site (reaction 3) is overcome, producing a reaction path which is competitive with reaction 2. 

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