Cytosine adduct

However, according to the calculations of the cytosine adducts, both trans and cis isomers should form experimentally in nearly equal amounts. 

The methyl group of thymine is susceptible to hydrogen abstraction resulting in a carbon-centred allyl radical. Further oxidation of this radical intermediate can yield thymine-specific products, 5-hydroxymethyluracil and 5-formyluracil. Cytosine adducts also yield unique products under further... 

Figure 3.10 Formation of cytosine adducts (43) by reaction of reactive aldehyde arising from C4 hydrogen abstraction in DNA.

Scheme 1.12 Pathways of photochemical damage to pyrimidine bases fonnation of a thymine-thymine adducts b thymine-cytosine adducts...

The reaction mechanism of the DNA (cytosine-5)-methyltransferase-catalyzed cytosine methylation was investigated at the MP2 and DFT levels [98JA12895]. This system has been modeled by 1-methylcytosine 117, methylthiolate, and trimethylsulfonium. The cytosine methylation is initiated by an attack of the anionic methylthiolate at Cg of the cytosine ring (Scheme 77). The formation of the methylthiolate adduct 118 of the neutral 117 was found to be endothermic in the gas phase and in solution. However, the MP2 and DFT results differ... 

The analogons deamination reaction is not observed in l-methyl-2 -deoxy-adenosine nncleosides. ° Rather, in the adenine series, the Dimroth rearrangement occnrs (Scheme 8.4). On the contrary, in styrene adducts of 2 -deoxyadenosine, the hydroxyl residue of the adduct undergoes intramolecular reaction with the base to initiate deamination (Scheme 8.6). ° ° Similarly, cytosine residues bearing styrene adducts at the N3-position undergo rapid deamination (nearly complete deamination is seen within 75h). °°... 

The data in Table 2.1 suggest that the O-benzylated adduct cannot be isolated since it is less stable than reactants. The N3-benzylated adduct should be generated faster, but it should also decompose under mild conditions into free reactants, because the activation free energy in aqueous solution for the decomposition into free QM and methylcytosine is only 21.4 kcal/mol.14 In other words, these data suggested that the QM-N3-cytosine conjugate could act as QM-carrier, few years before the experimental data related to the stability of QM-conjugates became available.4... 

The ability of o-QM to form several metastable adducts with pyrimidine (at cytosine N3) and purine bases (at guanine N7 and adenine Nl) in water suggested that the above adducts may be exploited as o-QM carriers under mild conditions, anticipating that o-QM could actually migrate along the structure of an oligonucleotide.35... 

TABLE 2.3 Stability of the QM-9-Methyladenine and QM-9-Methylguanine Adducts (QM-A and QM-G, Respectively) Relatively to Reactants in the Gas Phase (AGgas) and in Aqueous Solution (AGaq). Activation Energies for Their Decomposition into Free QM and Cytosine (AG e )... 

The interstrand cross-link also induces DNA bending.72 X-ray and NMR studies on this adduct show that platinum is located in the minor groove and the cytosines of the d(GC) base pair involved in interstrand cross-link formation are flipped out of the helix stack and a localized Z-form DNA is observed.83-85 This is a highly unusual structure and very distorting—implications for differential repair of the two adducts have been addressed. Alternatively, the interstrand cross-link of the antitumor inactive trans-DDP is formed between a guanine (G) and its complementary cytosine (C) on the same base p a i r.86,87/ nms- D D P is sterically incapable of producing 1,2-intrastrand adducts and this feature has been cited as a dominant structural reason for its lack of antitumor efficacy. It is clear that the structural distortions induced on the DNA are very different and likely to induce distinctly different biological consequences. 

Two types of addition to pyrimidine bases appear to exist. The first, the formation of pyrimidine photohydrates, has been the subject of a detailed review.251 Results suggest that two reactive species may be involved in the photohydration of 1,3-dimethyluracil.252 A recent example of this type of addition is to be found in 6-azacytosine (308) which forms a photohydration product (309) analogous to that found in cytosine.253 The second type of addition proceeds via radical intermediates and is illustrated by the addition of propan-2-ol to the trimethylcytosine 310 to give the alcohol 311 and the dihydro derivative 312.254 The same adduct is formed by a di-tert-butyl peroxide-initiated free radical reaction. Numerous other photoreactions involving the formation by hydrogen abstraction of hydroxyalkyl radicals and their subsequent addition to heterocycles have been reported. Systems studied include 3-aminopyrido[4,3-c]us-triazine,255 02,2 -anhydrouri-dine,256 and sym-triazolo[4,3-fe]pyridazine.257 The photoaddition of alcohols to purines is also a well-documented transformation. The stereospecific addition of methanol to the purine 313, for example, is an important step in the synthesis of coformycin.258 These reactions are frequently more... 

Solomon JJ, Segal A. 1985. Direct alkylation of calf thymus DNA by acrylonitrile. Isolation of cyanoethyl adducts of guanine and thymine and carboxyethyl adducts of adenine and cytosine. Environ Health Perspect 62 227- 230. 

The N-3 position of uracil also can be modified with carbodiimide reagents. In particular, the water-soluble carbodiimide CMC [l-cyclohexyl-3-(2-morpholinoethyl) carbodiimide, as the metho p-toluene sulfonate salt] can react with the N-3 nitrogen at pH 8 to give an unstable, charged adduct. The derivative is reversible at pH 10.5, regenerating the original nucleic acid base (Figure 1.47). Cytosine is unreactive in this process. 

Although relatively few structural studies of the interstrand GG adduct [42, 45, 46] have been reported, the data presented reveal the structural distortion to be significantly different from that of the intrastrand adduct. The prime feature of this adduct is the cross-linking between the two strands at GC sequences, thereby causing a kink in the double helix. In this instance, however, the kink is towards the minor groove, with a value of -47° (Fig. 4.3). Another feature of this adduct not present in the other intrastrand adducts is the complementary cytosine bases extruding from the lesion site. 

This quinone reacts in aqueous solution with OH and H adducts of cytosines and uracils by an electron transfer/addition mechanism, similar to Eq. 18 [28], Addition takes place at the quinone carbonyl oxygen to produce an anthroxyl radical. This then undergoes spontaneous C-O heterolysis ... 

To model the crucial step of covalent adduct formation, adducts resulting from quenching of lO-azaBaP-4,5-epoxide with cytosine via the exocyclic amino group were computed, and their geometrical features and relative energies were compared (Fig. 24). The most stable stereoisomer was the one with the cytosine moiety trans to the hydroxyl, with both groups in pseudoequatorial conformation. Two structures... 

Fig. 24 Lowest energy conformations of the adducts of lO-azaBaP-4,5-epoxide with cytosine, (a) Trans conformation, (b) cis conformation (OH pseudoequatorial), and (c) cis conformation (cytosine residue pseudoequatorial).

Murata T, Saito G (2006) Properties of reaction products between cytosine and F4TCNQ in MeOH two hemiprotonated cytosine salts with F4TCNQ radical anion and methoxy adduct anion. Chem Lett 35 1342-1343... 

The less basic purines generate different adducts. Both a C-8 adduct 107 and an 0-6 adduct 108 are produced in the presence of I, while the exclusive product of the reaction of A with 75n and 75o is the unique benzene imine 109. ° These purines also exhibit lower selectivity for trapping of the nitre-nium ions (Table 3). The pyrimidine nucleosides thymidine (T), uridine (U), and cytosine (C) showed negligible reactivity with these two nitrenium ions. ° The selectivity ratios for T, U, and C given in Table 3 are upper limits based on the decrease in the yield of the hydrolysis products at high nucleoside concentration (ca. 50mM). ° Since no adducts were isolated it is not clear that these selectivities represent nucleophilic trapping by the pyrimidines. 

Some other interesting observations regarding free radicals in these systems are noteworthy. In many instances, multiple conformations of radicals are found at lower but not higher temperatures. This indicates that the radicals exist in shallow energy wells at low temperature this phenomenon was observed very early, in the 4 K ENDOR investigation of radical formation in amino acids.23 Unlike the process in DNA. In which it is well understood that the thymine anion radical protonates at C6 to form T(C6)H-, in the crystalline state there is a not clear link between pyrimidine electron adducts and H-addition radicals. We finally note that a deuterium isotope effect of protonation/deprotonation processes was found in cytosine.HCl and 2 -deoxycytidine.HCl, as evidenced by a lower propensity for these processes to occur in partially deuterated systems than in predated ones. 

On warming, 39 persisted to 77 K (in one experiment) also, despite a thorough search, no H adducts to the C5 C6 double bond of cytosine were found at any temperature. 

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