Radical Pyrimidine

There are examples in which base radicals undergo reaction with adjacent base residues. The 5-(2 -deoxyuridinyl)methyl radical (63, Scheme 8.30) can forge an intrastrand cross-link with adjacent purine residues. Cross-link formation is favored with a guanine residue on the 5 -side of the pyrimidine radical and occurs under low-oxygen conditions. A mechanism was not proposed for this process, but presumably the reaction involves addition of the nucleobase alkyl radical to the C8-position of the adjacent purine residue. Molecular oxygen likely inhibits crosslink formation by trapping the radical 63, as shown in Scheme 8.24. The radical intermediate 89 must undergo oxidation to yield the final cross-linked product 90,... 

A different strategy has been applied in our work, that emphasizes the importance of DNA stability on hole transfer within double-stranded DNA. This work is based on determination of the overall yield of oxidized nucleosides that arise from the conversion of initially generated purine and pyrimidine radical cations within DNA exposed to two-photon UVC laser pulses. On the one hand, this work benefits from the excellent current knowledge of chemical reactions involving the radical cations of DNA bases, and on the other hand, from major analytical improvements that include recent availability of the powerful technique of high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (CLHP-ESI-MS/MS) [16-18]. 

However, the biochemical significance of the latter studies is challenged by the fact that the transformation of transient purine and pyrimidine radicals into diamagnetic decomposition products is oxygen-independent in the solid state. Therefore, it is necessary to study the chemistry of one-electron nucleobase intermediates in aerated aqueous solutions in order to investigate the role of oxygen in the course of reactions that give rise to oxidation products within DNA and model compounds. In this respect, type I photo-... 

A number of papers have reported studies on pyrimidine radical cations. 1-Methylthymine radical cations generated via a triplet-sensitized electron transfer to anthraquinone-2,6-disulfonic acid were detected by Fourier transform electron paramagnetic resonance (FTEPR). The parent 1-methylthymine radical cation, and its transformation to the N(3)-deprotonated radical cation, were observed. Radical cations formed by addition of HO and POs" at C(6) were also detected depending on the pH. Similarly, pyrimidine radical cations deprotonated at N(l) and C(5)-OH were detected from the reaction of 804 with various methylated pyrimidines." These radicals are derived from the initial SO4 adducts of the pyrimidines. Radical cations of methylated uracils and thymines, generated by electron transfer to parent ions of... 

An almost complete description of both OH radical-mediated and one-electron oxidation reactions of the thymine moiety (3) of DNA and related model compounds is now possible on the basis of detailed studies of the final oxidation products and their radical precursors. Relevant information on the structure and redox properties of transient pyrimidine radicals is available from pulse radiolysis measurements that in most cases have involved the use of the redox titration technique. It may be noted that most of the rate constants implicating the formation and the fate of the latter radicals have been also assessed. This has been completed by the isolation and characterization of the main thymine and thymidine hydroperoxides that arise from the fate of the pyrimidine radicals in aerated aqueous solutions. Information is also available on the formation of thymine hydroperoxides as the result of initial addition of radiation-induced reductive species including H" atom and solvated electron. 

In a comment on this work,39 Close expresses doubt regarding the DFT calculations that indicate a lack of planarity in pyrimidine radical anions, contrary to what is experimentally found in low temperature single crystal studies. He notes that using an extended basis set results in reasonable agreement between the experimental and calculated values of hyperfine coupling constant for the a-proton without the need to move the proton significantly out of the... 

Table VII Principal Pyrimidine Radicals in DNA at Low Temperatures in D2O solutions C(N3)H is described as C(N3)D- or CD )...

Short-lived adducts may be formed as intermediates in the reactions of the oxidizing inorganic radicals with the nucleobases, and it is therefore not always fully excluded that processes observed at very short times and attributed to the reactions of radical cations are in fact due to such intermediates. It may be mentioned that, for example, a long-lived S04 -adduct is observed in the reaction of S04, with maleic acid (Norman et al. 1970). It has been suggested that S04, in its reactions with the pyrimidines forms only an adduct and does not give rise to radical cations (Lomoth et al. 1999). The observation of heteroatom-centered radicals by EPR from the nucleobases Ura, Thy and Cyt (Catterall et al. 1992) as well as dCyd (Hildenbrand et al. 1989) (see below) has been taken as evidence that in the reaction of S04 with pyrimidines radical cations are likely, albeit... 

Pyrimidines. Photoexcited anthraquinone-2,6-disulfonate undergoes ET with Thy and its methyl derivatives as indicated by Fourier transform EPR (Geimer et al. 1997). These pyrimidine radical cations deprotonate at N( 1) thereby giving rise to the corresponding N-centered radicals [reaction (6)]. 

It has been mentioned above that the pyrimidine radical cations are reasonably strong acids and rapidly deprotonate at a heteroatom. As all protonation/ deprotonation reactions at heteroatoms are reversible [e.g., equilibrium (22)], the radical cations are regenerated upon reprotonation. Deprotonation at carbon or reaction with water yield the final free-radical products. For the l,3Me2Thy system, where the deprotonation/reprotonation equilibria such as reaction (22) fall away, reactions (25)-(28) have been postulated to account for the fact that in the presence of 02 l,3Me25HOMeUra and l,3Me25(CHO)Ura [reaction (29)] are formed in a combined yield of 80% of primary S04 radicals (Rashid et al. 1991). The formation of these products has been taken as evidence that a free radical cation must be an intermediate. It is, however, also possible that the allylic radical is formed in a concerted reaction HS04 elimination. For such a process, a six-membered transition state can be written. 

The radical anions may be formed by reacting the nucleobases with eaq which may be either generated radiolytically or in a two-step reaction, e.g in the laser flash photolysis of anthraquinonedisulfonate in the presence of pyrimidines (yielding the pyrimidine radical cation and an anthraquinonedisulfonate radical anion) and subsequent photoionization of the anthraquinonedisulfonate radical anion (Lii et al. 2001). The latter approach, combined with Fourier transform EPR spectroscopy, yielded detailed information as to the conformation of the radical anions of Ura and Thy in aqueous solution (for a discussion see Close 2002 Naumov and Beckert 2002). Similarly valuable EPR information has been obtained from y-irradiated single crystals (cf. Box and Budzinski 1975 Boxet al. 1975 Sagstuen et al. 1998). 

Table 10.20. Rate constants for protonation of the pyrimidine radical anion at C(6) by H2P04 using various approaches of evaluating the data (Deeble et al. 1985) ...

Decarroz C, Wagner JR, Cadet J (1987) Specific deprotonation reactions of the pyrimidine radical cation resulting from the menadione mediated photosensitization of 2 -deoxycytidine. Free Rad Res Commun 2 295-301... 

Repair reactions of pyrimidine radical anions protonated at the C6 position... 

The following pyrimidine radical anions protonated at the C6 position were studied, U (C6H), T C6H, and C (C6H) (Chart 3), to monitor their repair reactions [reaction (5)] ... 

Hydration of the thymidine radical cation leads to the predominant formation of the oxidizing 6-hydroxy-5,6-dihydrothymid-5-yl radical whereas deprotonation mostly generates the methyl-centered radical (Fig. 4). As already pointed out, these two pyrimidine radicals are also produced upon reaction with OH. However, the methyl-centered radical represented only 5% of base radicals when produced by OH while it corresponds to 30% of the thymidine radicals produced upon one-electron oxidation. Type I photosensitization of 2 -deoxy-cytidine leads to the formation of the 6-hydroxy-5,6-dihydro-2 -deoxycytidil-5-yl radical also produced upon reaction with OH. Additional oxidative pathways involve the formation of 2-deoxyribonolactone and free cytosine as well as production of 2 -deoxyuridine as the result of deprotonation ofthe pyrimidine radical cation at Cl and NH2 group, respectively. 

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